ANNUAL REPORT 2016/17

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1 ANNUAL REPORT 2016/17

2 National Health Laboratory Service Annual Report 2016/17

3 Table of Content Part A: General Information...3 General Information...4 Abbreviations and Acronyms...5 Foreword by the Chairperson...9 Acting Chief Executive Officer s Overview...12 Board Members...15 Statement of Responsibility and Confirmation of Accuracy for the Annual Report...18 Strategic Overview...19 Legislative and Other Mandates...21 Organisational Structure...23 Part B: Performance Information...24 Auditor s Report: Predetermined Objectives...25 Situational Analysis...26 Performance Information by Programme...28 Business Unit Performance...43 Performance Information by Province...90 Performance Information by Subsidiary Performance Information by Institute Part C: Governance Introduction Portfolio Committees Executive Authority The Accounting Authority/Board Risk Management Internal Audit Compliance with Laws and Regulations Fraud and Corruption Minimising Conflict of Interest Code of Conduct Health Safety and Environmental Issues Social Responsibility Report of the Audit and Risk Committee Part D: Human Resources Introduction Human Resources Oversight Statistics Part E: Financial Information Chief Financial Officer s report Summary of Group salient information National Health Laboratory Service

4 PART A General Information

5 General Information Registered name of the public entity Legal form Practice number Registered office address National Health Laboratory Service Schedule 3A public entity PR Modderfontein Road Rietfontein Sandringham Johannesburg, 2000 Postal address Private Bag X8 Johannesburg 2131 Contact telephone number address Website address Company Secretary: External auditors Adv. Mpho M Mphelo SizweNtsalubaGobodo Inc Chartered Accountants (SA) (SNG) Bankers First National Bank Limited, Rand Merchant Bank Limited, Investec Limited and Nedbank Limited 4 National Health Laboratory Service

6 Abbreviations and Acronyms AAR AARQA ACGT AIDS AMP AMR app ART ARV ASLM ASOT AU BhCG BHSc BLUC CCCP CCMA CCMT CDC CDW CHC CM CMA CMJAH CMSA CMV CNV CPD CPUT CrAg CSF CTB CU CUT DBS DCS DGM DHA DMP DNA PCR DoH DR-TB DST DUT DVS EBS EBV ECM EDTA EE EFI EGK Academic Affairs and Research Academic Affairs, Research and Quality Assurance AIDS Clinical Trials Group Acquired Immune Deficiency Syndrome Antibody-Mediated Prevention Antimicrobial Resistance Application Antiretroviral Therapy Antiretroviral African Society for Laboratory Medicine Antistreptolysin O Titer African Union Beta-Human Chorionic Gonadotropin Bachelor of Health Science Blood and Laboratory User Committee Cervical Cancer Control Policy Commission for Conciliation Mediation and Arbitration Comprehensive Care, Management and Treatment (of HIV and AIDS) Centers for Disease Control and Prevention Corporate Data Warehouse Community Healthcare Cryptococcal Meningitis Cytogenomic Microarray Analysis Charlotte Maxeke Johannesburg Academic Hospital College of Medicine of South Africa Cytomegalovirus Copy Number Variation Continuing Professional Development Cape Peninsula University of Technology Cryptococcal Antigen Cerebrospinal Fluid Centre for Tuberculosis Comprehensive University Central University of Technology Dried Blood Spot Department of Correctional Services Dr George Mukhari Department of Home Affairs Diagnostic Media Products Deoxyribose Nucleic Acid Polymerase Chain Reaction Department of Health Drug-Resistant TB Drug Susceptibility Testing Durban University of Technology Dried Virus Spot E-Business Suite Epstein Barr Virus Enterprise Content Management Ethylenediaminetetraacetic Acid Employment Equity European Federation of Immunology Electronic gate-keeping Annual Report 2016/17 5

7 EID Early Infant Diagnosis ELISA Enzyme-Linked Immunosorbent Assay EQA External Quality Assurance/Assessment EXCO Executive Committee FA Flow Assay FBC Full Blood Count FFP Fit for Purpose FIND Foundation for Innovative New Diagnostics FLQ Fluoroquinolones FNA Fine Needle Aspiration FSASP Federation of South African Societies of Pathology GDSP Global Data Services Platform GFAP Glial Fibrillary Acidic Protein GIS Geographic Information System GPC Green Point Complex GRAP Generally Recognised Accounting Practice GSH Groote Schuur Hospital GXP GeneXpert HAST HIV/AIDS and Sexually Transmitted Diseases and TB HBV Hepatitis B Virus HCT HIV Counselling and Testing HCW Healthcare Worker HEV Hepatitis E Virus HGSIL High Grade Squamous Intraepithelial Lesion HID Human Identification HIS Health Information System HIV Human Immunodeficiency Virus HIV CCMT HIV Comprehensive Care, Management and Treatment HIV VL HIV Viral Load HL7 Health Level 7 HLA Human Leukocyte Antigen HOD Head of Department HPCSA Health Professions Council of South Africa HPV Human Papillomavirus HTA Health Technology Assessment IALCH Inkosi Albert Luthuli Central Hospital IAPC Institutional Academic Pathology Committees ICC International Conventional Centre IgG Immunoglobulin G IgM Immunoglobulin M ILDAC Integrated Laboratory Data Analysis for Care ILO International Labour Organization INH Isoniazid IP Intellectual Property IPC Infection Prevention and Control IQC Internal Quality Control ISO International Standards Organization IT Information Technology ITGC IT Governance Committee KEH King Edward VIII Hospital KM Knowledge Management KPI Key Performance Indicator LAM Lipoarabinomannan LFA Lateral Flow Assay 6 National Health Laboratory Service

8 LFT LIS LPA LPA MCDS MDO MDR-TB MSF MTB MUT NAPC NAPHISA NEPAD NGO NHI NHLS NHRC NICD NIOH NMAL NMMU NPP OEHS OHASIS OHS OHSS ORU OSH PAHWP PathRed PCR PDP PEPFAR PFMA PHC PID PIVOTAL PLG PMC PMMH PMO PMTCT POC PPP PSA PTS QA QC QCA QMS R&D R&R RACL RDT Liver Function Test Laboratory Information System Line Probe Assay Lipoprotein(a) Minimum Clinical Data Set Missed Diagnostic Opportunity Multidrug-Resistant-TB Médecins Sans Frontiers Mycobacterium tuberculosis Mangosuthu University of Technology National Academic and Pathology Committee National Public Health Institute of South Africa New Partnership for Africa s Development Non-Governmental Organisation National Health Insurance National Health Laboratory Service National Health Research Committee National Institute of Communicable Diseases National Institute for Occupational Health Nelson Mandela Academic Laboratories Nelson Mandela Metropolitan University National Priority Programmes Occupational and Environmental Health and Safety Occupational Health and Safety Information System Occupational Health and Safety Occupational Health and Safety Systems Outbreak Response Unit Occupational Health and Safety Pan African Harmonisation Working Party Pathology Research and Development (Congress) Polymerase Chain Reaction Personal Development Plans President s Emergency Plan for AIDS Relief (US) Public Finance Management Act Primary Healthcare Primary Immune Deficiency Professional, Vocational, Technical and Academic Learning PanLeucogate Peri-Mining Community Prince Mshiyeni Memorial Hospital Project Management Office Prevention of Mother-to-Child Transmission Point-of-Care Public Private Partnership Prostate Specific Antigen Proficiency Testing Scheme Quality Assurance Quality Control Quality Compliance Audit Quality Management Systems Research and Development Remuneration and Reward Relational Algebraic Capacitated Location Rapid Diagnostic Test/Testing Annual Report 2016/17 7

9 RHRC RIF RM RPR SADC SAFETP SAIOH SANAS SANDF SASOHN SASOM SAVP SAVQA SCOPA SDG SHE SIA SL SLA SLID SLIPTA SLMTA SMU SOP STI TAT TB TBH TUT U&E UAL UCT UFS UKZN UL UJ UN UNAIDS UNION UNIV UoT UP UPS US UTT UWC VL VMV VUT WHO Wits WRHI WSP WSU Remuneration and Human Resources Committee Rifampicin Records Management Rapid Plasma Reagin Southern African Development Community South Africa Field Epidemiology Training Programme Southern African Institute for Occupational Hygiene South African National Accreditation System South African National Defence Force South African Society of Occupational Health Nursing Practitioners South African Society of Occupational Medicine South African Vaccine Producers South African Viral Quality Assessment Standing Committee on Public Accounts Sustainable Development Goal Safety Health and Environment Strip Interpretation Analysis Second Line Service Level Agreement Second-Line Injectable Drugs Stepwise Laboratory Quality Improvement Process towards Accreditation Strengthening Laboratory Management towards Accreditation Sefako Makgatho Health Sciences University Standard Operating Procedure Sexually Transmitted Infection Turnaround Time Tuberculosis Tygerberg Hospital Tshwane University of Technology Urea and Electrolytes Universitas Academic Laboratory University of Cape Town University of the Free State University of KwaZulu-Natal University of Limpopo University of Johannesburg United Nations United Nations Programme on HIV and AIDS International Union of Tuberculosis and Lund Disease Universitas Hospital University of Technology University of Pretoria Uninterrupted Power Supply University of Stellenbosch Universal Test and Treat University of the Western Cape Viral Load Vision, Mission and Values Vaal University of Technology World Health Organization University of the Witwatersrand Wits Reproductive Health Institute Workplace Skills Plan Walter Sisulu University 8 National Health Laboratory Service

10 Foreword by the Chairperson INTRODUCTION The laboratory and pathology services that the NHLS provides makes it integral to the South African public healthcare system and its performance. Efficiency and effectiveness of both clinical and public health functions including surveillance, diagnosis, prevention, treatment, research, teaching, training and health promotion are all influenced by reliable laboratory services. Laboratories provide confirmatory diagnosis, information for improved care of patients, essential public health information and disease surveillance. The NHLS continues to provide these services at a much lower rate than what a similar basket of tests would cost in the private sector, in spite of also carrying higher costs of providing services to remote areas and deploying funds for academic and research service, which private laboratories do not have to incur. The NHLS makes laboratory services affordable for all South Africans. In fact, without an effective laboratory service patient diagnosis and care is often compromised, expensive drug treatments are squandered, diagnoses are missed and information about public health is inaccurate. It is also impossible to measure the true effectiveness of interventions and to conduct accurate disease surveillance. Effective performance of these roles was the cornerstone of the NHLS in 2016/17. Chairperson Prof. Eric Buch During this past financial year, the Board has continued to diligently fulfil its governance, strategy and oversight roles. The Board is supported by its sub-committees on Audit and Risk, Information Technology Governance, Finance, National Academic Pathology, Remuneration and Human Resources and Research. There has been a focus on human resources and finance and systems and processes. This diligence led, for example, to the Board identifying and acting on matters ahead of them being identified in the audit. The ongoing development of the NHLS is underpinned by the NHLS Act and by its core values: Care: Unity of Purpose: Caring about the environment and society All working together towards a common goal Service Excellence: Valuing good work ethics and striving towards service excellence for customers Transformation: Innovation: Integrity: Looking forward to the future and growing together Pioneering relevant research solutions and training Working with integrity and responsibility The overall aim of the NHLS is to be an affordable, efficient and accessible world-class laboratory service. OVERVIEW The NHLS has five overall programmes: administration; surveillance of communicable diseases; occupational health and safety; academic affairs, research and quality; and laboratory services. To achieve the latter, the NHLS has a national footprint of laboratory services. While the NHLS achieved most of its performance indicators, the Board is cognisant that there is still much to do for the NHLS to reach the performance levels it aspires to and to ensure its sustainability. Our programmes during the year under review included: Administration A number of measures were taken to improve administration and most of the administration performance indicators were met. However, the Board identified significant challenges in procurement systems and information technology and in payments by some Annual Report 2016/17 9

11 provinces, and has sought measures to address these. The Board also addressed the legacy of below inflation increases in staff remuneration. Stability in NHLS financing is dependent on provinces paying in full for their consumption. Underpayments by some provinces have put pressure on the NHLS, including on our ability to reduce our debt to our creditors and our ability to fund new equipment and IT infrastructure and systems.. Surveillance of communicable disease The National Institute for Communicable Diseases (NICD) continues to provide exceptional surveillance and disease outbreak services. The re-engineered surveillance system is proving to be robust. The NICD s 100% response to reported disease outbreaks within 24 hours of notification is critical to informing how the national, provincial and local government respond to outbreaks with a view to containing them. Importantly, all NICD laboratories are SANAS accredited, providing the assurance of quality. Occupational health and safety The National Institute for Occupational Health (NIOH) celebrated its 60th anniversary this year. It remains at the forefront of occupational health and safety in the country providing unique and specialised services in the field and continuing to undertake unique research. Academic affairs, research and quality assurance (AARQA) The NHLS is not only a laboratory service. Its other mandates are education and research. The NHLS provides the academic platform for the training of medical and other health science students and for specialist training of pathologists and medical technicians and technologists. Of concern is the low pass rate of medical registrars, for which measures have been put in place to redress. Research output remains high and relevant. Improvements in grant management would advance research output. This programme is also responsible for quality assurance in the laboratories. While internal quality assurance is ongoing the Board requires more focus on increasing the number of laboratories which are fully SANAS accredited. Laboratory services Laboratory services are the core of the NHLS, through which most services are provided and most revenue generated. There are 268 NHLS laboratories in the country which performed tests of varying complexity and cost. The national footprint of the NHLS makes laboratory and pathology services accessible to all South Africans, reaching the most distant rural hospitals and clinics. The improvements in laboratory turnaround times are especially pleasing. We look forward to increasing the number of laboratories with state-of-the-art facilities. STRATEGIC RELATIONSHIPS The NHLS is a Section 3A Public Entity. It is therefore incumbent on the NHLS and the Board to forge meaningful and sustainable relations and partnerships with all the key players in the public healthcare sector. The Board values the role that the Parliamentary Portfolio Committee on Health has played in its oversight role and guidance. The Board expresses its deep appreciation to the Minister and the Director-General of Health for their commitment to enabling the NHLS to fulfil its mandate and for their ongoing support, wisdom and attention to the NHLS. They have been ably supported by the Deputy- Director General of Health Regulation and Compliance, and his team. The Board has also been engaging and strengthening NHLS relations with the Provincial Departments of Health and we appreciate the attention that MECs and Heads of Department have given to the NHLS. We continue our valuable, mutually beneficial partnership with universities as we strive to jointly fulfil our academic and research responsibilities and ensure that the service learning platform provided in our laboratories and pathology services are of the standard required for training future generations of health professionals and provide the platform for our cutting edge research focussed on priority diseases in South Africa and Africa. The NHLS also engages positively with national industry bodies and associations and appreciates the role the trade unions have played in bringing concerns to our attention. Their contribution to the NHLS cannot be underestimated and will be vital to the Board as we seek to enhance our value proposition. The NHLS is well positioned internationally and in Africa. The African Society for Laboratory Medicine (ASLM), the United States Centre for Disease Control (CDC) and many others continue to be our key stakeholders, from whom we gain and with whom we share knowledge and best practice. The NHLS will continue to engage with international structures not only with the aim of improving laboratory medicine practice in our country, but on the continent as a whole, for the advancement of Africa s public healthcare systems. 10 National Health Laboratory Service

12 CHALLENGES AND THE YEAR AHEAD The NHLS is an extraordinary national asset that needs to be protected and nurtured and geared for a central role in the National Health Insurance programme. The Board has played its part in advancing and positioning the NHLS and working to ensure its sustainability, efficiency and quality. The foundation for this is financial stability. While the NHLS has asked for (and received) low tariff increases over the past years, it is positioned to be financially secure if provinces pay in full for the services they procure and if inroads are made into historic debt. The Board trusts that ongoing engagements with the provinces will facilitate payments, without which the NHLS status as a going concern could be threatened. Cash flow will be enabled by the replacement of the fee-for-service model with a modified capitated reimbursement model. Tariff structures must be updated to more accurately reflect costs as some tests are being undercharged and others overcharged. The NHLS Board will continue to drive good governance and fiscal management and seek efficiency gains to continually provide better value for money. This will require the NHLS to review its service platform to identify points of duplication and seek possibilities of merging sections of laboratories where the workload is too low for efficiency, while ensuring that we do not compromise services to remote areas. The year ahead will see a focus on increased operational efficiencies, improved turnaround times and improved customer relations. The NHLS is privileged to be served by staff of the calibre it employs and the low turnover rate suggests that our staff are committed to the organisation. However, this cannot be taken for granted and was the basis for the Board addressing historical anomalies in remuneration in the NHLS, albeit that challenges were faced in implementation. Staff also need to be rewarded for their expertise and performance and the Board will be putting systems in place to ensure that this happens. The Board has been concerned by the weak implementation of procurement policies including: contracts, especially those above R10 million being signed without Board approval, poor asset management, IT infrastructure essential to our systems, too few laboratories being externally accredited and the high failure rate in pathologist examinations. The Board is guiding the way forward to address these and other challenges as it expresses its commitment to ensuring the efficient and principled running of the NHLS. Step by step, obstacles to achieving this are being removed, and new and better practices are being embedded into the organisation. The Board s responsiveness to allegations and our vigilance in governance have led to the unearthing of some alleged irregularities and inefficiencies in the NHLS. These are being addressed in accordance with the prescripts of the Public Finance Management Act. ACKNOWLEDGEMENTS I would like to thank the Minister of Health, Dr Aaron Motsoaledi and the National Department of Health, for their commitment to the NHLS, to the MECs and Heads of Provincial Departments of Health for the fruitful relationships fostered during the year under review. My heartfelt thanks to my predecessor as Chairperson of the Board, Professor Barry Schoub. He led the NHLS for most of the year under review. I thank my fellow Board members who have shown deep commitment to and passion for their roles on the Board and to its subcommittees and to the Governance Committee for the additional responsibilities they have taken on. It has been a privilege to Chair a Board with such commitment. At the heart of any organisation are its staff. My sincere gratitude goes to all NHLS employees who put the organisation and its role in service to our country and community first and who continually strive for excellence and efficiency. It is our duty to provide value for what is effectively public money that is being entrusted to the National Health Laboratory Service and for its Board to ensure the governance, oversight and strategy to accomplish this. Prof. Eric Buch Chairperson of the NHLS Board Annual Report 2016/17 11

13 Acting Chief Executive Officer s Overview GENERAL FINANCIAL REVIEW OF THE NHLS As an agency of the Department of Health, the NHLS is mandated to provide efficient and quality assured laboratory services to almost 85% of the population that are dependent on the public health service. This mandate will become all the more important as the country strives toward the implementation of a National Health Insurance model. During the 2016/17 financial year, the NHLS has been successful in bringing about some stability to the financial status of the organisation, albeit still challenged by the outstanding debts owed to it. Acting CEO Prof. Shabir Madhi During 2016/17, the NHLS observed an increase in service provision and laboratory test consumption, partly due to the Department of Health initiative for enhancing the screening of South Africans for HIV infection and tuberculosis. This resulted in an increase in billing for laboratory tests from R6.4 billion in 2015/16 to R7.0 billion in the 2016/17 financial year. Average test revenue per capita increased from 5.2% to 7% in the 2016/17 financial year. Ninety-five percent of consumption of NHLS services is incurred by the provincial Departments of Health. The NHLS, however, only received 82% of the billed amounts from the provinces, resulting in it operating under cash-flow constraints. This resulted in further suspension of capital investment, including in the field of Information Technology, which has required urgent attention for the past few years. Furthermore, production costs at the NHLS increased from R4.8 billion to R5.8 billion, driven by factors such as direct labour cost (including salary adjustments over and above annual salary increases), unfavourable exchange rate fluctuations and growth in procurement of material. This represented a production cost increase of 21% year-on-year, compared to an increase of 14% in the previous financial year. Labour constituted 46% of the total expenses in 2016/17 compared to 37% in the previous financial year. The overall personnel costs exceeded the 2016/17 budget by 8.2%, largely driven by the negotiated addition of a 13 th cheque for the A-C band staff, and compounded by the phasing in of further salary adjustments across the organisation. Material expenditure, as a percentage of revenue, remained constant at 36%. Although operational costs decreased overall by 39%, this too occurred within the context of limited capital infrastructure renewal, resulting in prolonging the already existing and muchneeded investment in capital revitalisation. Although there has been an improvement in receipt of payment for the majority of the provincial departments of Health, collection of current and accrued debt by some provincial departments of Health, continues to hamper the efficient functioning of the NHLS. As of 31 March 2017, the debt payable by provincial departments of Health amounted to R6.15 billion, including R4.7 billion that is older than 90 days. There are ongoing negotiations between the NHLS and the provinces that have accrued most of this debt, to settle these arrear amounts and enable the NHLS to continue contributing to the provision of quality laboratory services to the public health sector. IMPROVING OPERATIONAL EFFICIENCIES In the human resources management environment, the NHLS ensured that all leadership and critical positions were filled as speedily as possible, in both the support and laboratory situations. The turnaround time for filling positions was reduced to 59 days, against an annual target of 90 days. The NHLS prides itself in having a stable workforce that is committed to staying with and working for the organisation. This is evidenced by a turnover ratio of only 0.3% at the end of March 2017, against the set target of 10%. Furthermore, the vacancy rate stood at 5%, against a target of 18%. Going forward, the NHLS is in the process of implementing a new performance management system, to motivate high flyers and reward them at an appropriate level, while also addressing the issue of poor performance. 12 National Health Laboratory Service

14 The management of the NHLS recognises that ICT is a strategic vehicle that enables and supports the business as it strives to meet its strategic objectives. The ICT function plays a critical role, not only in enabling the business to operate, but also in improving customer service, through innovation and modernisation of the ICT infrastructure. During the period under review, the NHLS Management focused on implementing a number of initiatives to address challenges in the following three key areas: Unstable ICT infrastructure Shortage of ICT skills Inadequate ICT governance (processes and controls). The ICT environment of the NHLS remains under pressure due to chronic under-investment in this critical component, required for the optimal functioning of the organisation. This has had ramifications on other key functions of the organisation, including Supply Chain Management (SCM). The procurement of goods and services is an integral part of the overall success of the NHLS. The leadership of the organisation has to ensure that the procurement of goods and services is within the framework of the Public Finance Management Act (PFMA) and all related pieces of legislation. It is also the responsibility of management to ensure that these goods and services are procured from the right providers, at the right price, and as speedily as possible, without compromising quality. During the year under review, a number of structural shortcomings in the control of the awarding of tenders and SCM were identified. Some of these were in part due to the vigilance of NHLS employees in reporting suspected irregularities. These have been diligently followed up by the Board and the NHLS has now embarked on a rigorous programme to revamp and reposition its SCM Unit, which plays a strategic role within the organisation. The key objectives of this initiative will be to ensure adherence to all SCM processes and systems, and more importantly, to allocate properly skilled people and resources to this critical unit. The NHLS aims to have fully re-engineered this Unit and its operations by the end of the 2017/18 financial year. Despite the financial stress faced by the NHLS during 2016/17, it has refurbished old laboratories and buildings, some of which were at various stages of decay. This improved the morale and working conditions of employees, as well as enhanced health and safety. This project will continue until all outstanding and identified laboratories have been refurbished. IMPROVEMENT IN TURNAROUND TIMES Total test volumes for the year under review amounted to Turnaround times for various tests performed continued to show an improvement. On average, all tests were performed within the defined time frames, as indicated for some of the key tests in the table below: Performance Indicator Full-Year Actual Annual Target Status Percentage TB microscopy tests performed within 48 hours 95.72% 90% Achieved Percentage TB GXP tests performed within 48 hours 96.68% 90% Achieved Percentage CD4 tests performed within 48 hours 94.44% 85% Achieved Percentage viral load tests performed within 96 hours 87.3% 65% Achieved Percentage HIV PCR tests performed within 96 hours 81.90% 70% Achieved Percentage cervical smear tests performed within 5 weeks 96.87% 50% Achieved Percentage laboratory (FBC, U&E and LFT) tests performed within timeframes defined 85.83% 80% Achieved The above were achieved because of the NHLS continued focus on improving efficiencies in its laboratories, as well as raising the bar on customer service. CUSTOMER SATISFACTION SURVEY During the year, the NHLS conducted an External Customer Satisfaction survey to measure how its various customers perceived the quality of NHLS services. Overall, the feedback received was positive, although there are a number of areas that need to be worked on in order to meet the needs and expectations of customers, most importantly communication, training and skills development. In general, customers were pleased with the NHLS service culture, process efficiency, handling and resolution of queries and the quality of testing services. In the coming year NHLS Management will be working on addressing the issues that customers are not satisfied with, as well as on strengthening those areas where the NHLS is doing well. Annual Report 2016/17 13

15 REGISTRAR PASS RATE One critical area that the NHLS will be seeking to improve in the medium to long term is the pass rate of registrars. In the 2016/17 financial year, the pass rate stood at 36%, against a set target of 55%. Clearly, this situation needs to be addressed as a matter of urgency. Although the NHLS will be putting in more effort to improve this pass rate, it cannot do this alone and is very much dependent on its partnering academic institutions to assist. This includes ensuring greater exposure for under-graduate medical students to the pathology disciplines in their under-graduate years, failing which pathology as a career pathway will remain under-recognised and the current shortage of pathologists in South Africa will be further aggravated. STAKEHOLDER RELATIONS Continued engagement with customers and various stakeholders is critical to the success of the business. During the reporting period, various layers of management interacted with their stakeholders in their areas of control mostly to reach mutual understanding on areas of common interest and possible co-operation. At corporate level, the leadership continued to engage with stakeholders on issues pertinent to the business of the NHLS. These included engagement with the National and Provincial Departments of Health, CDC (US), donor organisations, Universities, the Parliamentary Portfolio Committee on Health, and other industry bodies and associations. PLANS FOR THE FUTURE Operating and maintaining a financially viable and stable organisation is a top priority for the leadership of the NHLS. Management will continue to work closely with all customers to ensure timeous payment for services rendered, so that the organisation can meet its liabilities and commitments. At the same time, the organisation will continue to ensure that all monies received are utilised for fulfilling its mandate, and will do everything possible to manage its operational costs very carefully through a robust cost-containment plan. ACKNOWLEDGEMENTS In conclusion, I would like to thank the Board of the NHLS for its continued support towards building a strong and stable organisation. I would also like to thank all NHLS staff members for their contribution to what has been a year of hard work, challenges and some achievements which are worthy of celebrating. We have seen some real and practical changes to the service delivery environment, but a lot still needs to be done to enable us to take the organisation to where we want it to be. I congratulate all our people, who, despite the pressures exerted on them during the period under review, have continued to maintain a dedicated and professional approach to their responsibilities, in the interest of developing a spirit of renewal and revitalisation. The strategic direction of the NHLS continues to evolve, our efficiency and effectiveness continue to grow, and our professional relationship with our customers is moving to a more mature level. We have an important role to play in the country s public healthcare system, and I believe that the NHLS is well placed to play its part. Prof. Shabir Madhi Acting CEO NHLS (effective 23 February 2017) 14 National Health Laboratory Service

16 Board Members Prof. Barry D Schoub Chairperson until December 2016 Dr Sibongile Zungu Vice-Chairperson Prof. Eric Buch Chairperson from January 2017 Mr Stanley Harvey Ms Ntombi Mapukata Mr Michael Shingange Ms Nelisiwe Mkhize Prof. Mary Ross Annual Report 2016/17 15

17 Prof. Haroon Saloojee Prof. Willem Sturm Dr Gerhard Goosen Mr Andre Venter Mr Michael Manning Dr Timothy Johan Tucker Mr Lunga Ntshinga Mr Ben Durham 16 National Health Laboratory Service

18 Prof. Larry Obi Dr Patrick Moonasar Ms Sphiwe Mayinga Prof. Shabir Madhi Dr Zwelibanzi Mavuso Dr Balekile Mzangwa Annual Report 2016/17 17

19 Statement of Responsibility and Confirmation of Accuracy for the Annual Report To the best of our knowledge and belief, we confirm the following: All information and amounts disclosed in the Annual Report are consistent with the Annual Financial Statements audited by SizweNtsalubaGobodo Inc. The Annual Report is complete, accurate and free from any omissions. The Annual Report has been prepared in accordance with the Annual Report Guidelines as issued by the National Treasury. The Annual Financial Statements (Part E) have been prepared in accordance with the Standards of Generally Recognised Accounting Practice (GRAP) applicable to the NHLS. The Accounting Authority is responsible for the preparation of the Annual Financial Statements and for the judgments made in this information. The Accounting Authority is responsible for establishing, and implementing a system of internal control, designed to provide reasonable assurance as to the integrity and reliability of the performance information, the human resources information and the Annual Financial Statements. The external auditors are engaged to express an independent opinion on the Annual Financial Statements. In our opinion, the Annual Report fairly reflects the operations, the performance information, the human resources information and the financial affairs of the NHLS for the financial year ended 31 March Yours faithfully Prof. Shabir Madhi Acting Chief Executive Officer Prof. Eric Buch Chairperson of the Board 31 July National Health Laboratory Service

20 Overview ABOUT THE NHLS The National Health Laboratory Service (NHLS) is a national public entity, established in terms of the National Health Laboratory Service Act, No. 37 of 2000, to provide quality, affordable and sustainable health laboratory and related public health services. It has approximately 288 laboratories across the nine provinces of South Africa, excluding depots, and serves approximately 80% of the South African population. The NHLS is the main provider of clinical support services to the national, provincial and local departments of Health through its countrywide network of quality assured diagnostic laboratories. It also provides surveillance support for communicable diseases, occupational health and cancer. The NHLS is managed according to the provisions of the National Health Laboratory Services Act; the NHLS Rules, gazetted in July 2007; and the Public Finance Management Act (PFMA), No. 1 of It is a state owned organisation governed by a Board and a Chief Executive Officer. It has a clear organisational structure consisting of a Head Office in Sandringham, Johannesburg, six regions (Mpumalanga and Limpopo; KwaZulu-Natal; Eastern Cape; Western and Northern Cape; Free State and North West; and Gauteng) and three institutes (National Institute for Communicable Diseases (NICD); National Institute for Occupational Health (NIOH); and National Cancer Registry). Each region is headed by a Business Area Manager who reports directly to a Chief Operations Officer. The creation of six regions is designed to ensure that the NHLS plans, agrees budgets and monitors laboratory services jointly with provincial health partners, with the intention that laboratory services are seen and accepted as part of the public health delivery system. The NHLS delivers services throughout the public sector from academic, provincial tertiary, regional and district hospitals to primary healthcare facilities. The level of complexity and sophistication of services increases from the peripheral laboratories to the central urban laboratories (with specialised surveillance infrastructure existing at specific sites). South African Vaccine Procedures (SAVP) is a wholly owned subsidiary of the National Health Laboratory Service and provides the following services: The manufacture of biologicals, namely polyvalent, Echis, Boomslang, spider, and scorpion antivenom Safety testing for pharmaceutical companies Research on routine products authorised via the animal ethics committee involving animals Preparation of horse and sheep serum Preparation and sampling of horse blood. VISION Africa s centre of excellence for innovative laboratory medicine MISSION To provide quality, affordable and sustainable health laboratory medicine, provide training for health science education and undertake innovative and relevant research. Annual Report 2016/17 19

21 VALUES The National Health Laboratory Service (NHLS) has identified the following values as the principles that will govern behaviour of all employees within the organisation: Value Description 1. Care Caring about the environment and society: This involves consideration of our impact on the environment and local communities, acting with concern and sensitivity. The National Health Laboratory Services (NHLS) is committed to behave ethically and contribute to the economic development of the workforce, community and society at large. It s about giving back to society and the environment as well as capacity building for a sustainable future. 2. Unity of Purpose All Working together towards a common goal: All employees should be united by a common vision and support each other in contributing to a beneficial and safe working environment. Teamwork and cohesion are key and collaboration should include pooling resources and communicating about each other s roles. Teamwork and cohesion are key and collaboration should include pooling resources and communicating about each other s roles. Foster trust and honesty in interactions with colleagues and behave professionally. Value all contributions, treat everyone consistently and fairly and capitalize on diverse viewpoints. Address and resolve conflicts effectively. Listen to others to fully understand and give clear, concise information when communicating expectations and accountabilities and providing feedback during coaching. Making NHLS goals a priority, using NHLS resources wisely and effectively and taking responsibility for your work. 3. Service Excellence Valuing good work ethics and striving towards service excellence for customers: This represents being committed to working with customers and building good relationships with them by understanding their needs, responding quickly and providing appropriate solutions. We treat them with respect at all times; we are helpful, courteous, accessible, responsible and knowledgeable in our interactions. We understand that we have internal and external customers who we provide services and information to. This information should be presented in a clear and concise form, where the message is adapted to the audience. 4. Transformation Looking forward to the future and growing together: This encompasses investing in professional growth of staff by sharing knowledge and experience, peer networking, education through training and seeking opportunities to develop. It covers creative problem solving, informed risk-taking, learning from our mistakes and experiences and behaving professionally. We should adapt to change timeously and positively, address setbacks and ambiguity and adapt our thinking/approach as the situation changes. Ideas should be shared and implemented effectively. Leaders should develop innovative approaches and drive continuous improvement as well as effective and smooth change initiatives. 5. Innovation Pioneering relevant research solutions and training: Identifying needs to broad challenges present in local society. Creating space for research to be done and backing fresh ideas by bringing them to the market. Pursuing cost-effective solutions in research and training. Monitoring the impact of solutions on the challenges faced. Supporting the application of new ways of doing things at senior management level in the organisation. Encouraging pioneer personalities to operate outside the research box. Rewarding and publicising boundary-breaking initiatives. Giving credit to those to whom it is due. 6. Integrity Working with integrity and responsibility: Setting and achieving goals, consistently delivering business results while complying with standards and meeting deadlines. Displaying commitment to organisational success; proactively identifying ways to contribute and taking initiative to address problems/opportunities. Building efficiencies in the best use of public resources. 20 National Health Laboratory Service

22 Legislative and Other Mandates The legislative mandate of the NHLS is derived from the Constitution, the National Health Act, No. 61 of 2003, the NHLS Act, No. 37 of 2000, and several pieces of legislation, regulations and policies passed by Parliament. CONSTITUTIONAL MANDATE The Constitution of the Republic of South Africa Act, No. 108 of 1996, places obligations on the state to progressively realise socio-economic rights, including access to healthcare. Section 27 of the Constitution states as follows concerning healthcare, food, water, and social security: (A) Everyone has the right to have access to healthcare services, including reproductive healthcare; sufficient food and water; and social security, including, if they are unable to support themselves and their dependents, appropriate social assistance. (B) The state must take reasonable legislative and other measures, within its available resources, to achieve the progressive realisation of each of these rights; and (C) No one may be refused emergency medical treatment. THE NATIONAL HEALTH ACT, NO. 61 OF 2003 This Act provides a framework for a structured uniform health system within South Africa, taking into account the obligations imposed by the Constitution and other laws on the national, provincial and local governments with regard to health services. The objects of the National Health Act (NHA) are to: Unite the various elements of the national health system in a common goal to actively promote and improve the national health system in South Africa; Provide for a system of co-operative governance and management of health services, within national guidelines, norms and standards, in which each province, municipality and health district must address questions of health policy and delivery of quality healthcare services; Establish a health system based on decentralised management, principles of equity, efficiency, sound governance, internationally recognised standards of research and a spirit of enquiry and advocacy which encourage participation; Promote a spirit of co-operation and shared responsibility among public and private health professionals and providers and other relevant sectors within the context of national, provincial and district health plans; Create the foundations of the healthcare system that must be understood alongside other laws and policies that relate to health. THE NATIONAL HEALTH LABORATORY SERVICE ACT, NO. 37 OF 2000 The Act mandates the NHLS to provide cost-effective and efficient health laboratory services to all public sector healthcare providers; any other government institution inside and outside of South Africa that may require such services; and any private healthcare provider that requests such services. The Act also mandates the NHLS to support health research and provide training for health science education. ADDITIONAL GOVERNANCE CONTEXTS The NHLS is required to comply, inter alia, with the following: General rules made in terms of section 27 of the National Health Laboratory Service Act Companies Act, No. 71 of 2008 Protocol on Good Corporate Governance in the Public Sector Public Finance Management Act, No. 1 of 1999 (as amended) Treasury Regulations issued in terms of the PFMA, 1999 Annual Report 2016/17 21

23 Preferential Procurement Framework Act, No. 5 of 2000 Relevant legislation applicable to the Health Sector Annual Report Guide for Schedule 3A and 3C Public Entities King III Code on Good Corporate Governance. OTHER POLICY INITIATIVES The NHLS is committed, as articulated in its Strategic Plan 2015/ /20, to support the following: The National Health Insurance (NHI), which will cover a defined basket of pathology services that are aligned with the package of services required per level of care. The pathology service will be delivered at the public healthcare level as well as at higher levels of care as defined by the NHLS Act and in line with the National Health Act. The latter requires the setting, monitoring and enforcing of quality control standards applicable to pathology services, to ensure patient safety. The following are functions in the National Public Health Institute for South Africa (NAPHISA)»» Communicable disease»» National Cancer Registry»» Occupational Health»» Non-communicable disease»» Injury and violence prevention. The various departments are still to be determined but the NICD, NCR, NIOH will naturally be incorporated. 22 National Health Laboratory Service

24 Organisational Structure Minister of Health NHLS Board Audit and Risk Committee Company Secretary Chief Executive Officer Head: Risk Management Internal Audit Senior Manager: Monitoring and Evaluation Manager: Legal Support Senior Manager: Communication, Marketing and PR Chief Financial Executive Manager: Executive Manager: Executive Manager: Chief Information Officer HR Operations AARQA Officer Director NICD Director NIOH Executive Manager: NPP Manager SAVP Annual Report 2016/17 23

25 PART B Performance Information 24 National Health Laboratory Service

26 Auditor s Report: Predetermined Objectives The independent auditor performed the necessary audit procedures on performance information to provide reasonable assurance in the form of an audit conclusion. The audit conclusion on the performance against predetermined objectives is included in the report to management, with material findings being reported under the Predetermined Objectives heading in the Report on other Legal and Regulatory Requirements section of the Auditor s Report on pages 188 to 194. Annual Report 2016/17 25

27 Situational Analysis SERVICE DELIVERY ENVIRONMENT The NHLS continued to provide quality service to its stakeholders. The NHLS strives to make its services accessible to all communities by being present in all hospitals and collecting samples from all primary healthcare facilities on a daily basis. The NHLS successfully completed the rollout of its new Laboratory Information System (LIS) in all laboratories across the country, which resulted in seamless and integrated management of laboratory data. The NHLS Corporate Data Warehouse (CDW) enabled the development of the first National CD4/Viral Load Monitoring Dashboard, an online tool that monitors CD4 count and viral load in HIV positive patients, which was launched in November The NHLS s IT infrastructure, which has been a challenge for some time, was prioritised during the reporting period, and the aim is to build a strong IT foundation based on robust and agile infrastructure with core laboratory and enterprise capabilities and innovative solutions that help build state-of-the-art laboratory services in the country. The South African Vaccine Producers (SAVP), a wholly-owned subsidiary of the NHLS, has continued to supply strategic products, with excellent results. Excellent feedback was received from as far as Spain and Thailand, including a report from Kenya stating that the antivenom has saved lives in these serious snakebite areas. ORGANISATIONAL ENVIRONMENT Burden of Disease South Africa experiences a quadruple burden of disease comprising communicable diseases, non-communicable diseases and occupational health and injuries. The NHLS is the main provider of clinical support services to the national and provincial Departments of Health through its country-wide network of quality assured diagnostic laboratories. It also provides surveillance support for communicable diseases and cancer, as well as occupational and environmental health services, thereby assisting in addressing the burden of disease. The NHLS supports government s plans for addressing the challenges of HIV/AIDS and TB in an integrated manner. Hence, the NHLS has been and will remain an important partner in the successful implementation of the HIV/AIDS Counselling and Testing (HCT) Campaign, the Prevention of Mother-to-Child Transmission (PMTCT), and the Comprehensive Care, Management and Treatment (CCMT) Programmes through the National Priority Programme (NPP) Unit. The announcement by the Minister of Health, Dr Aaron Motsoaledi, during his budget speech on 10 th of May 2016 that the country would implement the World Health Organization (WHO) evidence-based guidelines on Universal Test and Treat (UTT) by 1 September 2016; is expected to have an impact on the demand of service by the Department of Health at various levels. The NHLS is a custodian of a wealth of valuable health data that could inform policy and guidelines through collaborative engagement and our diagnostic and monitoring services are critical in contributing to the reduction of disease progression, improving quality of care, quality of life and to ultimately reduce premature deaths. Accessibility to Pathologist Services Pathologists play a vital role in health laboratory services. There is a clear need to improve access to pathologists support outside of the major academic centres. Placement of clinical and mono-specialist pathologists at provincial, tertiary and regional laboratories is desirable. Any clinician working in the public sector should, at the least, have telephonic access to a pathologist/pathology registrar in the relevant discipline for clinically-related queries. Using a combination of on- and off-site pathologists, a pathologist hotline for relevant queries should be established and formally staffed with duty rosters communicated to clinicians. Furthermore, pathologists should participate in the District Clinical Support Teams (DCSTs) as envisaged under the NHI, which are incorporated in the clinical platform, thereby complementing patient care, and contributing to patient outcomes by adding value in clinical decision-making. Accessibility to Testing Services The current model involves an extended laboratory footprint with numerous services provided close to the periphery. The NHLS will be guided by the directives, policies and guidelines of the National Department of Health. Accessibility to services can be extended through electronic access to test results. Doctors and nurses rely on the NHLS to inform decisions about patient diagnoses and treatment. 26 National Health Laboratory Service

28 A technology-driven results system is far more superior in terms of time, cost and efficiency than courier-delivered paper results, and includes web-accessible results and results transmitted by SMS printers and mobile cellular devices. Point-of-Care Testing (POCT) could revolutionise laboratory and diagnostic services for patients and health providers and improve access. Rapid technological advances have ensured that this type of testing performed near or on site, has become a reality and is the fastest growing segment of the diagnostic industry. Aspects of quality assurance and control, instrument monitoring, as well as download of results into the LIS as part of patient pathology records and public health surveillance are currently receiving attention through pilot studies conducted by the NHLS. National Health Insurance (NHI) Government has tabled the NHI in a bid to expand accessible healthcare to all South Africans and to provide universal coverage of health services, while controlling costs. The NHLS, together with the Department of Health are working on means to reduce laboratory diagnostic test costs through rational laboratory usage or electronic gatekeeping projects. The NHLS is optimising its strategic position as a partner to the Department of Health through collaboration at various levels, from health facilities, district, region, provincial tertiary and national central institutions to the National Department of Health. The public pathology services in South Africa constitute less than 3% of the total health spend in the public sector, yet the benefit of pathology to health is established in both developed and developing countries, from training of undergraduate and postgraduate health professionals to clinical consultation, surveillance, infection control and prevention, diagnosis and monitoring of disease. Data from developed countries show that pathology services are important in 70 80% of critical medical decisions. Health promotion, strongly emphasised in the NHI policy, requires a thorough understanding of the epidemiology of disease in South Africa. National laboratory surveillance is crucial to providing detailed information on the national and local level to inform policy and drive appropriate interventions. The NHLS has significant surveillance capacity, with a data powerhouse supported by a seamless LIS. In this regard, the NHLS is a national asset. Management Information Systems The power of this database has already been demonstrated with the national mapping of multi-drug and extensive drug resistant tuberculosis. A national LIS is required to allow retrieval of patient results as patients are referred or migrate between districts. The establishment of a business intelligence unit dealing with patient data will improve decision-making and healthcare provision. Furthermore, such a system will allow the development of consistent gatekeeping to prevent requests of unnecessary testing and reduce wasteful expenditure. Affordability The pathology services provided by the NHLS are more affordable than that of the private sector. Despite being cheaper, the NHLS also covers the cost of additional responsibilities, such as teaching, training, surveillance, outbreak control, scientific research, etc. For example, on the comprehensive care management treatment tests, the NHLS is on average 27% lower than the private sector. The entity is also in the process of implementing a new funding model (Modified Capitation Funding Model), which will include the following programmes: Minimum Clinical Data Set (MCDS): The project serves to improve the completeness of information, relating to the patient and specimen, as received on the NHLS request form. The billing of provinces is intricately linked to the request form, which is the source document that provides a link to the clinician. The accuracy and completeness of the patient and clinician demographics is vital to improved efficiency and billing. Electronic Gatekeeping (EGK): EGK in a pathology laboratory is the process whereby access to laboratory testing is controlled by using rules that are programmed into the LIS. These rules will either allow or disallow laboratory test to be done. Currently a set of EGK rules (formulated by a Hospital Medical Committee) are embedded in the LIS to promote rational use of laboratory services and save costs by avoiding unnecessary testing (e.g. repetitions) without compromising patient care, while encouraging good clinical practice. These projects will further enhance the affordability of the service. Annual Report 2016/17 27

29 Delivery on the Academic Mandate Research has been mandated as a function of the NHLS by the NHLS Act, No. 37 of A balance needs to be established between the research interests of the NHLS, the National Research Priorities (NRPs) of the country, individual researchers and external funders. Clear alignment between the research and service delivery agendas should be the goal. NHLS is mandated to support and undertake the training of pathologists and health science students and therefore has joint appointment arrangements with all universities with medical schools and some with dental schools, as well as a formal relationship with a number of comprehensive universities and universities of technology. Clinical pathology, the generalist discipline in the field, needs greater focus, as the requirement for clinical pathologists to be placed at regional laboratories increases to improve accessibility to pathology consultancy services. Resource Constraints Given its strategic alignment with government programmes, the NHLS must ensure that it has sufficient capacity, whether human, technology or Infrastructure, to adequately respond to the increasing burden of disease outbreak, despite the resource-constrained environment faced. This will require innovation, creativity, flexibility, agility, foresight, prioritisation of tests and services. KEY POLICY DEVELOPMENTS AND LEGISLATIVE CHANGES During the reporting period, there were no policy developments or legislative changes that impacted on the operations of the NHLS. Performance Information by Programme Introduction Performance information enables the organisation to track how well it is progressing in meeting its planned strategic goals and strategic objectives. It is key to effective management, including planning, budgeting, implementation, monitoring and reporting. It also facilitates accountability and enables stakeholders and interested parties to track progress and identify the scope of improvement plans and better understand the issues involved (Framework for Managing Performance Information: National Treasury). The report below does not sufficiently indicate progress made year-on-year because performance indicators have changed over the years. These changes were introduced by successive new leaders in an effort to make the performance indicators specific, measurable, achievable, realistic and time-related (SMART). Programme 1: Administration Programme Purpose The administration programme plays a crucial role in the delivery of NHLS services through the provision of a range of support services, such as organisational development, Human Resources and labour relations, information technology, property management, security services, legal services, communication and integrated planning. The NHLS relies heavily on the effective management of financial resources and procurement processes as administered within the financial department. Generating sufficient revenue remains a critical focus area for NHLS to ensure financial viability and sustainability. The programme comprises four sub-programmes, as set out below. Sub-Programme Financial Management The purpose of this sub programme is to manage the finances of the NHLS. Strategic Objective 1.1: To improve the liquidity position of the NHLS Objective Statement: Improve the cash flow position of the NHLS by improving the cash flow coverage ratio from 2.2 to 2.6 by 2020 and thereby ensure that there is liquid capital to implement key plans and priorities. Increase the current ratio rating from 2.4 to 2.6 by 2020 to optimise the margin of current assets over current liabilities. 28 National Health Laboratory Service

30 Programme 1: Administration 1.1 Sub-Programme: Financial Management 2016/17 Planned Target Performance Indicator 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Actual Current ratio (current New New New 2.9 times 2.7 Not achieved assets/current liabilities) Cash flow coverage ratio New New New 2.7 times 2 Not achieved (operating cash in-flows/ total debt) Turnover (including other New 6.8bn 7.1bn Achieved income): R bn Percentage of materials to 29.9% 31.5% New 38% 39% Achieved sales Number of creditor days New Achieved Reason for Deviation from Planned Target Number of debtor days New This is due to delayed payments from the provinces, especially Gauteng and KZN Sub-Programme Governance and Compliance The purpose of this sub-programme is to provide support services and ensure compliance with relevant legislation. Strategic Objective 1.2: To maintain the unqualified audit opinion of the NHLS until 2020 Objective Statement: Provide support services and ensure compliance with relevant legislation. Uphold audit outcome by ensuring continuous management practices through compliance with standard operating procedures and systems within the NHLS. 1.2 Sub-Programme: Governance and Compliance Performance Indicator Audit opinion of the Auditor-General Expenditure as a percentage of turnover 2013/14 Actual 2014/15 Actual 2015/16 Actual New New Unqualified audit report 2016/17 Planned Target Unqualified audit report 2016/17 Actual Qualified Reasons for Deviation from Planned Target See detailed Auditor s Report New New New 96% 94% Improved efficiencies Sub-Programme Information Communication and Technology The purpose of this sub-programme is to develop and implement an integrated ICT governance framework by focusing on the business continuity plan and supporting the needs and requirements of end users by Strategic Objective 1.3: To ensure that 100% of registered users have access to the Trak Web View system by 2020 Objective Statement: Develop and implement an integrated ICT governance framework by focusing on the business continuity plan and supporting the needs and requirements of the end-users by 2020 utilise ICT mechanisms for improved communication, marketing and branding purposes. Strategic Objective 1.4: To increase the systems availability to 99.5% by 2020 Objective Statement: Improve and enhance systems and networks to improve and maintain uptime and accessibility of the system. Annual Report 2016/17 29

31 1.3 Sub-Programme: Information Communication and Technology Performance Indicator Percentage of registered users utilising the system (Trak Web View) 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual Reasons for Deviation from Planned Target New New New 75% 30% The NHLS will put strategies in place to encourage end-users to access the results on the web Percentage network uptime New New New 99% 99% Achieved Percentage uptime of the Laboratory Information System (LIS) Percentage uptime of Oracle Percentage uptime of Thusano system Percentage calls logged resolved within prescribed timeframes New New New 99% 95% Not Achieved. This is due aging IT infrastructure. New New New 99% 99% Achieved New New New 99% 82% Thusano crashed during the course of the year and was down for some time, this affected the average uptime. New New New 95% 83% Sometimes some jobs take longer than anticipated as a result the average turnaround time was negatively affected. Sub-Programme Human Resource Management The purpose of this sub-programme is to provide effective services through efficient processes and adequate human resources. Strategic Objective 1.5: To ensure adequate and skilled human resources by 2020 Objective Statement: Provide effective services through efficient processes and adequate human resources and improve the motivation and performance levels of all employees. 1.4 Sub-Programme: Human Resources Performance Indicator 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual Reasons for Deviation from Planned Target Staff turnover ratio 8% 9% New 10% 5.0% Implementation of reward and remuneration system Average turnaround time to New New New 90 days 62.2 days Improved efficiencies fill a vacancy (in days) Percentage of employment equity achieved 94% 82% New 83% 89% Achieved Percentage of contracted employees performance review concluded biannually Percentage of employees trained as per the WSP New New New 90% 63% Management of the system needs to be improved so that tracking of the agreements can be monitored easily New New New 85% 91% Achieved Vacancy Rate New 18% 5% Posts were filled much faster, dropping the vacancy rate to 5% Contribution to Strategic Outcome Orientated Goals Strategic Objective To improve the liquidity position of the NHLS To maintain the unqualified audit opinion of the NHLS until 2020 To ensure that 100% of the registered users have access to the Trak Web View system by 2020 To increase the systems availability to 99.5% by 2018 To ensure that the workforce of NHLS is capacitated and motivated Strategic Outcome Orientated Objective Sound governance and sound financial management Performance driven processes and systems Adequate and competent human capital 30 National Health Laboratory Service

32 Changes to Planned Targets There were no changes to planned targets for Programme 1 in 2016/17. Linking Performance to Budget 2016/17 Actual Expenditure 2015/16 Actual Expenditure Budget Over/Under Budget Over/Under Programme /17R 000 Expenditure 2015/16 Expenditure Administration Reasons for Deviations from the Budget Underspent in 2016/17 due to cash flow constraint (Infrastructure enhancement) Provision and bad debts Programme 2: Surveillance of Communicable Diseases Programme Purpose The National Institute for Communicable Diseases (NICD) is a national public health institute for South Africa, which in collaboration with the NHLS, provides reference microbiology, virology, epidemiology, surveillance and public health research to support government s response to communicable disease threats. Strategic Objective 2.1: To uphold communicable disease surveillance level at 90% by 2020 and beyond Objective Statement: Maintain a comprehensive communicable disease surveillance programme for leading infectious diseases associated with morbidity/mortality. Strategic Objective 2.2: To maintain response levels at 100% for outbreaks responded to within 24 hours after notification Objective Statement: Maintain capacity and resources to be able to respond to outbreaks of diseases within prescribed timeframes and requirements. Strategic Objective 2.3: To ensure all NICD laboratories remain SANAS accredited Objective Statement: Maintain standards and processes within laboratories to retain SANAS accreditation for all laboratories. 2.1 Sub-Programme: Surveillance of Communicable Disease Performance Indicator Percentage of identified prioritised diseases under surveillance Number of peer reviewed journals published annually Number of NICD communiqués published on website Percentage of outbreaks responded to within 24 hours after notification Percentage of provinces with appointed epidemiologists (1 per province) Number of field epidemiologists qualified Percentage of SANAS accredited NICD laboratories 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 90% 90% Achieved New New New Achieved New New Achieved New New New 100% 100% Achieved Reasons for Deviation from Planned Target New New 44% 80% 36% Some of the epidemiologists were appointed outside the period under review. There are however seven epidemiologists in seven of the nine provinces, resulting in a 67% coverage. New New New 5 14 Achieved New New New 100% 100% Achieved Annual Report 2016/17 31

33 Contribution to Strategic Outcome Orientated Goals Strategic Objective To uphold communicable disease surveillance level at 90% by 2020 and beyond To maintain response levels at 100% for outbreaks responded to within 24 hours after notification Strategic Outcome Orientated Objective Accessible Pathology Service Footprint Changes to Planned Targets There were no changes to planned targets for Programme 2 in 2016/17. Linking Performance to Budget Programme 2 Budget 2016/17R /17 Actual Expenditure Over/Under Expenditure Budget 2015/ /16 Actual Expenditure Over/Under Expenditure Surveillance and Communicable Diseases Reasons for Deviation from Budget Underspent on direct labour in 2016/17 and 2015/16. Programme 3: Occupational Health and Safety Programme Purpose The National Institute for Occupational Health is a National Public Health Institute, which provides occupational health and safety services across all sectors of the economy to improve and promote worker s health and safety. The Institute achieves this by 1. Providing occupational medicine, hygiene and laboratory services, 2. Conducting research and 3. Providing teaching and training in occupational health and safety. Included under the governance of the National Institute for Occupational Health is the National Biobank. There are five sub-programmes in this programme. Sub-Programme Occupational Health and Safety The purpose of this sub-programme is to provide quality and accredited laboratory services for all occupational health related matters. Strategic Objective 3.1: To increase the percentage of specialised laboratories accredited from 75% to 100% by 2020 Objective Statement: Provide quality and accredited laboratory services for all occupational health related matters. Strategic Objective 3.2: To conduct 95% of all occupational health laboratory services within turnaround times by 2020 Objective Statement: Improve efficiencies in conducting occupational health laboratory tests within predefined turn-around times. Strategic Objective 3.3: To increase the number of occupational hygiene assessments conducted from 17 annually to 175 by 2020 Objective Statement: Prevent occupational disease and injury and promote occupational health and safety through increased number of assessments conducted. 32 National Health Laboratory Service

34 3.1 Sub-Programme: Occupational Health and Safety Performance Indicator Percentage of NHLS laboratories utilising OHASIS Percentage of four specialised laboratories accredited with a relevant and recognised accreditation body Percentage of occupational health laboratory tests conducted within predefined turnaround time Number of occupational hygiene assessments conducted Percentage of occupational health and safety queries answered Number of projects conducted with an external partner 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 planned 2016/17 Actual New New New 100% 100% Achieved New New 88% 75% 75% Achieved New New New 85% 93% Achieved New New New Achieved New New New 100% 98% Not achieved Reasons for Deviation from Planned Target New New Many of the sections that had promised to contribute to this indicator lost senior staff members who were responsible for the projects, hence the target could not be met. Sub-Programme Technical Support for Occupational Health and Safety The purpose of this sub-programme is to provide occupational medical services to the NHLS and to be the occupational medical practitioner for the NHLS. Strategic Objective 3.4: To improve occupational health by increasing OHS assessments conducted to (cumulatively) by 2020 Objective Statement: Provide occupational medical services to the NHLS and to be the Occupational Medicine Practitioner for the NHLS. Strategic Objective 3.5: To perform 100% of all autopsy examinations within required timeframes by 2020 Objective Statement: Maintain existing efficiencies in performing autopsy examinations within determined timeframes. Strategic Objective 3.6: To annually produce and update the OHS technical guidelines by 30 March 2020 Objective Statement: Develop, review and promote the implementation of an evidence-based healthcare package of occupational health and safety. 3.4 Sub-Programme: Technical Support for Health and Occupational Safety Performance Indicator Number of Occupational Health and Safety assessments done for the NHLS Number of queries handled (including advisory services) for the NHLS 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New Achieved New New New Achieved Reasons for Deviation from Planned Target Annual Report 2016/17 33

35 3.4 Sub-Programme: Technical Support for Health and Occupational Safety Performance Indicator Percentage of autopsy examinations completed and reported on Number of OHS technical guidelines produced and disseminated 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 100% 101% Achieved Reasons for Deviation from Planned Target New New It has been completed but procedurally still needs to be endorsed by the legal team and the unions. This process may take time depending on the stakeholders availability. Sub-Programme Occupational Health and Safety Research The purpose of this sub-programme is to promote, conduct research and submit reports and publications pertaining to Occupational Health in South Africa. Strategic Objective 3.7: To increase research outputs and reports to 135 by 2020 to improve the surveillance of exposure to disease, and improve management and prevention of occupational disease and injury Objective Statement: Promote, conduct research and submit reports and publications pertaining to occupational health in South Africa. Strategic Objective 3.8: To increase the number of organisations which have implemented OHASIS to 3 by 2020 Objective Statement: Advance the implementation of the OHASIS within the public service and state-owned enterprises by Sub-Programme: Occupational Health and Safety Research Performance Indicator Number of published scientific articles including peer reviewed publications and reports Number of surveillance reports produced and disseminated Number of government departments or stateowned enterprises which have implemented OHASIS 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New Achieved New New New 2 2 Achieved New New Achieved Reasons for Deviation from Planned Target Sub-Programme Training and Development for Occupational Health and Safety The purpose of this sub-programme is to promote capacity building and strengthen Human Resources on Occupational Health and Safety by contributing to the teaching and training of doctors, nurses, scientists, hygienists and occupational health practitioners by Strategic Objective 3.9: To maintain and increase OHS professionals trained on an annual basis Objective Statement: Promote capacity building and strengthen human resources on occupational health and safety by contributing to the teaching and training of doctors, nurses, scientists, hygienists and occupational health practitioners by National Health Laboratory Service

36 3.9 Sub-Programme: Training and Development for Occupational Health and Safety Performance Indicator Number of occupational medicine registrars under training Number of medical scientist/experiential learners under training Number of medical doctors trained in Diploma in Occupational Health programmes by the NIOH Number of public health medicine registrars who received training at the NIOH Number of pathology registrars rotating at NIOH per annum Number of postgraduate students under supervision 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 4 5 Achieved New New New 5 7 Achieved New New New Achieved New New New 3 4 Achieved New New Achieved New New Achieved Reasons for Deviation from Planned Target Sub-Programme National Biobank The purposes of this sub-programme is to store and secure Bio materials and associated data to enable research through specimen storage with its associated data by using short, medium and long term storage of bio material and associated data for research purposes. Strategic Objective 3.10: To improve turnaround times to respond to specimen requests from five to three days by 2020 by using short, medium and long-term storage of biomaterial and associated data for research purposes Objective Statement: Store and secure biomaterials and associated data to enable research through specimen storage with its associated data by using short, medium and long-term storage of biomaterial and associated data for research purposes. Strategic Objective 3.11: To increase international relationships with Biobank societies from two to three for sharing of information and keeping up with international Biobank best practices by 2020 Objective Statement: Establish international relationships with Biobank societies for sharing of information and keeping up with international Biobank best practices Sub-Programme: National Biobank Performance Indicator Average turnaround time (in days) to respond to specimen requests Maintaining Membership with International Biobank Societies 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual Reasons for Deviation from Planned Target New New New 4 0 This is long-term storage of specimens in the biobank. During the reporting period, there were no specimen requests. In addition the ethical oversight is still being finalised New New New 2 0 Both memberships were paid and certificates subsequently sent Annual Report 2016/17 35

37 Contribution to Strategic Outcome Orientated Goals Strategic Objective To increase the percentage of specialised laboratories accredited from 75% to 100% by 2020 To conduct 95% of all occupational health laboratory services within turnaround times by 2020 To increase the number of occupational hygiene assessments conducted from 17 annually to 175 (cumulative) by 2020 To prevent occupational disease and injury and promote occupational health and safety through increased number of assessments conducted To perform 100% of all autopsy examinations within required timeframes by 2020 To increase research outputs and reports to 135 by 2020 to improve the surveillance of exposure to disease, and improve management and prevention of occupational disease and injury To improve turnaround times to respond to specimen requests from 5 to 3 days by 2020 by using short-, medium- and long-term storage of biomaterial and associated data for research purposes To increase international relationships with Biobank societies for sharing of information and keeping up with international Biobank best practices from 2 to 3 by 2020 Strategic Outcome Orientated Objective State-of-the-art laboratories Accessible to pathology service footprint Academic excellence International Best Practice Laboratory Medicine Improved stakeholder relations Changes to Planned Targets There were no changes to planned targets for Programme 3 in 2016/17. Linking Performance to Budget 2016/17 Actual Expenditure R /16 Actual Expenditure R 000 Budget Over/Under Budget Over/Under Programme /17 R 000 Expenditure 2015/16 R 000 Expenditure Occupational Health Reasons for Deviations from the Budget Underspent on direct labour in 2016/17 and 2015/16. Programme 4: Academic Affairs, Research and Quality Assurance Programme Purpose The main purpose of this programme is to strengthen the mandate of the NHLS of maintaining and providing quality assured and accredited laboratory medicine. One of the focus areas within this programme is to ensure that research is conducted to contribute to service delivery improvement and quality. The aim is to oversee and collaborate with various training institutions that contribute to the development of qualified and skilled people operating within the scientific field of pathology services. The programme comprises three sub-programmes. Sub-Programme Quality Assurance The purpose of this sub-programme is to improve Total Quality Management systems, processes, equipment and resources within laboratories to increase accreditation of laboratories. Strategic Objective 4.1: To increase levels of quality tests performed within the laboratories by ensuring laboratories are well equipped, resourced and maintained by 2020 and beyond Objective Statement: Improve Total Quality Management systems, processes, equipment and resources within laboratories to increase accreditation of laboratories. 36 National Health Laboratory Service

38 4.1 Sub-Programme: Quality Assurance Performance Indicator Percentage of laboratories accredited (National Central) Percentage of laboratories accredited (Provincial Tertiary) Percentage of laboratories accredited (Regional) 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual 88% 90% New 90% 90% Achieved Reasons for Deviation from Planned Target New New New 70% 47% Not achieved due to staff constraints 28% 55% 39% 40% 11% Percentage of laboratories achieving Proficiency Testing Scheme (PTS) performance standards of 80% New New New 80% 87% Improved efficiencies Sub-Programme Academic Affairs The purpose of this sub-programme is to promote capacity building of health professionals to strengthen a business case for sustained development for the NHLS through the development of pathologists, medical scientists and medical technologists Strategic Objective 4.2: To increase the pool of available pathology health professionals by 2020 Objective Statement: Promote capacity building of health professionals to strengthen a business case for sustained development for the NHLS through the development of pathologists, medical scientists and medical technologists. 4.2 Sub-Programme: Academic Affairs 2016/17 Planned Target Performance Indicator 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Actual Reasons for Deviation from Planned Target Registrar pass rate 75% 55% New 55% 29.0% This continues to be a New New New 55% 44.0% Medical Technologist pass rate Medical Technician pass rate New New New 60% 45.0% challenge, however, the NHLS has put strategies in place to improve the pass rate. Sub-Programme Research The purpose of this sub-programme is to increase the knowledge base on diseases and influence the decision taken to diagnose, treat and care for these diseases through research outputs and articles published. Strategic Objective 4.3: To increase research outputs that translate into diagnostic practice to 3 by 2020 Strategic Objective 4.4: To increase the number of peer reviewed articles published to 700 by 2020 Objective Statement: Increase the knowledge base on diseases and influence the decisions taken to diagnose, treat and care for these diseases through research outputs and articles published. Annual Report 2016/17 37

39 4.3 Sub-Programme: Research Performance Indicator Research reports submitted to influence policy R-value of grants attracted for health system strengthening (Rm) Percentage of personnel with library access and usage, electronic access coverage Number of research outputs translated into diagnostic practice Number of peer-reviewed articles published 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual 4 4 New 4 4 Achieved New New New R200 mil R276.6 mil Achieved New New New 70% 70% Achieved 9 12 New 10 5 Not Achieved New New New Achieved Reasons for Deviation from Planned Target Contribution to Strategic Outcome Orientated Goals Strategic Objective To increase levels of quality tests performed within the laboratories by ensuring laboratories are well equipped, resourced and maintained by 2020 and beyond To increase the pool of available pathology health professionals by 2020 To increase research outputs that translate into diagnostic practice to 3 by 2020 To increase the number of peer reviewed articles published to 700 by 2020 Strategic Outcome Orientated Objective Academic excellence Changes to Planned Targets There were no changes to planned targets for Programme 4 in 2016/17. Linking Performance to Budget Programme 4 Budget 2016/ /17 Actual Expenditure Over/Under Expenditure Budget 2015/ /16 Actual Expenditure Over/Under Expenditure Academic Affairs, Research and Quality Assurance Programme 5: Laboratory Service Programme Purpose This programme represents the core business of the NHLS, as mandated the NHLS Act, to provide cost-effective and efficient health laboratory services to all public sector health care providers; any other government institution within or outside the Republic that may require such services; and any private health care provider that requests such services. The Act also mandates the NHLS to support health research; and provide training for health science education. It is anticipated that the NHLS should provide a comprehensive, accessible, quality and timeous pathology service, resulting in improved patient care. The programme comprises five sub-programmes. Sub-Programme Increase accessibility to NHLS services The purpose of this sub-programme is to increase access to the NHLS laboratory services with the main aim of servicing all health care facilities as part of government health care services Strategic Objective 5.1: To increase the accessibility of pathology services to all health facilities by 2020 Objective Statement: Access to the NHLS laboratories should be increased with the main aim of servicing all health care facilities as part of government health care services. 38 National Health Laboratory Service

40 5.1 Sub-Programme: Increase accessibility to NHLS services Performance Indicator Percentage of Regional, Provincial Tertiary and National Central Hospitals with on-site NHLS services Percentage of district hospitals provided with NHLS services on site (numbers as gazetted in 2015/16) Percentage of primary health care facilities provided with daily NHLS specimen collection services 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 100% 100% Achieved New New New 70% 70% Achieved New New New 100% 100% Achieved Reason for Deviation from Planned Target Sub-Programme Operational Efficiency The purpose of this sub-programme is to decrease the overall turnaround times of all tests within every laboratory across South Africa and improve levels of quality of tests performed in the laboratories Strategic Objective 5.2: To improve the total turnaround time for tests performed by 2020 Objective Statement: Decrease the overall turnaround times of all tests within every laboratory across South Africa. Strategic Objective 5.3: To increase quality compliance of tests to 80% by 2020 Objective Statement: Improve levels of quality of tests performed in the laboratories. Performance Indicator Percentage TB Microscopy tests performed within 48 hours Percentage TB GXP tests performed within 48 hours Percentage CD4 tests performed within 48 hours Percentage Viral Load tests performed within 96 hours Percentage HIV PCR tests performed within 96 hours Percentage Cervical Smear tests performed within 5 weeks Percentage laboratory (FBC, U&E, LFT) tests performed within timeframes defined 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 90% 95.72% Achieved New New New 90% 96.68% Achieved New New New 85% 94.44% Achieved 86% 81% 64% 65% 87.30% Achieved 70% 82% 73% 70% 81.90% Achieved New New New 50% 96.87% Achieved New New New 80% 85.83% Achieved Reason for Deviation from Planned Target Sub-Programme Quality of Service The purpose of this sub-programme is to improve levels of quality of tests performed in the laboratories by ensuring that laboratories comply with quality standards set and attain accreditation status. Strategic Objective 5.4: To increase the percentage of SANAS accredited regional laboratories to 60% by 2020 Objective Statement: Improve levels of quality of tests performed in the laboratories by ensuring that laboratories comply with quality standards set, and attain accreditation status. Annual Report 2016/17 39

41 5.4 Sub-Programme: Quality of Service Performance Indicator Percentage compliance achieved by laboratories during annual quality compliance audits Percentage of National Central laboratories that are SANAS Accredited Percentage of Provincial Tertiary laboratories that are SANAS Accredited Percentage of Regional laboratories with SANAS Accreditation status 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 82% 83.0% Achieved 88% 91% New 90% 90.0% Achieved Reasons for Deviation from Planned Target New New New 70% 47.0% Not achieved due to staff constraints 28% 55% 49% 45% 11.0% Not achieved due to staff constraints Sub-Programme State of Art Laboratories The purpose of this sub-programme is to increase the number of adequately resourced laboratories by ensuring that all laboratories are equipped with advanced technology and equipment as well as having sufficient space and infrastructure available to perform functions. Strategic Objective 5.5: To increase the percentage of adequately resourced laboratories to at least 90% by 2020 Strategic Objective 5.6: To ensure that 90% of capital budgets are spent to improve quality of laboratories in South Africa Objective Statement: Increase the numbers of adequately resourced laboratories by ensuring all laboratories are equipped with advanced technology and equipment as well as having sufficient space and infrastructure available to perform functions. 5.5 Sub-Programme: State-of-the-art Laboratories Performance Indicator Percentage of laboratories complying with minimum legal requirements(oshact) as per NHLS annual safety audits Percentage of automated tests in the top 100 tests by volume list Percentage of Provincial tertiary laboratories with pre-analytical automation Percentage of capital budget spent 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual New New New 80% 85.5% Achieved Reasons for Deviation from Planned Target New New New 90% 78.0% Not achieved due to a delay in the automation of ABO testing and the fact that other tests in the top 100 list cannot be automated. New New New 25% 6.0% Not achieved due to a delay in the procurement of automated pre-analytical analysers. New New New 90% 101.0% Achieved Sub-Programme Productivity and Efficiency The purpose of this sub-programme is to provide highly efficient and productive laboratory service by adopting best practices and technologies. Strategic Objective 5.7: To ensure high levels of customer satisfaction results measured annually Objective Statement: Provide highly efficient and productive laboratory service by adopting best practises and technologies 40 National Health Laboratory Service

42 5.6 Sub-Programme: Productivity and Efficiency Performance Indicator 2013/14 Actual 2014/15 Actual 2015/16 Actual 2016/17 Planned Target 2016/17 Actual Reasons for Deviation from Planned Target Customer satisfaction index 78% New 69% 75% 72.0% Area of improvement is training, skills development and communication Percentage of acceptable direct material/revenue ratio 29.9% 31.5% New 38% 39.0% Achieved Percentage of preanalytical staff meeting the productivity targets (80 registrations per 8 hour shift) New New New 70% 43.0% Some of the clerks do other duties as well which are not related to data capturing, e.g. answering telephones, filing, scanning etc. this affected the average productivity rate. Contribution to Strategic Outcome Orientated Goals Strategic Objective To increase the accessibility of pathology services to all health facilities by 2020 To increase quality compliance of tests to 80% by 2020 To increase the percentage of SANAS accredited regional laboratories to 60% by 2020 To improve the total turnaround time for tests performed by 2020 To increase the percentage of adequately resourced laboratories to at least 90% by 2020 To ensure that 90% of capital budgets are spent to improve quality of laboratories in South Africa To ensure high levels of customer satisfaction results measured annually Strategic Outcome Orientated Objective Accessible Pathology Service Footprint Performance Driven Processes and Systems International Best Practice Laboratory Medicine Improved Stakeholder Relations Changes to Planned Targets There were no changes to planned targets for Programme 5 in 2016/17. Linking Performance to Budget 2016/17 Actual Expenditure 2015/16 Actual Expenditure Budget Over/Under Budget Over/Under Programme /17 Expenditure 2015/16 Expenditure Laboratory Services Reason for Deviation from the Budget Overspent on direct labour and direct material in 2016/17. Annual Report 2016/17 41

43 Linkage to Budget for all Programmes Programme 4 Administration Budget 2016/ /17 Actual Expenditure Over/Under Expenditure Comments Budget 2015/ /16 Actual Expenditure Over/Under Expenditure Comments R 000 R 000 R 000 R 000 R 000 R 000 Underspent due cashflow constraint (Infrastructure 1,122, , ,148 enhancement) 804,575 1,202,615 (398,040 ) Surveillance and Communicable Diseases 347, ,742 51,532 Occupational Health 107,866 93,117 14,749 Underspent on direct labour 266, ,672 (4,789) Underspent due to vacancies budgeted for were not filed and Operating expenses 109,451 90,106 19,345 Academic Affairs. Research and Quality Assurance - 219,241 (219,241) - 190,990 (190,990) Laboratory Services 5,232,459 5,675,692 (443,233) Overspent on direct labout and direct material 4,966,203 4,930,749 35,454 6,809,850 6,950,895 (141,045) 6,147,112 6,686,132 (539,021) Provission and Bad debts Underspent on direct labour Underspent due to vacancies budgeted for were not filed and Operating expenses CAPITAL INVESTMENT 2015/ /17 Budget Actual Over/Under Expenditure Budget Actual Over/Under Expenditure R 000 R 000 R 000 R 000 R 000 R 000 Capital Expenses 450, , , , ,123 (18,123) Total 450, , , , ,123 (18,123) Investment in capital expenditure overspend due to the roll out of computers and replacement of Innovant IT equpiments REVENUE COLLECTION 2015/ /17 Estimate Actual Amount Collected Under Collection Estimate Actual Amount Collected Under Collection Source of revenue R 000 R 000 R 000 R 000 R 000 R 000 Total test revenue 5,763,268 4,570,070 1,193,198 6,379,635 5,344,283 1,035,352 Of the total revenue of R6.3 billion for 2016/17, an amount of R5.3 billion was collected relating to the current year s debt. This related to an overall recovery rate of 83% compared to 79% in the prior financial year. There was a shortfall of R1.0 billion in collections for the 2016/17 financial year, mainly due to cash constraints from provinces. The main contributor to this shortfall was the Gauteng DoH, which short-paid the NHLS R836 million for 2016/17. R1.2 billion was collected from the provinces within the first quarter of the 2017/18 financial year, which related to 2016/17. Meetings were held with the provinces to follow up outstanding payments. The NHLS is constantly engaging with the provinces to follow up on outstanding debts. 42 National Health Laboratory Service

44 Business Unit Performance INFORMATION TECHNOLOGY The Information Technology (IT) Department supports and services the NHLS business departments across the country on a 24 hour a day, seven day a week basis. The IT landscape is constantly changing and the focus during the year was to ensure that NHLS IT infrastructure meets both the demands of the business and those required in terms of good IT governance and practice. An IT modernisation project was undertaken to revamp underlying infrastructure in the light of the NHLS IT Digitisation Strategy. This is in line with the objective of simplifying, standardising and rationalising the NHLS IT infrastructure. Laboratory Information Systems The Laboratory Information Systems (LIS) Unit implements, maintains and provides support for the IT systems used in the laboratories. Chief Information Officer Tintswalo Shilowa The implementation of the TrakCare Lab LIS was completed with the installation of TrakCare Lab at the National Institute for Communicable Diseases (NICD) and the National Institute for Occupational Health (NIOH). An updated version of the viewer for electronic results on TrakCare Lab, WebView, was installed. The updated WebView uses responsive design techniques so that the pages adapt to the size of the device from which they are being accessed. This allows for the easy viewing of results on a wide range of devices from desktop personal computers to tablets and mobile phones. The use of WebView continues to increase, with average searches per month exceeding 2 million in 2016/17. The implementation of patient demographic and result interfaces has continued. A new interface between the TrakCare Lab system and the Meditech system at the Inkosi Albert Luthuli Central Hospital was installed. The TrakCare Lab-Meditech interface at Universitas and Pelonomi hospitals was updated to allow order entries to be done by the hospital. An interface to the City of Johannesburg s electronic health record was also implemented. Further HL7 interfaces were implemented at Livingstone Hospital and at Anglo American s Witbank Highveld Hospital. Enterprise Resource Planning E-Business Suite (EBS) includes Financials, Supply Chain, Human Resource Management, Customer Relationship Management and Project Accounting. These products support a myriad of business processes, among them being Procure-to-Pay and Order-to-Cash cycles within the NHLS. The NHLS Procurement Department is required to adhere to National Treasury instructions regarding travel policies. Electronic requisitions will now be captured on Oracle iprocurement while Oracle Purchasing will send purchase orders directly to the supplier. Electronic requisitions for travel, and Blanket Agreement, will therefore allow users to add prices as per quote received from the supplier. Configuration was completed in time. Further, the NHLS Grants Management function was enhanced by the automation of some of the manual business processes within the NHLS Grants Management Department. Corporate Data Warehouse The Corporate Data Warehouse (CDW) merges result data from the legacy LIS with that of the current LIS to provide an integrated platform with more than a decade of national pathology information that can benefit research, epidemiology and operational requirements. Annual Report 2016/17 43

45 Further advances in include: Ongoing development and enhancement of dashboards for the monitoring and evaluation of the TB and the HIV Comprehensive Care, Management and Treatment (HIV CCMT) Programmes were made available online to stakeholders The alert reports distributed to provinces to assist with Linkage to Care for drug resistant TB patients and infants diagnosed with HIV have been strengthened. Extensive reporting has been developed in support of Antimicrobial Resistance (AMR) surveillance and the CDW is represented on the National Ministerial Advisory Committee on AMR. Information and Knowledge Management This department is responsible for the development, entrenchment and management of sustainable Knowledge Management (KM) and Records Management (RM) frameworks, and facilitates development, implementation and management of Enterprise Content Management (ECM) solutions. Key initiatives include: ECM CS Integration with TrakCare The integration of the ECM Content Server with TrakCare was successfully implemented. Scanned Laboratory Request Forms are accessible via the TrakCare interface, which assists laboratory staff to compare results with request forms in one interface. Rollout of Asynchronous Scanning Solution The ECM Scanning Solution has been implemented in 198 laboratories, allowing laboratory request forms to be scanned into the ECM repository. Benefits of the scanning solution are that laboratory request forms are easily accessible from anywhere with permission controls in place. This offers a better auditing experience as forms are easily retrievable from TrakCare Lab or the ECM Scanning Solution. IT Project Management Office The NHLS established the IT Project Management Office (PMO) to create efficiencies and effectiveness in delivering IT Projects. The initial aim of establishing the PMO is to centrally run and co-ordinate all IT projects in line with best practice. The ultimate goal is to later transition the IT PMO into an Enterprise Project Management Office, which will deal with enterprise-wide programmes and projects. Currently, the PMO tracks the status, progress, costs and resources committed to numerous projects each year. The current approach brings only a limited measure of project management to projects. Because of these limitations, the PMO has been capacitated through the appointment of the Head of Department; two Project Managers; and two Project Administrators. The PMO is assessing the current state and will be implementing a Project Management Framework that will ensure that the NHLS runs the PMO in line with best practice. IT Governance The NHLS has established an IT governance function to ensure the effective and efficient use of IT in enabling the NHLS to achieve its goals. To date, IT governance has been involved in reviewing all IT policies, contract and licence support alignment, IT risk management and the co-ordination of action items from audits and performance reporting, amongst other matters. IT governance works in alignment with the Risk Management Office on risks and audits. The process of developing a long-term IT Strategy and Enterprise Architecture has been initiated. 44 National Health Laboratory Service

46 COMMUNICATION, MARKETING AND PUBLIC RELATIONS Communications Department Communication is an important and strategic function in any organisation, hence seamlessness between stakeholders is very important. The Communications Department has therefore made every effort to ensure that the flow of information between the organisation s internal and external stakeholders in the 2016/17 financial year has been as continuous as possible. This has been achieved through an array of services such as public and media relations, editorial, photography, graphic design and website management. In addition, the department provides NHLS employees with timely, accurate, and clear information about policies, programmes, services and initiatives. Through these offerings, the department has achieved the following in the reporting period. Annual Report The 2015/16 NHLS Annual Report was co-ordinated and produced by the department as per schedule, by engaging with organisational departments in order to meet and comply with National Treasury Guidelines and delivery deadlines. Senior Manager Tebogo Seate Figure C&M1: The 2015/16 Annual report Launch of the New Vision, Mission and Values (VMVs) A decision was reached by NHLS Executive Management to revise the Vision, Mission and Values (VMVs) of the organisation, to bring them in line with the organisation s strategic plan for the period. The department undertook a launch of the VMVs, in an effort to educate NHLS employees on the importance of upholding organisational values. The VMVs were unveiled in Sandringham on 29 August The department was instrumental in designing banners, posters, folders and bookmarks, which were distributed to the entire organisation for awareness purposes. Further information was also published on the NHLS website, and in the organisational internal newsletter, LabRap. Annual Report 2016/17 45

47 Figure C&M2: Launch of the NHLS vision, mission and values at Sandringham Conferences The Communications Department is responsible for enhancing the reputation of the organisation and increasing its brand visibility. This is done, among others, through participation at relevant industry conferences and exhibitions. During the period under review, the NHLS participated in the following conferences and exhibitions: 21 st International AIDS Conference The department exhibited at the 21 st International AIDS Conference, which is a premier meeting where leaders and the scientific community meet to collectively advance the treatment and prevention of HIV/AIDS. The AIDS Conference was held at Durban s International Conventional Centre (ICC) from July 2016, and created an environment for the organisation to exhibit its services and engage with stakeholders. At the conference, numerous queries, comments, suggestions as well as concerns were noted and submitted to the organisation s leadership for follow-up. Figure C&M3: NHLS staff manning the stand during the International AIDS Conference with Nelisiwe Mkhize, NHLS Board member, in the middle 46 National Health Laboratory Service

48 African Society for Laboratory Medicine (ASLM) Congress The 2016 African Society for Laboratory Medicine Congress, which was hosted from 5 8 December 2016 at Cape Town s ICC, provided the opportunity for the department to highlight the good work carried out by the organisation. The congress served as a platform for the international laboratory medicine community to share best practices, acquire knowledge and debate innovative approaches for combatting global health threats. External Customer Satisfaction Survey The 2016/17 External Customer Satisfaction Survey was conducted by an independent research company. The results received showed an overall improvement in customer satisfaction levels amongst key stakeholders of the NHLS. The organisation achieved an overall score of 72%, compared to 69% in the previous financial year. It is encouraging to note that participation from external stakeholders also improved quite significantly. As service delivery is at the heart of the NHLS Strategic Plan, the department will be working with various departments in the organisation to ensure that all areas of improvement identified in the survey are sufficiently addressed in the coming financial year. Media Relations and Editorial Services The department continued to play an important role in facilitating NHLS presence in the media to highlight some of its work, either through media interviews, media releases or placement of advertorials in selected publications. During the period under review, the following activities were co-ordinated by the department: Profiling of the organisation in Leadership Magazine as well as the Pan African Parliament publication Profiling of the NHLS and its employees in Science Career, a leading science career magazine targeting Grade 10 to 12 learners, in order to stimulate their interest in pursuing various careers as cytologists, microbiologists, biomedical technologists, medical scientists and medical technicians SABC interview on Talk SA with Prof. Himla Soodyall, in May 2016, on her paper entitled The Lemba origins revisited: Tracing the ancestry of Y chromosomes in South African and Zimbabwean Lemba Profiling of the NHLS in the African Business Network online publication Interview on Motsweding FM on the role of the NHLS in the public healthcare system Interview on the SABC s Interface programme, about paternity testing Interview on Ubuntu FM on the launch of the CD4 monitoring dashboard Interview with Prof. Himla Soodyall on SABC regarding Mapungubwe and DNA Ancestry. In addition to the above, the department collaborated with Umhlobo Wenene FM s Career Guidance programme to educate listeners about haematology and cytology. Photographic Services The photographic function performed by the department helps to retain organisational memory by capturing and storing all organisational images. In the review period, the unit captured images, including those submitted by the NHLS regions. Graphic Design Services The department continued to offer graphic design services and layout of many conceptual artworks including organisational corporate identity maintenance and branding, designing of marketing brochures and newsletters, mailer artwork pieces, exhibition stands, and display posters for conferences for various divisions, including the National Institute for Communicable Diseases and the National Institute for Occupational Health. The service was also responsible for the formatting and layout of strategic documents for the organisation and satisfied the needs of internal stakeholders. Web Management Services The purpose of this function is to keep internal and external stakeholders informed of activities in the organisation by updating, uploading and communicating organisational information on the intranet, internet and on all communication channels. During the year under review, usage of the NHLS internet and intranet was as follows: Annual Report 2016/17 47

49 Table CMP1: Internet usage Year Unique Visitors Number of Visitors Pages Hits 2015/ / Difference Percentage Table CMP2: Intranet usage Year Unique Visitors Number of Visitors Pages Hits 2015/ / Difference Percentage Conclusion A new Communications Strategy was developed, aimed at revitalising and repositioning the function of communication within the organisation, as well as ensuring that all communication activities are executed in a co-ordinated and orderly fashion. The strategy is further aimed at re-inventing the function so that it becomes a strategic business partner within the NHLS. The focus in the coming financial year will therefore be on: Implementing best practices on communication, reputation management and brand positioning Improving relations with all stakeholders Revamping and improving existing communication platforms Increasing NHLS visibility in the media Providing ongoing support to the leadership of the organisation to improve internal communication and employee engagement. 48 National Health Laboratory Service

50 ACADEMIC AFFAIRS, RESEARCH AND QUALITY ASSURANCE Academic Affairs and Research Academic Affairs, Research and Quality Assurance (AARQA) incorporates the Academic Affairs and Research (AAR) and the Quality Assurance departments. It is accountable for the teaching, training and research mandate of the NHLS and oversees the quality assurance support and management programmes for the organisation. AARQA strives to ensure consistent adherence to accreditation and compliance measures across all the laboratories through the benchmarking of quality assurance standards for the NHLS. The in-house Health Technology Assessment (HTA) programme focuses on the pre-evaluation of new in vitro Diagnostic Devices in order to facilitate the effective and reliable introduction of technology advancement in the service platform and provide an opportunity for competitive and open selection of innovative approaches to diagnostic technology. AARQA has continuously supported these activities in conjunction with its academic partners to contribute towards the NHLS mission and to promote excellence in the delivery of highquality pathology services. A formal relationship between AARQA and the ten South African Medical Universities is endorsed through an Umbrella Agreement signed by all the institutions. Discussions to finalise the bilateral agreements with each of the institutions continue, with final agreement having been reached between the NHLS and the following medical universities: Walter Sisulu University and the University of the Free State. The relationship with the six Universities of Technology (UoT) and two comprehensive universities (CUs) continues through their faculties of Health and Biomedical Sciences. Acting Executive Manager Dr Sergio Carmona In December 2016 the NHLS was included as a Schedule 1 Institution in terms of the Intellectual Property Rights from Publicly Financed Research and Development Act, No. 51 of This strengthens the position of the NHLS and the role it plays in research within the country. AARQA also completed and implemented an Intellectual Property (IP) Policy that provides guidance on the ownership of, and procedures for, the disclosure, protection and commercialisation of any form of IP generated through research supported by the NHLS. Core Professionals in Training The number of registrars and medical scientist interns on the training platform during the 2016/17 financial year decreased slightly by 1%, from 269 to 250. There were 220 registrars and 30 medical scientist interns (Figure A1). The NHLS has Health Professions Council of South Africa (HPCSA) accredited positions through its academic laboratories and the National Institute for Communicable Diseases (NICD) to train more than 150 interns, and only ~19% of these positions are occupied. It is planned that 50 interns will be placed in the 2017/18 financial period. Qualifying registrars and medical scientist interns contribute towards strengthening the skilled pathology laboratory workforce and improved coverage. Annual Report 2016/17 49

51 / / / / /17 Registrars Intern Scientist Figure A1: Number of registrars and intern scientists on NHLS platforms: 2012/ /17 In total, 39 registrars wrote the examination through the College of Medicine of South Africa (CMSA) in September 2016 and 14 (36%) passed. The majority (50%) of those who passed the written examination were in the field of anatomical pathology (7), followed by medical microbiology (4) haematology (2), and clinical pathology (1) (Figure A2a). During the March 2017 CMSA examinations 42 registrars wrote and 15 passed, and the pass rate remains at 36% (Figure A2b). Figure A2c shows the distribution of registrars who passed CMSA written examinations by discipline in the 2016/2017 Financial year (September 2016 & March 2017 combined). The total pass rate for registrars for the 2016/17 period has improved. Nineteen registrars qualified as pathologists and have subsequently registered with the HPCSA (Figure A3). This is less than the number of newly qualified pathologists in the previous financial year. 1(7%) 4.29% 2(13%) Anatomical Pathology Anatomical Pathology Chemical Pathology 2.14% 1.7% 7.50% Clinical Pathology Heamatology Microbiology 7(47%) 3(20%) 2(13%) Clinical Pathology Heamatology Medical Microbiology Figure A2a: Distribution of registrars who passed CMSA written examinations by discipline in September 2016 Figure A2b: Distribution of registrars who passed CMSA written examinations by discipline in March (38%) 8 (28%) 2 (7%) Anatomical Pathology Chemical Pathology Clinical Pathology Heamatology 5 (17%) 3 (10%) Medical Microbiology Figure A2c: Distribution of registrars who passed CMSA written examinations by discipline in 2016/2017 Financial year (September 2016 & March 2017 combined) 50 National Health Laboratory Service

52 / / / / /17 Qualified Pathologists Medical scientist Figure A3: Newly qualified pathologists and medical scientists registered with the HPCSA trained on the NHLS platform, 2012/ /17 A total of 755 core pathology workers and trainees are on NHLS platforms, including the NICD and NIOH, with 578 placed in NHLS service platforms (excluding NIOH and NICD). The majority are White (242) followed by African (199), Indian (109), Coloured (26) and Chinese (2). Figure A4 shows distribution by race and profession, with the majority of the core staff category being white and the majority of the trainees being black. This will improve the transformation strategy, as trainees qualify and are placed on the platform African Chinese Coloured Indian White Medical Scientist Medical Scientist Intern Pathologist Registrar Figure A4: Number of pathologists, medical scientists and trainees in the NHLS platform (excluding NICD and NIOH) by race Academic Support and Development The NHLS continues its support for academic and development activities in close collaboration with its academic partners (Table A1). An umbrella agreement has been signed with all ten Medical Universities, and consultations on the umbrella agreements continue. Review of the umbrella agreement with the six UoTs and two CUs continues, in order to capture new and emerging developments in the higher education sector relating to the medical technologists/medical laboratory scientist professions and the changed management structure of the NHLS. Consultative meetings will be carried out with each UoT and CU to formalise bilateral agreements as soon as the umbrella agreement has been endorsed and signed by all. Quarterly National Academic Pathology Committee meetings are held with representatives from all these institutions to gather input on pathology developments and academic strategic initiatives. Annual Report 2016/17 51

53 Table A1: Universities in collaboration with the NHLS University Sefako Makgatho Health Sciences University (SMU) University of Cape Town (UCT) University of KwaZulu-Natal (UKZN) University of Limpopo (UL) University of Pretoria (UP) University of Stellenbosch (US) University of the Free State (UFS) University of the Western Cape (UWC) University of the Witwatersrand (Wits) Walter Sisulu University (WSU) University of Technology (UoT) Cape Peninsula University of Technology (CPUT) Central University of Technology (CUT) Durban University of Technology (DUT) Mangosuthu University of Technology (MUT) Tshwane University of Technology (TUT) Vaal University of Technology (VUT) Comprehensive University (CU) Nelson Mandela Metropolitan University (NMMU) University of Johannesburg (UJ) The research, teaching and training activities are supported through collaboration with academic partners. Funding for scientific travel and events continues to be restricted due to internal financial constraints. However, the NHLS encourages and supports these activities with the majority supported through grants and time allocation for attendance. Driving the Research Agenda The NHLS, in collaboration with its academic partners, published 618 journal articles in the 2016/17 financial year. More than a third of the articles were published in collaboration with UCT (201: 34%) followed by Wits University (156: 25%) and UP (97: 17%), Figure A5. Figure A6 indicates the total number of publications per discipline. The majority of publications were contributed by the departments of Medical Microbiology (136: 22%), followed by Haematology (114: 18.4%). 9.1% 7.1% 74.12% SMU % SU UCT 9.2% 19.3% % UKZN UP UFS UWC 97.16% 46.7% Wits WSU Figure A5: Number of peer reviewed journal articles by institution 2016/17 52 National Health Laboratory Service

54 Anatomical Pathology Chemical Pathology Haematology Human Genetics Immunology Medical Microbiology Medical Virology Number per Discipline Percentage per Discipline Figure A6: Number of peer reviewed journal articles by discipline 2016/17 PathRed Congress The NHLS-organised Pathology Research and Development (PathRed) Congress 2017 will be held from 23 to 24 June The Congress is designed to actively develop, strengthen and support young and emerging researchers (including pathologists, medical scientists and technologists) by incorporating programmes that will promote collaboration, learning and skills development. Now organised in partnership with the Federation of South African Societies of Pathology (FSASP), the congress aims to reach out to the broader pathology community to promote clinical and diagnostic pathology excellence. The PathRed 2017 Congress will include targeted skills training and development workshops for young, emerging and junior researchers to enhance their skills on advanced technologies, scientific knowledge and initiatives in laboratory medicine. Currently South Africa faces an ever-increasing shortage of skilled pathology researchers. This Congress highlights the importance of investment in skills development programmes to address skills shortfalls and add much needed capacity to the economy. Confirmed Key Speakers include two renowned South African A-rated researchers and leaders, Prof. Shabir Madhi, Executive Director of the NICD and acting CEO of the NHLS; and Prof. Glenda Gray, Director of the South African Medical Research Council. Grant Programme Management The programme management section of AAR strives to improve the grant management process by consistently reviewing and interpreting grantor regulations, promoting adherence, advising principal investigators accordingly and facilitating timely processing of contracts, cost centre opening, submissions of project progress and financial reporting. The NHLS continues to attract grant funds to support research initiatives and strengthen the laboratory diagnostic platform. During the 2016/17 financial period, R275.2 million was attracted and contractual agreements were completed with the grantors. Table A2 indicates the total grants attracted per grantor. Most of the grant funding managed by the NHLS Grants Office was from international sponsors. CDC remains the main grantor, followed by the Department of Health: Global funds. Annual Report 2016/17 53

55 Table A2: Total Grant Funding attracted in 2016/17 International Centers for Disease Control and Prevention (CDC) Epicentre Healthy Business German Federal Ministry of Health Makerere University College of Health Sciences World Health Organization South Africa Department of Health: Global Fund National Research Foundation NHLS Research Trust Poliomyelitis Research Foundation South African Medical Research Council Grand Total Quality Assurance The Quality Assurance (QA) Department is responsible for the following portfolios at the NHLS: Accreditation of laboratories Certification of support service departments Document control Health technology assessment (Evaluation of new in vitro Diagnostic Devices) Monitoring and compliance of laboratories Proficiency testing schemes (External quality assurance) Quality assurance related projects. During 2016/17, the NHLS Executive Committee (EXCO) and other top management members showed support and commitment to the QA Department. Three significant events during the period were: Approval of seven new QA positions to complement available staff and increase the support offered to business (laboratories) and support services departments both at head office and throughout the country Five of these positions were filled during the financial year and the remaining two were re-advertised more than once The first Quality Assurance Management Review meeting, which was held in October 2016 to address the accreditation of laboratories and certification of support departments Two International Standards Organization (ISO) standards namely, 9001 and were reviewed at the meeting, which was attended by the NHLS (EXCO), Area Managers and Quality Assurance Managers Two laboratories (Kroonstad and Northdale) were recognised by the CEO for achieving 5 Stars during the World Health Organization (WHO) Stepwise Laboratory Quality Improvement Towards Accreditation (SLIPTA) audits during the Business Units meeting held in November Figure A7: Northdale Laboratory (from left to right) Praneel Budhu Northdale Laboratory Manager, Patience Dabula National Manager: Quality Assurance, Joyce Mogale NHLS CEO, Sibulele Bandezi KZN Area Manager and Brian Naidoo UMgungundlovu and UThukela Business Manager 54 National Health Laboratory Service

56 Figure A8: Kroonstad Laboratory (from left to right) Jone Mofokeng Free State and North West Area Manager, Frik Craukamp retired Kroonstad Laboratory Manager, Noma Bosman Free State Business Manager, Joyce Mogale NHLS CEO and Patience Dabula National Manager: Quality Assurance Accreditation and Certification Accreditation of Medical Laboratories The number of medical laboratories accredited by the South African National Accreditation Systems (SANAS) against ISO 15189:2012 increased during the reporting period (see Figure A9). Four new facilities were accredited and another three submitted applications to SANAS but had not been assessed by the end of March The accredited laboratories are one national central laboratory in KwaZulu- Natal, two provincial tertiary laboratories in North West and Northern Cape and one regional laboratory in Mpumalanga. One national central laboratory in the Free State was suspended in June The accreditation target for 2016/17 was only achieved by the national central laboratories, with the other tiers performing below target. The percentage of accredited laboratories per tier at the end of March 2016 was as follows: 94% (49/52) of national central laboratories 47% (8/17) of provincial tertiary laboratories 17% (7/42) of regional laboratories. Figure A9 shows the percentage of accredited laboratories per laboratory tier in 2016/17 and 2015/16 compared to the target set for the 2016/17 financial year National Central Laboratories Provincial Tertiary Laboratories Regional Laboratories FY 16 Accredited Laboratories FY 17 Accredited Laboratories FY 17 Accredited Target Figure A9: Percentage of NHLS laboratories accredited per laboratory tier Annual Report 2016/17 55

57 ISO 9001 Quality Management System in Support of Service Departments During the review period, the department trained 143 Support Service Department staff members (45 in 2015/16) on ISO 9001:2015 through the NHLS Skills Department. The training varied from introduction to internal audits. Little progress was made in addressing the non-conformities identified during the gap assessments conducted in the previous financial year. Human Resources remains the only department that has divisions where gap assessments had not been done by the end of March In total, 56 QA meetings (36 in 2015/16) were held in both corporate and area offices with executives, managers, departmental QA representatives and other staff members, to address quality management topics relating to ISO 9001:2015 requirements. These included introduction/overview meetings with support service managers and staff, as well as planning/follow-up meetings with QA representatives and department managers. All the departments were part of the National Management Review Meeting. The QA Manager for Support Services was appointed in February An ISO 9001:2015 quality manual was drafted and three standardised procedures were written. Proficiency Testing Schemes During 2016/17, the number of ISO accredited Proficiency Testing Schemes (PTSs) increased by one scheme (C Reactive Protein) from 17 in the previous financial year to 18 during the SANAS Reassessment in May Centers for Disease Control and Prevention (CDC) Atlanta transferred seven more sites for Human Immunodeficiency Virus (HIV) Early Infant Diagnosis (EID) PTS to the NHLS. This increased the total HIV EID PTS participants to 83 sites in 11 countries compared to 76 in the same number of countries in the previous financial year. Further piloting of cryptococcal antigen PTS continued, with favourable results. This scheme is now offered at 71 sites. A costing model was finalised and used to develop pricing for non-nhls participants. Despite the high increase in price compared to previous years, the number of participants and countries enrolled increased. PTS Enrolments The number of countries enrolled on the NHLS PTS increased from 22 to 24 when compared to the previous financial year. The number of enrolments by NHLS laboratories, the South African private sector and laboratories in other countries increased by 16% from in 2015/16 to in 2016/17. Table A3 lists non-south African countries participating in the schemes in alphabetical order. Table A3: Countries with laboratories enrolled in NHLS PT Schemes: 2016/17 No. B G No. I N No. N Z 1. Botswana 9. Ivory Coast 17. Nigeria 2. Cameroon 10. Kenya 18. Rwanda 3. Democratic Republic of Congo 11. Lesotho 19. Swaziland 4. Eritrea 12. Malawi 20. Tanzania 5. Ethiopia 13. Mauritius 21. Uganda 6. Gabon 14. Mozambique 22. United States of America 7. Ghana 15. Namibia 23. Zambia 8. Guinea 16. Niger 24. Zimbabwe Performance of NHLS Laboratories on PTS Performance on NHLS PTSs was excellent, due to improved laboratory practice and management, with 97% of the laboratories performing above 80% (17% more than the annual target of 80%). The national average performance of laboratories increased to 90% during 2016/17 compared to 84% during 2015/16. Figure A10 shows the average performance of laboratories for the six areas as well as the national average for 2016/17 compared to the same areas in 2015/ National Health Laboratory Service

58 National Score Western and Northern Cape KwaZulu-Natal Limpopo and Mpumalanga Gauteng Free State and North West Eastern Cape / /16 Figure A10: Average results of NHLS laboratories in the NHLS PTS (shown as a percentage) QA Monitoring and Compliance Two internal audit tools were used during the review period. The Quality Compliance Audit (QCA) tool was used in 218 laboratories that are not yet accredited. Accredited laboratories were audited using the SANAS tool. The overall performances of laboratories audited using the QCA tool showed an increase from 82% in the previous financial year to 87% in 2016/17 (see Figure A11). In total, 83% of the laboratories achieved at least an 80% score compared to 71% in the previous financial year. 100 QCA % Score / / / / / / / / / /17 Figure A11: Quality Compliance Audit results from 2007/08 to 2016/17 Health Technology Assessment (HTA) The HTA unit of the NHLS complies with various ISO standards to select suppliers of equipment yielding critical results. The unit works closely with the Department of Health HTA unit, suppliers of in vitro devices in the NHLS and other international bodies to evaluate the performance of devices before they are eligible for procurement. During the reporting period, 64 projects were processed in the units, covering all disciplines. A good working relationship now exists with suppliers since major challenges have been resolved. Quarterly meetings with the Executive of the Diagnostic Association have consequently been modified to include other common interests such as regulations and supply chain management. Annual Report 2016/17 57

59 QA Research or Grant Projects Project title: Strengthening Laboratory Management Towards Accreditation (SLMTA) in South Africa Investigator: Patience Dabula Project period: October 2012 to date Reporting period: April 2016 to March 2017 Funded by: President s Emergency Plan for AIDS Relief (US) (PEPFAR), Centres for Disease Control (CDC) South Africa Progress during the reporting period: 18 Laboratories were enrolled in Cohort 3 of the SLMTA programme. Baseline audits for the 18 laboratories and all laboratories that were in cohort 1 and 2 and not yet accredited were conducted during the review period. The African Society for Laboratory Medicine (ASLM) audited seven selected laboratories using the WHO-SLIPTA audit checklist»» Audits were conducted in June 2016»» Auditors were from Nigeria, South Africa (NHLS trainees) Tanzania, and Zimbabwe»» Figures A13 and A14 show the results of the NHLS laboratories that were audited by the ASLM in both percentages and star ratings. The baseline and exit audits were internal audits conducted by NHLS trained SLIPTA auditors while the third results are from the ASLM auditors Kroonstad Kalafong Tembisa R K Khan Pelenomi Leratong Edenvale Baseline Exit ASLM Figure A12: SLIPTA results for seven laboratories audited by ASLM given as percentages 58 National Health Laboratory Service

60 Kroonstad Kalafong Tembisa R K Khan Pelenomi Leratong Edenvale Baseline Exit ASLM Figure A13: SLIPTA results for seven laboratories audited by ASLM given in star ratings Through the NHLS, South Africa is the first country to achieve multiple 5-Star ratings among the 18 countries audited by the ASLM. Nigeria was the first country to obtain a 5-Star rating but to date has only one laboratory.»» Figure A14 shows the 18 countries audited by ASLM as at September 2016, namely Angola, Botswana, Burundi, Cameroon, Ethiopia, Ghana, Lesotho, Malawi, Mozambique, Namibia, Nigeria, Rwanda, Tanzania, Uganda, South Africa, Swaziland, Zambia and Zimbabwe.»» Over the past three years, 14 NHLS staff members have been certified by the ASLM as external auditors and have audited in nine of the above countries on behalf of the ASLM. Annual Report 2016/17 59

61 Counties Visited 197 Labs Audited South African Data Zero Stars One Star Two Stars Three Stars Four Stars 3 Five Stars Zero Stars One Star Two Stars Three Stars Four Stars Five Stars Figure A14: Results of 197 laboratories in 18 countries audited by ASLM by September 2016 (Source: ASLM) The first laboratory to obtain 5 Stars in South Africa was Northdale in July 2014 and the second was Kroonstad in June Figure A15: delegates from Kroonstad Laboratory led by Mr Frik Craukamp (retired) with the NHLS CEO, Free State QA Coordinator and Kroonstad SLMTA Trainer during the closing meeting Project title: Implementation of Proficiency Testing in South African Voluntary Counselling and Testing Sites Investigator: Prof. Adrian Puren Co-investigator: Patience Dabula Project period: January 2014 to date Reporting period: April 2016 March 2017 Funded by: PEPFAR and CDC South Africa, with ASLM as an implementing partner 60 National Health Laboratory Service

62 Activities during the period: Two staff members were appointed to the Regional Rapid Testing Quality Improvement Initiative project In total, sites enrolled for Rapid HIV PTS in eight of the nine provinces in the country the Northern Cape is the only province that has not yet enrolled Two PTS surveys were sent out, with results showing an improvement from 62% in the first survey to 77% in the second survey. OTHER QA ACTIVITIES Pan African Harmonisation Working Party (PAHWP) Membership of the PAHWP remains 18 African countries namely: Burkina Faso, Burundi, Ethiopia, Ghana, Kenya, Malawi, Mozambique, Nigeria, Rwanda, Senegal, Sierra Leone, South Africa, Uganda, United Republic of Tanzania, Togo, Zambia, Zanzibar and Zimbabwe. The transfer of the PAHWP website for hosting by the NHLS was completed in July During the year, the committee continued to communicate by conference call, and finalised a draft PAHWP Constitution and Concept Note. The PAHWP was represented at the African Medicines Regulatory meeting in Senegal in May 2016, where a relationship was established between PAHWP and the African Union s (AU) New Partnership for Africa s Development (NEPAD). The PAHWP was represented at a WHO meeting in Geneva during October 2016, where funding was obtained for a regulatory meeting to be held in Cape Town. The London School of Hygiene and Tropical Medicine hosted this regulatory forum on behalf of the PAHWP in December 2016 during ASLM PAHWP was represented at the WHO pre-qualification team regulatory meeting, held at the same venue, to update industry, regulators and countries on the latest requirements for submissions. At the end of the meeting, the Concept Note and Draft Constitution were discussed, and agreement was reached to submit a funding application letter to AU NEPAD. In Dec 2016, the funding application letter was written and forwarded to the AU NEPAD Technical body and the committee awaits feedback. Scientific Meetings Table A4 reflects the seven presentations made at scientific meetings during the review period a decrease compared to 14 in the previous financial year. Table A4: Presentations by QA head office staff at scientific meetings No. Meeting Name, Venue Month Title of Presentation Presenter 1. African Health Economics and Policy Association (AfHEA), Rabat Morocco 2. 21st International AIDS Conference September 2016 NHLS HTA Programme Sarvashni Moodliar July 2016 The impact of the NHLS CD4 PTS/EQA in resource limited settings the last 13 years 3. ASLM 2016, Cape Town December 2016 Are Point-of-Care Testing sites producing reliable CD4 results? Findings from the NHLS CD4 Proficiency Testing Scheme/External Quality Assessment 4. ASLM 2016, Cape Town December 2016 The South African NHLS Proficiency Testing Scheme 5. ASLM 2016, Cape Town December 2016 Implementation of HIV for POCT sites in South Africa 6. ASLM 2016, Cape Town December 2016 Implementation and update of WHO/SLIPTA audit programme in the National Health Laboratory Service in South Africa 7. ASLM 2016, Cape Town December 2016 Implementation of ISO 9001 in the NHLS Support Service departments [Human Resources, Finance, AARQA, Communication, Information Technology]: supporting laboratories with compliance to the Quality Management System Hazel Aggett Hazel Aggett Mahlatse Maleka Mahlatse Maleka Patience Dabula Stephina Makena Type of Presentation Oral Oral Poster Oral Poster Oral Poster Annual Report 2016/17 61

63 NATIONAL PRIORITY PROGRAMMES Overview The National Priority Programmes (NPP) was established in 2010 to address the Department of Health s (DoH) need to provide increased access to patient testing in order to enhance treatment and care programmes with a focus on certain priority areas in public healthcare, including HIV and associated opportunistic infections (such as tuberculosis), and Cryptococcal disease. Director Prof. Wendy Stevens The NPP has been responsible for the implementation of several national laboratory programmes such as Early Infant Diagnosis (EID) of HIV; CD4 testing; HIV viral load (HIV VL) testing; pulmonary and extra-pulmonary tuberculosis (TB) diagnosis by molecular testing; HIV drug-resistance testing; and reflexing cryptococcal antigen testing following CD4 determination. Many lessons have been learnt, skill sets developed, and much experience has been gained during the implementation of these programmes. Implementation was extended to the specific diagnostic needs of vulnerable populations in South Africa such as the mining and peri-mining communities (PMC), and offenders in the Department of Correctional Services (DCS). The NPP comprises a multidisciplinary technical and clinical team with members representing both the NHLS and the Wits Health Consortium. The multidisciplinary team allows for a complete systems approach in supporting the implementation process through research and development of diagnostic platforms; determining diagnostic needs; conducting site assessments; offering technical assistance during and subsequent to implementation; overseeing quality assurance aspects; providing ongoing technical and clinical training; ongoing monitoring and evaluation to ensure programme maturation; and research activities to support programme improvements such as connectivity strategies and innovations. Implementation science is further expanded to guide surveillance for programmatic purposes; highlight disease transmission hot spots; improve linkage-to-care needs; identify service delivery gaps; and integrate management at all levels of a tiered laboratory structure. Operations Manager Dr M Pedro da Silva Programme implementation and development would not be possible without public-private partnerships as has been demonstrated in research work done with suppliers of diagnostic platforms and engineering groups for application, software, and SMS Printer development. The team continues to work closely with international and national stakeholders, and funders such as the Global Fund; Centers for Disease Control and Prevention (CDC): USAID through the NGO, Right to Care; Bill and Melinda Gates Foundation; the Grand Challenges Canada; the World Health Organization (WHO); London School of Hygiene and Tropical Medicine; and UNITAID, to name a few. Activities of the respective programmes conducted for the period 1 April 2016 to 31 March 2017 (2016/17) are detailed in this section. National CD4 Programme Staff Prof. Debbie K Glencross: Director CD4 National Priority Programme Dr Lindi Coetzee: National CD4 Co-ordinator Naseem Cassim: Health Economics and Data Analyst Sherry Drury: Senior Trainer (Retired February 2017) Sithembile Mojalefa: Trainer Glodean Mokone: Trainer 62 National Health Laboratory Service

64 Overview CD4 testing continues as an integral component of the Comprehensive Care, Management and Treatment of HIV and AIDS (CCMT) programme in South Africa to assess the immune status of newly diagnosed HIV patients not yet on therapy or those initiating therapy for the first time. During 2016, ~3.4 million CD4 tests were performed across the organisation with a ~10% reduction in test volumes expected for the 2017/18 financial year. This reduction in testing volumes is anticipated considering the World Health Organization (WHO) 2016 HIV for Antiretroviral Therapy (ART) Guidelines, adopted locally by the DoH and the South African HIV Clinicians Society, which recommend a universal test and treat (UTT) approach where CD4 counts are no longer necessary to define patient eligibility for ART. The welcomed UTT approach however, does not mean that there is no longer a need for CD4 counting, largely due to the local burden of HIV disease 1 and reported high proportion of HIV-positive patients in South Africa who are severely immuno-compromised at time of presentation. CD4 counts thus remain an important laboratory determinant of patient immune suppression and a means to identify patients at risk for opportunistic co-infections and/or stratify long-term risk and fast-track ART for patients with CD4 counts <350cells/ µl. In this context, cryptococcal meningitis (CM) is a common opportunistic infection in HIV patients, frequently associated with high mortality that can be prevented by early detection and presumptive fluconazole treatment. In this regard, reflexed cryptococcal antigen (CrAg) testing in patients whose routinely submitted CD4 samples are shown to have counts less than 100 cells/µl, has been shown to be a cost effective strategy to identify patients at risk 2. With the support of the National Institute of Communicable Diseases (NICD) and the DoH, the CD4 Programme rolled out the national cryptococcal disease screening service to all NHLS CD4 laboratories by October The CD4 unit continues to support 49 testing facilities across South Africa through training, site visits, on-site audits and preparation for SANAS accreditation for both CD4 and reflexed CrAg testing. The unit further provides for the ongoing updating of national Standard Operating Procedures (SOPs) related to all aspects of CD4 testing and monitors laboratory performance on the NHLS External Quality Assessment (EQA) programme and supplier-provided external quality assurance programme, i.e. the Beckman Coulter IQAP. Test volumes and turnaround times (TATs) are routinely monitored to focus on operational interventions and developing systems to strengthen the national laboratory network, including assessing laboratory capacity to ensure continued quality of testing with appropriately placed equipment that matches service needs and volumes of tests performed. The unit also continues its programme to evaluate new and emerging CD4 and related technologies and platforms, to support the current integrated tiered service delivery model into national CD4 and related testing services that can be performed in CD4 laboratories. Operations CD4 tested volumes for 2016/17 were million, with KwaZulu-Natal processing 1.08 million samples (32% of annual volumes), followed by Gauteng with samples (22%). CD4 volumes vary monthly between and , and overall less tests were performed in comparison to 2015/16 (3.2% decline) Refer Figure NPP1 for details. 1 Coetzee LM, Cassim N and Glencross DK. Analysis of HIV disease burden by calculating the percentage of patients with CD4 counts <100 cells/ µl across 52 districts reveals hot spots for intensified commitment to programmatic support. SAMJ June 2017, in press. 2 Larson BA, Rockers PC, Bonawitz R, Sriruttan C, Glencross DK, Cassim N, Coetzee LM, Greene GS, Chiller TM, Vallabhaneni S, Long L, Van Rensburg C, Govender NP. Screening HIV-Infected Patients with Low CD4 Counts for Cryptococcal Antigenemia prior to Initiation of Antiretroviral Therapy: Cost Effectiveness of Alternative Screening Strategies in South Africa. PLOS ONE DOIi: /journal.pone ecollection 2016 (11(7):1-23). Annual Report 2016/17 63

65 (a) CD4 Annual Tests Monthly April 2016 May 2016 June 2016 July 2016 August 2016 September 2016 October 2016 November 2016 December 2016 January 2016 February 2016 March (b) CD4 Regional Eastern Cape Free State and North West Gauteng KwaZulu-Natal Figure NPP1: Annual CD4 volumes per month (a) and volume contributions per region (b) in 2016/17 Limpopo and Mpumalunga Western Cape and Northern Cape Three MPL/CellMek platform training workshops were conducted between April 2016 and March 2017, with 24 staff members representing NHLS laboratories from Limpopo/Mpumalanga, Gauteng, Free State/North West, Eastern Cape and Western Cape. In addition, on-site training for a further 11 staff members was conducted at Ngwelezane, Polokwane and Welkom laboratories on the MPL/CellMek cytometer. Four site visits for the purpose of audits were performed at Tshepong, Tambo Memorial, Dr George Mukhari (DGM) and Rustenburg laboratories, with pre-sanas audits conducted at Tshwane Academic and Tshepong. Twenty-three CD4 laboratory personnel from the Eastern Cape attended a PLG CD4 Testing and Quality Assurance presentation in October During 2016/17, the new Beckman Coulter Aquios cytometer was introduced to replace the ageing XL MCL technology at lower throughput CD4 laboratories. Cytometers were initially commissioned at two pilot laboratories, Witbank and Vryheid, with the aim of developing a national SOP, and providing for TrakCare laboratory information system (LIS) interface development. Subsequently, cytometers were commissioned at a further 15 laboratories between January and June 2016, with 68 staff members trained on site and deemed competent to perform CD4 testing on the Aquios. Fit for purpose (FFP) testing was completed after each installation prior to commencing with patient testing, and once acceptable agreement between the Aquios instrument and the MPL/Cellmek system had been confirmed. Extended monitoring confirmed both instrument and operator consistency. Aquios is an automated load and go instrument, designed to be fully operational with minimal operator input. All 17 laboratories have maintained an in-laboratory TAT of <24 hours since implementation. The load and go capability of the Aquios has also contributed to a median decrease in the mean in-lab TAT from 13 to 10 hours (January to November 2016). 64 National Health Laboratory Service

66 Figure NPP2: Aquios system training for NHLS laboratory staff Reflexed Cryptococcal Antigen Screening Following the successful implementation of the US CDC and NICD-funded CrAg screening pilot programme, a national NHLS-based reflexed testing programme was introduced across CD4 testing laboratories, in a staggered fashion by NHLS business region, between June and September Standardised methodology such as the Lateral Flow Assay (LFA) (IMMY, US), procured through a national tender, enabled ease of implementation with absorption and full integration into existing CD4 workflow, without the need to incur additional staffing costs. TrakCare LIS was used to automatically reflex the CrAg test in laboratories and enable worklist generation to facilitate identifying samples for CrAg testing in CD4 laboratories. Onsite training for 49 staff members was conducted at each facility and 225 operators were deemed competent prior to commencement of patient testing. CrAg Annual Volumes CrAg Positivity Rates ND Pos 1 0 EC FS and NW GT KZN LP and MP WC and NC Neg 0 EC FS and NW GT KZN LP and MP WC and NC Figure NPP3: CrAg volumes for 2016/17 per NHLS region (Left). CrAg positivity rates for the same period, per region From June 2016 (national implementation) to March 2017, CrAg samples were processed across the NHLS, with Gauteng performing samples (27% of national volumes), KwaZulu-Natal (19%) and Limpopo/Mpumalanga (18%). The lowest recorded numbers were reported for the Western and Northern Cape (9%). Positivity rates ranged from 4.57 (Western and Northern Cape) to 6.94% (KwaZulu-Natal) for this period. The current month-to-month percentage of CD4 <100 cells/µl reflexing to CrAg testing has stabilised at 98.5% since October 2017, with an average 10% of tested CD4 samples having counts <100 cells/µl. Annual Report 2016/17 65

67 Outputs The unit continued its evaluation and validation of new and existing CD4 technologies in terms of laboratory and in-field studies. These included the Partec MiniPOC/CyFlow Partec CyFlow Counter instrument study (February 2017) on behalf of Sysmex for the WHO validation, as well as the Becton Dickinson FACSPPresto CD4 point-of-care (POC) instrument. Validation studies on the CrAg LFA and automated CrAg EIA systems were completed in The unit has continued the development of the flow cytometry assay for CrAg testing to get CD4 and CrAg testing onto the sample testing platform, with built in quality control measures and direct reporting through connectivity with the LIS. The unit participated in developing connectivity/interfacing solutions for the FACSPresto and Beckman Coulter Aquios. Development of the Becton Dickinson connectivity solution for their POC CD4 instrument continued through 2016, with a prototype tested in January Field testing is scheduled later in 2017 at a POC hub laboratory where essential HIV tests are provided as per the Integrated Tiered Service Delivery Model introduced in 2015/16. The unit is involved in implementation science for the routine implementation of new assays, platforms, or systems. The implementation of reflexed cryptococcal antigen screening in CD4 tests across South Africa was a major focus in gaining an understanding of unit test costs, clinical cost effectiveness, pilot site evaluation, and strategies for best practice implementation. National HIV Viral Load Programme Staff Dr Sergio Carmona: Pathologist in Charge Somayya Sarang: Programme Manager Overview There are 16 HIV VL laboratories located throughout South Africa. These are managed by the respective laboratory managers and supported by business and area managers who are directly responsible for ensuring continuous service delivery. The role of the NPP is to ensure ongoing support, integrate, and monitor the HIV VL Programme at national level. This is achieved through site evaluation, equipment commissioning, equipment verification, accreditation support, monthly supplier meetings, monthly indicator reports, Abbott mview monitoring of laboratory performance in real time, Roche Axeda for remote connectivity when laboratories experience downtime, and the ART dashboard providing reports for internal and external stakeholders relating to test volumes and test ranges at national, provincial and district levels. On 1 September 2016, the DoH adopted the UTT strategy in line with the WHO s guidelines, allowing all people living with HIV access to treatment, regardless of their CD4 count. In view of the guideline change and alignment with targets (90% of individuals tested, 90% on treatment, and 90% virologically suppressed) it is estimated that patients will be placed on ART by the 2018/19 financial year, with HIV VL tests required. Operations The rollout of the Roche Cobas 6800 and 8800 systems, as part of the upscaling of the HIV VL Programme, was successfully completed in December The process was challenging and required substantial renovations to be undertaken within strict timelines. Eight laboratories were equipped with these systems. A combination of Cobas 6800/8800, Cobas Ampliprep Cobas Taqman (CAPCTM) and Abbott m2000 systems, equate to 41 systems that now cater for the increased HIV VL testing capacity. Table NPP1: Instrument placements at the 16 HIV VL laboratories Instrument Cobas 6800/8800 CAPCTM Abbott m2000so, m2000rt Laboratory Charlotte Maxeke Johannesburg Academic (CMJAH), Inkosi Albert Luthuli Central Hospital (IALCH), Ngwelezane, Rob Ferreira, Mankweng, Port Elizabeth, Mthatha Madadeni, Frere, Tshepong, Groote Schuur, Tygerberg Addington, Universitas, DGM On-site training for new staff members as well as refresher training sessions are conducted by the suppliers. Two successful Abbott superuser training workshops were conducted from 21 to 22 April 2016 and 26 to 27 October The first super-user training workshop for Roche Cobas 6800/8800 users was held at the Roche Training Centre in Midrand from the 6 to 10 February Delegates from CMJAH, IALCH, Edendale, Ngwelezane, Mankweng, Rob Ferreira (Nelspruit), Mthatha and Port Elizabeth attended. It was an intensive but fun-filled weeklong workshop, which equipped delegates to successfully operate and troubleshoot the high throughput analysers. 66 National Health Laboratory Service

68 Figure NPP4: Delegates, the Roche training team, and the HIV VL Programme Manager attending the first HIV-1 VL Cobas 6800/8800 super-user training workshop in Midrand, Gauteng In total, HIV VL tests were performed in the 2016/17, with 88.23% of these tested within 96 hours. This exceeds the NHLS Annual Performance Plan HIV VL target of 65% within 96 hours. Monitoring and Evaluation All HIV viral load testing laboratories are enrolled with the QCMD EQA Programme. The EQA activities are co-ordinated by the NHLS Quality Assurance (QA) Department. The Roche Dashboard for the Cobas 6800/8800 systems is currently in development and is expected to be available in Quarter 3 of National HIV Genotyping Programme Staff Dr Kim Steegen: Chair NHLS HIV Drug Resistance Committee, Senior Medical Scientist Operations Four of the five NHLS laboratories allocated to perform HIV drug resistance testing are operational. These laboratories include CMJAH, Tygerberg (TBH), IALCH and Universitas Hospital (UNIV). The fifth laboratory, DGM, is yet to complete assay validations before commencing HIV drug resistance testing. Between the four laboratories, a total of samples was processed for HIV drug resistance testing in 2016/17, with CMJAH and TBH bearing the bulk of the volumes (Figure NPP5) Apr 16 May 16 Jun 16 Jul 16 Aug 16 Sep 16 Oct 16 Nov 16 Dec 16 Jan 17 Feb 17 Mar 17 CMJAH IALH TYG UNIV Figure NPP5: HIV drug resistance testing volumes across the four testing facilities for the 2016/17 FY Annual Report 2016/17 67

69 The average accepted TAT for HIV drug resistance testing is 21 days. This target is not met consistently and requires improvement. Often the increase in TAT is related to high specimen volumes or, at the opposite extreme, small specimen volumes leading to specimen batching to maintain cost-efficiency (Figure NPP6) Apr 16 May 16 Jun 16 Jul 16 Aug 16 Sep 16 Oct 16 Nov 16 Dec 16 Jan 17 Feb 17 Mar 17 CMJAH IALH TYG UNIV Figure NPP6: HIV drug resistance testing TAT (hours) across the four testing facilities in 2016/17 Monitoring and Evaluation An HIV drug resistance dashboard is being developed. National Early Infant Diagnosis Programme Staff Dr Sergio Carmona: Pathologist in Charge Somayya Sarang: Programme Manager Tsakani Mhlongo: Project Manager Training Nthabiseng Mhlongo: Clinical Trainer Overview The EID Programme aims to assist in the delivery of quality HIV diagnostic services for infants and children, in collaboration with the DoH, and other partners. This is accomplished through training, the provision of technical assistance, support visits, monitoring, and advocacy. The Prevention of Mother-to-Child Transmission (PMTCT) guidelines were amended in 2015, requiring that a Polymerase Chain Reaction (PCR) test be done at birth for all babies born to HIV positive mothers. With this change in policy, training on EID at hospitals and maternity units around the country was deemed a priority. The training activities include correct collection of dried blood spot (DBS) specimens, interpretation of PCR results, the significance of performing HIV rapid tests in babies, and guidance on the initiation of prophylaxis for the babies. Through these activities, it is ensured that all identified HIV-infected babies will have access to care. Operations Training activities have led to an increase in HIV PCR test uptake of ~14% in 2016/17 when compared to the previous fiscal period. The number of HIV PCR tests performed in 2016/17 was , of which 50.07% were tested in KwaZulu-Natal and Gauteng provinces alone. According to the NHLS Annual Performance Plan targets, 70% of HIV PCR should be tested within 96 hours. The target was exceeded, with 81.9% of HIV PCR tests being completed within the required period. 68 National Health Laboratory Service

70 Table NPP2: Early infant diagnosis training conducted in 2016/17 Year Month HCWs Trained Province 2016 April 108 Gauteng May 127 Gauteng, Free State June 169 Gauteng, Mpumalanga July 200 Limpopo, Gauteng, Free State August 211 Free State, Limpopo, Gauteng September 314 Gauteng, Free State, Eastern Cape October 303 Eastern Cape, Gauteng, Free State November 160 Gauteng, Free State, KwaZulu-Natal 2017 January 35 North West February 42 Free State March 674 Limpopo, Mpumalanga, KwaZulu-Natal, Gauteng Total Monitoring and Evaluation The Corporate Data Warehouse (CDW) distributes monthly statistics on the top 50 facilities with the most missed diagnostic opportunities (MDO). These samples have been rejected for clinical, clerical or administrative reasons. The NPP team uses the statistics to identify the facilities that are not performing well in terms of DBS collection and communicates its findings to the provincial PMTCT co-ordinators. A strategy is then developed to improve the quality of specimen collection in problematic facilities. Through these activities, there has been a significant reduction in MDO nationally, and in 2016/17 a further decrease of 1.9% was recorded. Outputs The NPP team assisted Gauteng Province in developing the facility-based PCR register, which captures data elements and improves PCR result reporting. The EID team forms part of the PMTCT working group and contributes to the national PMTCT guidelines. National GeneXpert MTB/RIF Programme Staff Puleng Marokane: Programme Manager Sylvia Ntsimane: Clinical Trainer Mbuti Radebe: Technical Trainer Overview The NPP is responsible for the implementation and continued programmatic monitoring of the GeneXpert MTB/RIF Programme, for the diagnosis of pulmonary and extra-pulmonary TB disease. This test was implemented in 2011, in conjunction with the DoH, to improve TB healthcare services due to its increased sensitivity for TB detection and reduced testing time. The technology identifies the causative agent of TB, Mycobacterium tuberculosis, and its susceptibility to rifampicin (RIF), a drug used in TB treatment. The programme oversees 326 GeneXpert instruments of varying capacity (GX4 platforms: 127, GX16 platforms: 190, GX48 platforms: one, and GX80 platforms: eight) distributed across 207 laboratories in South Africa. To date tests have been performed, with of these proving positive for TB, and with detectable rifampicin resistance. In 2014, testing was extended to vulnerable populations by the addition of seven on-site laboratories at the DCS and six mobile laboratories to support the PMC. Annual Report 2016/17 69

71 Figure NPP7: GeneXpert placements across nine provinces in South Africa (green circles) Operations From April 2016 to March 2017, GeneXpert MTB/RIF tests were performed nationally by NHLS laboratories. The average national TB positivity rate among those tested was 9.13%. Rifampicin resistance detection rates have remained at an average ~6%. The number of unsuccessful tests remained below 2%, with corrective actions implemented where necessary. Ninety-five percent of national GeneXpert MTB/RIF tests were performed within 48 hours, exceeding the NHLS Annual Performance Plan target of 90% within this time. Table NPP3: National GeneXpert MTB/RIF cumulative positivity results since programme inception Year MTB Detected MTB not Detected Test Unsuccessful Total % MTB Detected Total Table NPP4: National GeneXpert MTB/RIF rifampicin cumulative results since programme inception Year Inconclusive Resistant Sensitive No RIF Result Total % RIF Resistant Total The NPP team is responsible for monitoring GeneXpert testing nationally and provides training on quality procedures to healthcare workers (HCWs) such as appropriate sputum collection procedures, amongst other topics. This is an ongoing process to support DoH training in relation to the GeneXpert diagnostic and clinical algorithm. 70 National Health Laboratory Service

72 In total, 214 laboratory staff and HCWs were trained in 2016/17. Training activities included advanced GeneXpert workshops, which were conducted in collaboration with the supplier, Cepheid. These workshops produced 73 GeneXpert super-users across all nine provinces. In addition to training, visits to sites with poor performance were carried out and troubleshooting support provided. Table NPP5: Laboratory staff trained on the GeneXpert system in 2016/17 Province Basic-Users Super-Users Eastern Cape Free state 10 2 Gauteng KwaZulu-Natal Limpopo 8 7 Mpumalanga 6 5 Northern Cape 0 1 North West 0 2 Western Cape 29 6 Total Table NPP6: HCWs trained on GeneXpert-related topics in 2016/17 Year Month HCWs Trained Province April 24 Gauteng May 304 Mpumalanga, Limpopo June 207 Mpumalanga, Limpopo 2016 July 84 Mpumalanga, Limpopo August 154 KwaZulu-Natal, Mpumalanga, Gauteng September 84 Mpumalanga October 220 Gauteng, Mpumalanga November 204 Mpumalanga, North West, KwaZulu-Natal 2017 February 57 Gauteng, KZN March 157 Northern Cape, KwaZulu-Natal, Gauteng Total Monitoring and Evaluation All GeneXpert laboratories are monitored monthly for test volumes, instrument utilisation, in-laboratory TAT, TB positivity, RIF resistance and error rates via data extraction from the CDW. Summary reports on laboratory performance are compiled and distributed monthly to the area and business managers to assist with continuous monitoring of the programme. Quality assurance: To monitor ongoing quality of the testing service, all NHLS GeneXpert MTB/RIF testing laboratories are enrolled in an EQA programme for GeneXpert using dried culture spots. Three dried culture spot panels (Phase 1 to 3), each containing four samples, are distributed to all GeneXpert sites and the results of submissions analysed online. The EQA Programme has reported an improved site submission rate from phase 1 to 3 for the 2016 cycle. A consolidated national report is prepared at the end of each phase and sent to the NHLS QA Department. Connectivity: In 2016, NPP and Cepheid initiated the rollout of a real-time monitoring dashboard, C360, to enhance productivity and performance. The dashboard provides a detailed overview of national, provincial and laboratory performance by identifying geographical trends, system issues and user training needs. Installation of C360 software has been completed successfully in >70% of GeneXpert sites. Annual Report 2016/17 71

73 Figure NPP8: Benefits of the Cepheid C360 connectivity software Outputs A GeneXpert MTB/RIF Information Booklet was developed for HCWs to assist in improving TB diagnosis. The NPP GeneXpert Programme organised a successful Lessons Learnt half-day seminar at the 2016 African Society for Laboratory Medicine (ASLM) Conference. The aim was to share experiences regarding the national implementation of the GeneXpert MTB/RIF Programme in South Africa. Additional Items Training The GeneXpert NPP staff took part in national and provincial TB and HIV campaigns Monitoring of GeneXpert specimen rejection rates was initiated, leading to targeted clinical training interventions Ongoing training remains a practical tool to guarantee improvement in specimen collection and labelling. Technical and Maintenance Retro back covers were installed on all white skinned GX4 platforms to improve temperature related failures Optics cleaning maintenance was introduced for all GeneXpert platforms to reduce modular dust accumulation High voltage Uninterrupted Power Supply (UPS) systems were procured to ensure that GeneXpert power is maintained for at least 2 hours during power outages The following UPS systems were installed according to instrument capacity: 6 Kva for the GeneXpert Infinity platforms, 2 kva for the GX16 platforms, and 1 kva UPS for the GX4 platforms. Software updates In 2016, Cepheid released version 4.7b of the GeneXpert DX Software. Software 4.7b was deployed throughout the programme in preparation for the upcoming rollout of the more sensitive GeneXpert MTB/RIF Ultra assay. National Correctional Services TB and HIV Programme Staff Dr Leigh Berrie: Head Grants and Special Programmes Andani Phaswana: Programme Manager 72 National Health Laboratory Service

74 Yomvula Skhosana: Clinical Trainer S Nomatshaka, I Diale, T Mofokeng, L Mosasa, S Mona, S Sikazwe, T-L Mathews: Technicians Overview Previously, the Right to Care Global Fund Grant focused on 12 selected correctional centres and ensured that seven on-site GeneXpert MTB/RIF laboratories were set up. The seven centres with NHLS laboratories are Barberton, Kgosi Mampuru, Mondeor, Groenpunt, Westville, St. Albans and Pollsmoor prisons. The DCS TB and HIV Programme received additional funding from the Global Fund to ensure that inmates are screened and tested for TB, HIV and sexually transmitted infections (STIs) in all the correctional centres in the country. The CDC President s Emergency Plan for AIDS Relief (US) (PEPFAR), through the Aurum Institute, provided additional funding, ensuring HCWs at the DCS centres are trained on the GeneXpert MTB/RIF diagnostic testing algorithms, SOPs relating to specimen collection, infection prevention and control (IPC), and internal quality control for POC HIV testing. Funds were also secured for adequate monitoring and evaluation and to enrol all DCS centres in the internal quality control (IQC)/EQA proficiency HIV testing schemes. Operations DCS TB Programme In total, GeneXpert MTB/RIF tests were performed in 2016/17 (with 81.1% of tests conducted in four provinces: Western Cape, Eastern Cape, Gauteng, and KwaZulu-Natal); tests were positive for TB (4.9%); and 145 (4.7%) detected rifampicin resistance. Rates of rifampicin resistance were highest in the Western Cape (32%) followed by Eastern Cape (20%), KwaZulu-Natal (19.3%), Gauteng (11.7%), and 17.2% in the remaining five provinces. DCS HIV Programme The number of CD4 tests performed in 2016/17 was , of which (4.3%) had CD4 counts <100 cells/µl. Of the HIV VL tests performed for the same period, (35.7%) registered >1 000 copies/ml with three provinces (Gauteng, KwaZulu-Natal, and Mpumalanga) contributing 62.6% of these. Training Activities IPC training was given to 243 DCS officials in 116 (48.9%) centres across the 48 management areas. Training on appropriate specimen collection and handling was delivered at 223 (92.1%) of DCS centres. All 48 management areas were visited at least once (35% of areas visited at least twice) and meetings were held on matters related to service delivery. Figure NPP9: Nomvula Skhosana (front row, far right) at a training session at Modderbee Correctional Facility Centre, Gauteng Annual Report 2016/17 73

75 Training for HIV IQC was provided to 62 DCS centres (25.6%) with quality controls now being run weekly. This will significantly increase result reliability. It is intended that all 242 DCS centres will be performing internal quality controls by March With respect to GeneXpert diagnostic testing algorithm training, 138 DCS centres (57%) were targeted. The training leads to improved specimen collection with reductions in specimen rejections and thus increases in TB detection. Monitoring and Evaluation Test data from the DCS TB and HIV Programme, rates of specimen rejections, and SMS Printer functionality are monitored by programme staff. All 242 DCS centres have been enrolled on the NHLS EQA scheme and will participate from the first quarter of 2017/18. Courier routes for specimen collection at the DCS centres were re-aligned to improve testing TAT. Mine and Peri-Mining Communities TB and HIV Programme Staff Abel Makuraj: Programme Manager P Marule, F Kwinda, L Mamafa, T Motlogeloa, A Jonas, M Muntswu: Mobile Drivers J Phasha, M Booysen, O Mampe, M Kgotle, M Marumule, M Nkhobo: Mobile Technicians Overview Through financial support from the Global Fund, the NHLS, together with the Aurum Institute, was appointed by the DoH to provide services aimed at improving TB and HIV/AIDS management for vulnerable peri-mining communities, estimated at around people in six mining districts. The six districts with a high proportion of mines are Lejweleputswa, Dr Kenneth Kaunda and Bojanala districts in the North West; West Rand in Gauteng; and Waterberg and Sekhukhune in Limpopo. The NPP has provided six GeneXpert-mobile units within these communities since January 2015 to undertake GeneXpert MTB/RIF testing for TB diagnosis. The mobile units consist of vans equipped as mini-laboratories, with refrigeration facilities, water supply, and generators supplying electricity for the analysers. There are four GXP4 platform analysers per mobile laboratory, each with a testing capacity of 16 GeneXpert MTB/RIF tests every two hours. The mobile laboratories are supported by an LIS that provides patient results on site. Six drivers and six technologists have been employed through the Global Fund Grant to conduct the required testing. Operations The mobile units support the staff of the Aurum Institute during TB campaigns and undertake door-to-door visits to the informal settlements. Visits include taxi ranks, and mines. Further, provincial and district heath campaigns are supported by the mobile units, and on-site testing services are provided. This PMC programme tested GXP specimens in 2016/17, of which 232 (1.08%) specimens tested positive for TB, with 16 (6.9%) identifying rifampicin resistance. For the new fiscal year, the Aurum Institute has changed its TB strategy to contact tracing and this will likely increase TB detection rates. Figure NPP10: PMC Carletonville GeneXpert mobile laboratory conducting testing at Randgate Clinic, 13 September National Health Laboratory Service

76 Regular site visits and meetings are conducted with the mobile team members, parent laboratory managers, district DoH, and Aurum Institute teams for monitoring purposes in terms of meeting the set targets as stipulated by the grant funders. Quarterly meetings between the district health partners and DoH are intended to foster better relations and optimise resources. At these meetings, TB transmission hot spots are identified and action plans developed to improve the TB campaigns. National and Provincial HIV Counselling and Testing/Tuberculosis Campaigns and Events Overview The NPP takes part in various HIV counselling and testing/tb campaigns throughout the year, including activities around World TB Day, World AIDS Day, and others. The GeneXpert mobile laboratories are deployed at the events and provide on-site TB diagnostic services. Campaigns Supported Figure NPP11: PMC Jane Furse Mobile Unit at Heritage Day celebrations at Babubatse Primary School, 22nd September 2016 Figure NPP12: PMC Mobile team active at the DOH/Rustenburg Rotary Club TB Outreach Programme, 13 October 2016 Figure NPP13: NUM National Mineworker s TB Campaign, James Motlatsi Stadium, 22 October 2016 Annual Report 2016/17 75

77 Figure NPP14: Welkom Provincial World AIDS Day event, 1 December 2016 Figure NPP15: National Department of Transport Health Campaign, Bosman Station in Pretoria, 8 December 2016 Figure NPP16: National World TB Day event, Clive Solomon Stadium, Bloemfontein, 31 March 2017 Figure NPP17: NHLS and Aurum Institute partners at the National World TB Day event, Hoffman Square, Bloemfontein, 31 March National Health Laboratory Service

78 Other Events Attended 3 to 8 December 2016 Meeting of the African Society for Laboratory Medicine (ASLM), Cape Town 10 February 2017 National Department of Transport Campaign, Bosman Station in Pretoria 24 March 2017 Gauteng World TB Day event, Saul Tsotetsi Stadium, Carletonville 14 to 18 March 2017 Department of Transport TB Campaign, Bosman Station in Pretoria. mhealth Programme Staff Lynsey Isherwood: Programme Manager Floyd Olsen: Special Projects Manager Portia Madumo: POC Co-ordinator Rapid Testing Overview The mhealth programme was established in March 2014, with the primary aim of extending NPP services to HIV and TB health services in South Africa, using mobile technology. The unit began with the development of simple android notification applications (apps), and has now been extended to include automated readers and mobile POC technologies. Laboratory Result Notification and Linkage-to-Care Applications: Treat-TB Notify Application This is an android mhealth app, developed to send real-time notifications to pre-authenticated end-users (HCWs, TB co-ordinators and tracing/injection teams) of newly diagnosed drug-resistant TB (DR-TB) patients. Currently, the app is only accessible to the Ekurhuleni district of Gauteng and six TB Co-ordinators are receiving these notifications via their personal mobile devices. The Gauteng DoH has requested a provincial rollout. Therefore, an additional 50 TB Co-ordinators have been trained, in preparation for the rollout. Through separate funding, Version 2 of Treat-TB app has been developed by TLC Engineering. This updated version incorporates newly diagnosed drug-sensitive TB patients. One hundred android phones have been purchased to support the rollout. The procured android mobile will be locked through an APN connection, which will allow for remote device management and monitoring. Exception reporting tools have been designed to notify programme managers of patients not linked into care within three days of diagnosis. Laboratory Result Notification and Linkage-to-Care Applications: milinc Application A prospective observational cohort research of persons with symptoms of TB presenting to primary healthcare clinics in peri-urban KwaZulu- Natal, was conducted between June and November Enrolment was undertaken by clinic staff into the mobile interface Linkage to Care milinc app. A specimen bar code was placed on the sputum specimen bottle and was scanned directly into milinc, creating an immediate direct patient-specimen match. The sputum specimen followed the standard laboratory submission processes and the results were transmitted from the NHLS to milinc. TB results were available immediately on milinc for the clinic nurse, while linkage officers were simultaneously notified of rifampicin resistant patients for tracing and linkage. Three clinics enrolled patients. Among patients without results, the majority (56.5%) resulted from rejection at laboratory level. All rejected specimens resulted in an immediate notification for repeat testing. TB was identified in 292/2 880 (9.9%) patients and rifampicin resistant TB in 38/292 (13%). Of the DR-TB patients, 33/38 (87%) were traced. Patients with DR-TB were linked to care and appropriate anti-tb treatment was initiated within ~ 2 days 23 hours. The combined impact of rapid diagnosis and enrolment with milinc resulted in linkage and initiation of DR-TB treatment in <3 days from diagnosis. The DoH evaluated the milinc programme through an independent company Cyber Pro Consulting, commencing on 25 July The evaluation ended in December 2016 and the decision was taken to discontinue the project. Laboratory Result Notification and Linkage-to-Care Applications: SmartLTC Application This was a multi-site randomised controlled study Do smartphones increase linkage to and retention in care in newly diagnosed HIVpositive patients in Johannesburg? The Principal Investigator was Prof. WDF Venter, Wits Reproductive Health Institute (WRHI), funded by The World Bank. The app was designed by the NPP, in conjunction with the WRHI. The primary aim was to educate newly diagnosed HIV patients on the CD4 and HIV VL results, thereby empowering them to take charge of their own health. Recruitment status target was patients with no mobile phone, and patients with access to android mobile devices. The study ended in September 2016 and was replaced by a new programme, Phila SMS. This is part of a decanting project at one of the City of Johannesburg s healthcare facilities (decanting of patients to community sites for HIV treatment aiming to decongest clinics). Phase 1 was launched on 26 September 2016 and involves only the SMS platform. Phase 2 will see the launch of an app version during the first quarter of Annual Report 2016/17 77

79 Automated Rapid Diagnostic Testing (RDT) Devices: Fio Deki Readers Feasibility and performance of an automated rapid test reader for improving HIV Counselling and Testing services in South Africa (Ethics Approval No: M150160). The Deki is an automated portable reader with touchscreen technology that provides data capture, quality control checks, workflow prompting and automated result analysis for any standard, commercially available lateral flow test strip. The Deki Reader is used to capture an image of a processed RDT (after exposure to a clinical specimen), analyse the captured image, and provide a qualitative determination of the presence or absence of a visual marker that results from the reaction between the RDT reagents and the clinical specimen. The Deki Reader is an alternate to performing visual interpretation of the RDT result. Figure NPP18: An illustration of the Fio Deki Reader and placement of the RDT The NPP conducted a laboratory evaluation of the Deki Reader (ethics approval #M150160) to determine the concordance between automated result interpretations by the Deki versus the visual result interpretation of various commercially available HIV rapid tests. Overall, the Deki reader had a 99.5% concordance (for 774 individual RDTs measured) with visual result interpretation. A clinical evaluation will be conducted to determine the performance and feasibility of the Deki reader within the South African healthcare setting. The evaluation data was presented to the DoH on 21 January 2017 and approval for the clinical evaluation was given. The clinical evaluation protocol has been developed together with Right to Care (ethics approval #M150160). Twenty Deki readers will be available for this phase of the study (15 in use and five spare). Five Deki readers will be placed at the healthcare service of the Right to Care offices, Helen Joseph Hospital, and 10 readers will be placed with community teams working within sub-districts A and B of the Johannesburg Health District. The evaluation is divided into two phases: 1. Phase A - Evaluation of the Deki reader robustness, operability, data capture and connectivity capabilities (2 months), and 2. Phase B - Determine the performance (concordance) between visual interpretation by a HCW and the automated Deki interpretation of residual HIV rapid tests used in HCT (4 months). Automated Rapid Diagnostic Testing (RDT) Devices: MobiHealth Laboratory performance evaluation of an android powered blood testing innovation: MobiHealth (Ethics Approval No. M150160). MobiHealth is an Android (mobile phone), blood diagnostic platform that can be used for patient self-testing or diagnostic testing at the site of patient care. MobiHealth tests for 51 different diagnostic parameters using disposable test strips, requiring 25-40µl blood. Test results are provided in 5 90 seconds and these results can be automatically transmitted to a cloud-based server to ensure data management. The validation study is due to commence in May Figure NPP19 (Left): An illustration of the MobiHealth glucose and cholesterol analytes. (Right): An illustration of the MobiHealth patient management and test result data 78 National Health Laboratory Service

80 Strengthening of Pre- and Post-Analytics for HIV VL Testing, using Mobile Technology: milabs Strengthening and Improving Access to HIV VL Testing in South Africa. (Grant number: 5U2GGH ). Through this grant, the use of a mobile ICT (mhealth) solution to assist in service delivery in HIV VL testing will be developed. The mobile workflow automation solution will comprise a monitoring system that will track HIV VL testing activities through a mobile app installed on a mobile device operated by the HCW. The proposed solution will provide a standard and integrated mechanism with which services can be effectively recorded, analysed, improved and reported to the relevant stakeholders (e.g. government health departments, management, and funding parties). HCWs at health facilities and drivers will be equipped with smart phones, pre-loaded with the app, which is customised to match the required HIV VL testing workflow. Data will be zero-rated to ensure that access to the app is possible at all time. Features will include 1. Automated order entry pilot in 27 PEPFAR Districts, 2. Cold chain management (sample integrity) for both plasma and DBS for HV VL monitoring, 3. TAT and traceability monitoring of HIV VL specimens, and 4. Technical training for all stakeholders who will use the app. SMS Printers Between November 2013 and December 2015, bi-directional laboratory SMS Printers were rolled out in a phased approach in all provinces, excluding KwaZulu-Natal. Bi-directional laboratory SMS Printer technology has improved the rapid delivery of HIV and TB diagnostic data of patients throughout South Africa, providing HCWs with patient results immediately they have been authorised by the testing laboratory. Training of HCWs was aligned to the phased rollout. The NHLS bi-directional SMS Printer has the ability to send results from the LIS to the printer placed at Primary and Community Healthcare clinics ( Push ). This occurs for CD4, reflexed cryptococcal antigen, HIV VL, infant HIV PCR, TB microscopy, and GeneXpert MTB/RIF results. The printer can also retrieve patient results ( Pull ) from the LIS database by scanning the barcode on the specimen requisition form at the healthcare clinic. Automated heartbeat messages allow for daily monitoring of SMS Printers, ensuring their functionality. To date, bi-directional laboratory SMS Printers have been installed in healthcare facilities and 242 DCS centres. The TAT from specimen collection to result delivery has reduced substantially. Weekly reports are generated, listing facilities where SMS Printers are not functioning. In addition, a real-time monitoring website has been developed and implemented. Connectivity within remote areas across South Africa continues to challenge the system, aggravated by staff rotation within facilities and inappropriate device handling of critical components of the printers. On average, results are queried Eastern Cape Free State Gauteng KwaZulu-Natal Limpopo Mpumalunga 27 North West Northern Cape Western Cape ART Initiating Facility SMS Printers Figure NPP20: Coverage by SMS Printers of ART initiating healthcare facilities by province A number of challenges have been experienced with the utilisation of SMS Printers, and the NHLS is working on improving the following: 1. Implementing a move from SMS to Global Data Services Platform (GDSP) accompanied by national roaming to improve network connectivity, 2. Scanners, power supplies and external antennas will be modified and internalised in updated models to limit component removal, and 3. The potential for pushing additional laboratory tests. During the financial period, 348 healthcare facilities were visited and support services provided, and 576 HCWs trained (at 471 facilities) on all aspects of SMS Printer operation. Annual Report 2016/17 79

81 Information and Data Management Staff Dr M Pedro da Silva: NPP Operations Manager Oriel Mahlatsi: Data analyst Silence Ndlovu: Database administrator Overview For programmatic monitoring and evaluation purposes, the NPP generates a vast array of monthly and quarterly reports for distribution to partners, funders, national and provincial DoH/s, and co-ordinators. These reports are prepared as Excel-based spreadsheets, providing multiple user-friendly views of specimen and facility-level laboratory data. The data is extracted via the CDW. Data variables include test volumes, positivity rates, laboratory workflow analyses, TAT, instrument percentage utilisation rates, exception reporting such as tests with CD4 values <100 cells/µl, HIV VL >1 000 copies/ml, and test data disaggregated by sex and/or age. Ethics approval was obtained in December 2016 (Clearance M160978) from the Wits Human Research Ethics Committee for the analysis of LIS data, by the NPP, for programmatic monitoring and evaluation purposes under the established Integrated Laboratory Data Analysis for Care (ILDAC) programme. Programmatic data requests are directed to the Operations Manager who ensures the data request complies with the conditions of the ethics approval, prior to data release, under the ILDAC programme. Grants and Special Programmes Staff Dr Leigh Berrie: Head - Grants and Special Programmes Lucky Ngwenya: Grants Financial Manager Asiashu Bongwe: Point-of-Care Co-ordinator HIV Viral Load Portia Madumo: Point-of-Care Co-ordinator Rapid Testing Global Fund to Fight AIDS, Tuberculosis and Malaria (Year 1) The NHLS has been awarded a total of R for both HIV and TB activities for the entire grant period. NHLS interventions fall into the following categories: 1. Provision of GeneXpert MTB/RIF testing either on site or at the nearest referral laboratory for improved case detection in PMC, 2. Provision of GeneXpert MTB/RIF testing either on site or at the nearest referral laboratory for improved case detection in the DCS, 3. GeneXpert MTB/RIF diagnosis in informal settlements, 4. Provision of GeneXpert training for both clinical and laboratory staff, 5. Provision of IPC training for the DCS, 6. Expansion of HIV VL testing services to address gaps in service delivery, and 7. Improving quality of HIV rapid testing in the field. Provision of Xpert MTB/RIF Testing for Improved Case Detection in PMC Interventions in this programme are to assist the DoH in improving TB/HIV case findings by working closely with the Aurum Institute, another sub-recipient and the clinical partner, to screen and test for TB with the GeneXpert in the PMC. In the previous round of the Global Fund Grant, the DoH identified six districts for the PMC roll-out; Lejweleputswa in the Free State, Dr Kenneth Kaunda and Bojanala districts in the North West, Waterberg and Sekhukhune in Limpopo and West Rand in Gauteng Province. These six districts are provided with GeneXpert MTB/RIF-equipped mobile laboratories. The mobile laboratories are run with two employees, a driver/clerk and a technician and are linked to the closest NHLS laboratory, which supports the mobiles for reagents, consumables, and overflow of GeneXpert specimens. Provision of Xpert MTB/RIF Testing for Improved Case Detection in the DCS The NHLS, as a pathology group servicing the state sector in South Africa, is responsible for testing the inmate population in the DCS for TB, using the GeneXpert MTB/RIF test. In 2016/17, specimens were tested. The success of this programme can be attributed to the intensive visits to all the DCS management areas by the NHLS staff, where all issues pertaining to a comprehensive care package are discussed and mentoring is done, ensuring that DCS clinical staff members follow the national testing guidelines and algorithms. Provision of GeneXpert Training for both Clinical and Laboratory Staff The NHLS implemented the Xpert MTB/RIF test as the initial TB diagnostic test for individuals suspected of having MDR-TB or HIV/TB from 80 National Health Laboratory Service

82 March Training of personnel is an ongoing process to support the DoH on the clinical algorithm as well as to train laboratory staff on the most efficient operation of the analysers, whilst ensuring result quality. In the review period, HCWs and laboratory technical staff were trained. IPC Training for the DCS Prof. Adriano Dusé and his IPC team at the University of the Witwatersrand (Wits), together with the NPP, have developed an IPC Training Course with Trainer and Trainee manuals. Training is currently being rolled out to all DCS regions and will re-commence in May Follow-up assessments will be done for the regions that have been trained from April Expansion of HIV VL Testing Services to Address Gaps in Service Delivery The NHLS provides HIV VL testing services across 16 high-throughput, centralised laboratory sites but gaps remain in service coverage. A pilot project is being undertaken to close identified service-related delivery gaps through decentralisation of HIV VL testing services in South Africa. A tiered, hybrid model has been developed, consisting of centralised laboratory-based and decentralised testing, to facilitate improved access to HIV VL testing services, reduce HIV VL testing TATs, and decrease the testing burden at centralised sites. This model identified 13 district-level laboratories across six provinces for placement of additional HIV VL testing services. As the NHLS has extensive technical and operational expertise regarding the GeneXpert platform (Cepheid), this assay was selected and placed, utilising the Xpert HIV-1 VL assay. Improving Quality of HIV Rapid Testing in the Field Rapid diagnostic tests (RDTs) or dip-sticks are performed in large numbers in both rural and urban settings but have little or no innate quality control and thus are difficult to monitor at a central level. In South Africa, there are over facilities which offer HIV Counselling and Testing (HCT) services to the public sector using RDTs. Innovative solutions using wireless technologies such as reader/smartphone applications are a potential strategy to ensure quality assurance through automated test result interpretation and data capture for real-time quality monitoring. One option, which is commercially available and has already shown promise in malaria testing, is the Deki Reader (Fio Corporation, Toronto, Canada), discussed earlier. AURUM/CDC Grant (Year 3) The focus of the grant is on Comprehensive HIV and TB Prevention, Care and Treatment Services and Systems Strengthening in Facilities of South Africa s DCS. The key deliverables for the NHLS are to support and train DCS facility staff on laboratory procedures, including stock control of collection materials; specimen handling, including recording and storage of samples; IPC; and procedures for containment and disposal of hazardous waste. In addition, the NHLS is required to support and train facility management to 1. Address bottlenecks in processing specimens and results, 2. Improve laboratory service utilisation, and 3. Address billing procedures. The NHLS is required to provide QA for point-of-care testing and to standardise SOPs for collection of laboratory specimens according to guidelines and in line with current DoH algorithms. Further, the NHLS is to monitor the performance of the SMS Printers at DCS centres. Training Clinical Training on GeneXpert technology, GeneXpert TB clinical algorithm, laboratory procedures, QA for POC testing and SOPs has been undertaken for the DCS. In the Gauteng, Limpopo, KwaZulu-Natal, Free State and Northern Cape Management Areas, 100% training coverage has been achieved on the revised GeneXpert algorithm and drug-resistant TB reflex testing to support the rollout of the shortened multidrug-resistant-tb (MDR-TB) regimen. In the Free State, Northern and Western Cape Management Areas, 100% coverage on IPC practices training has been achieved. Remarkable improvement in specimen collection has been noted with minimal error rate following training. IQC Rollout To date, 53 of the targeted 121 DCS centres have received IQC material for quality assurance of HIV rapid testing. In addition, 237 functional centres have been successfully enrolled on the NHLS EQA proficiency scheme for HIV rapid tests. GeneXpert and CD4 Data Collection and Reporting Of the active DCS centres, 100% have accurate laboratory data collection and reporting for GeneXpert MTB/RIF, CD4, and HIV VL results. SMS Printers All the centres in the DCS have received SMS Printers. SMS Printer functionality is monitored remotely. NHLS CDC CoAg: HIV Viral Load Project (Year 1) This project is aimed at strengthening the pre- and post-analytical phases at facility level (Laboratory-Clinic interface) to ensure the timely Annual Report 2016/17 81

83 return of quality laboratory results, with a focus on the use of innovative technologies for the strengthening and improvement of pre- and post-analytical processes for HIV VL monitoring in the 27 PEPFAR-supported districts in South Africa. The ultimate goal is to strengthen and improve access to HIV VL monitoring. NPP activities under this project include the procurement of three pre-analytical systems for the Roche Cobas 6800/8000 for Mankweng, Nelspruit and Charlotte Maxeke; as well as the development of mhealth solutions for specimen tracking, cold chain monitoring, and results delivery. Research and Development Group Staff Professor Lesley Scott: Senior Research and Development Scientist and Group Head Anura David: Research and Development Scientist Lara Noble: Research and Development Scientist Matilda Nduna: Registered Nurse Violet Molepo: Auxiliary Nurse Dr Natasha Gous: Point-of-Care Manager for the NPP (Resigned November 2016) Overview The NPP Research and Development (R&D) group comprises a multidisciplinary team, specialising in applied research and implementation of new laboratory diagnostics for HIV and TB, including quality management systems of high to low throughput testing platforms. The group s outputs under the leadership of Professor Lesley Scott contribute to improved services within the NHLS, knowledge transfer to the NPP, policy development for the DoH, and global quality management for several diagnostic tests. Contributing to Africa s Innovation through Science: Verification and External Quality Assurance Programmes Xpert MTB/RIF EQA Programme The R&D team continues to supply the dried culture spot technology programme (developed by the group) for verification and EQA of GeneXpert MTB/RIF platform. In 2016, the programme supplied EQA material to 207 NHLS sites (326 instruments) and 75 international sites (90 instruments). The programme is now managed by SmartSpot Quality Pty (Ltd), a Wits Enterprise spin-off company. In 2017, an automated dried culture spot preparation instrument was evaluated and the 2017 verification and EQA panels were prepared using this instrument. MTB Combo EQA Programme The MTB Combo EQA, comprising the GenoType MTBDRplus (HAIN diagnostics, Behren, Germany) EQA and the Strip Interpretation Analysis (SIA) programmes, was piloted in 2016 (11 sites, 15 instruments over three phases) to provide additional educational support to sites performing the MTBDRplus assay. The automated upload platform was tested in the final quarter of 2016 to simplify result capture and reporting, and is currently being finalised. The 2017 programme will be prepared in April HIV Viral Load Programmes The R&D team supplies the South African Viral Quality Assessment (SAVQA) panel for instrument verification and evaluation. In 2016, 46 SAVQA panels were prepared (Twenty-three for NHLS/research and the equivalent for EQUIP). The SAVQA panel is currently being adapted to a dried virus spot (DVS) programme to enable sites in remote areas to obtain quality assessment panels, without the requirement of refrigeration or complicated shipping. The verification panels will be piloted in the NHLS Point-of-Care Xpert HIV-1 VL trial sites in mid Contributing to National Health TB Policy: Aiming for Improvements in Sensitivity of TB Molecular Diagnostics Several new technologies are being evaluated in the R&D group: The multicentre (10 site, 8 country) study to evaluate the new Xpert MTB/RIF Ultra sputum test for TB, in collaboration with the Foundation for Innovative New Diagnostics (FIND) and WHO, was completed in Quarter 4 of The overall data analysis reports non-inferiority of 82 National Health Laboratory Service

84 the Xpert MTB/RIF Ultra to the current in-use Xpert MTB/RIF TB test used in the SA National TB programme. A 17% increased sensitivity in MTB diagnosis among smear-negative cases was noted. The R&D team presented the South African data to the NHLS Microbiology Expert Review Committee, and an implementation plan is being developed. The final report can be accessed at bitstream/10665/254792/1/who-htm-tb eng.pdf The Abbott (Abbott Molecular, Des Plains, IL, USA) RT MTB and RT MTB RIF/INH assays, designed for the Abbott m2000 platform, were evaluated against the Xpert MTB/RIF, on a cohort of presumptive TB infected individuals. In total, 206 complete results were analysed. The results are promising, especially since the RT MTB assay includes a reflex test to determine RIF and Isoniazid (INH) susceptibility. A manuscript was submitted to the Journal of Clinical Microbiology in March 2017 as an evaluation of the technology performance in HIV-TB co-infected individuals and reviewer queries are being addressed. The Hain FluoroType MTB and FluoroType MTBDR are two new assays being developed for use on the GenoXtract 96 and Fluorocycler instruments from Hain as a potential automated option over the current MTBDRplus assay. Dried culture spots were tested on the system with 100% concordance with Xpert MTB/RIF. Biosafety data has recently been made available and further R&D is planned prior to testing on patient specimens. The investigation (NIH R21, EXIT-RIF) into whether new diagnostics impact on improved patient care is complete and has been published. The study assesses whether rapid diagnosis of rifampicin resistance by GeneXpert testing leads to improved TB treatment outcomes, determines phenotypic and genotypic drug resistance profiles in patients diagnosed with Xpert-RIF resistance, and documents management decisions and patient actions in the 12 months following diagnosis of Xpert-RIF resistance. A second NIH R21 study is under way in the Eastern Cape to evaluate laboratory and clinic indicators for TB transmission and control. Permission to evaluate the DHIS data has been received from the DoH. A new grant (Wendy Stevens, Principal Investigator; Lesley Scott, Project Leader) has been awarded through the Newton/MRC funder, to investigate Technology supported systems for rapid impact on TB control, and commenced in March The first grant report feedback has been completed. Ethics and relevant approvals for both projects are under way and the first connectivity solution C360 (Cepheid) has been evaluated in collaboration with the NPP GeneXpert programme staff. Lesley Scott collaborated with the HIV Network Co-ordinating TB Diagnostic Laboratory Working Division of the National Institute of Allergy and Infectious Diseases, to survey the TB infection control practices in low- and middle-income countries. In collaboration with biomedical engineers at the Thayer School of Engineering in Dartmouth, R&D is under way to determine the likelihood of identifying M.tuberculosis from sputum, using volatile acids collected through air sampling and fatty acid profiling. This study is in the preliminary phases, but shows promising results. Contributing to National Health TB Policy: Information Technology s Superpower and its Place in Global Disease Control This year the team further expanded its knowledge base in Information Technology (IT) applications for developing concepts in disease control using molecular indicators from the Xpert MTB/RIF programme. The team realised the importance of the molecular characteristics, such as cycle threshold, of each GeneXpert TB test performed, and formed the hypothesis that the cycle threshold could be used as an indicator of mycobacterial disease burden and be used to monitor trends in RIF resistance in relation to space and time. The > MTB positive GeneXpert results are being analysed using various statistical and geographic information system (GIS) models across districts to present and evaluate disease trends over time and across geographically variable regions. Several multidisciplinary collaborations have evolved through the need to better understand and evaluate the findings. These collaborations include epidemiology groups at University of North Carolina, Health Economists at Right to Care and the Wits School of Public Health. Included in this is the evaluation of the Remote Xpert, which is a dashboard-driven laboratory monitoring tool, to assist the NPP on GeneXpert instrument and site performance. Several projects are ongoing and funded through mechanisms such as CDC, the NIH and recently the South African Medical Research Council, with funds received from the UK Medical Research Council Newton Grant. Results of these interventions are shared with the NPP and DoH. In addition to evaluating new TB diagnostics, the R&D group, together with the NPP, is evaluating the connectivity software from Cepheid. The C360 remote access software allows real time analysis of the quality of all Xpert MTB/RIF tests performed in the field. The R&D team is currently developing an evaluation grid of audit indicators to monitor test/instrument/user performance quality. Embracing Future HIV Testing Needs with New Molecular Technologies The R&D group is involved in performing evaluations of various new high throughput and POC platforms for HIV VL testing, with a focus on the integration of TB-HIV care: Annual Report 2016/17 83

85 The performance of the Aptima HIV-1 Dx assay on the Panther system (Hologics Inc, Bedford, MA, USA) as an alternative assay for high throughput laboratories, using both EDTA-plasma and DBS, was evaluated. These results were presented at the ASLM Conference in 2016 and a manuscript is being prepared for publication. The Cepheid Xpert HIV-1 viral load (Xpert VL; Cepheid Sunnyvale, CA, USA) for GeneXpert was evaluated in a high-burden HIV setting (Johannesburg, South Africa), using EDTA-plasma, with a sub-study on EDTA-whole blood, DBS, and EQA material. This evaluation has been published and a tiered HIV VL testing model has been developed for the extension of HIV VL testing services, to address gaps in service delivery. The use of off-label specimens for VL testing, using the Xpert HIV-1 VL to expand VL testing further, is currently being evaluated. A clinical trial is scheduled to begin in Quarter 1 of 2017/18, to determine the potential of the Xpert HIV for HIV VL testing using different blood collection tubes, whole-blood finger stick specimens (for true point-of-care testing), DVS and low volume EDTA-plasma. Preliminary results will be presented at the Interest Meeting 2017, in Malawi. An abstract showcasing the VERIS HIV-1 (Beckman-Coulter) SAVQA pre-qualification results will be presented at the Interest Meeting 2017, in Malawi, and a clinical trial is being discussed. Additional Activities Implementation of the Shortened MDR-TB Treatment Regimen and Line Probe Assay to Detect Second-Line Resistance On 12 May 2016, the WHO announced recommendations for a shortened MDR-TB treatment regimen. With the shortened regimen, MDR-TB treatment can be completed in 9 12 months compared to the conventional regimen of months. In addition, the WHO endorsed the MTBDRsl line probe assay (LPAsl) as the rapid initial test to be performed on patients with confirmed rifampicin resistant-tb, in place of second-line drug susceptibility testing (DST) to detect resistance to fluoroquinolones (FLQ) and second-line injectable drugs (SLID). The shortened regimen is expected not only to improve patient outcomes due to greater treatment adherence, but also to reduce the number of patients lost to follow-up. LPAsl detects resistance to the FLQ based on the gyra/gyrb genes and the SLID based on the rrs/eis promoter gene. As the WHO recommendations for LPAsl apply to both direct testing of sputum specimens (irrespective of smear status) and indirect testing on positive TB cultures, exclusion of resistance to second-line drugs will be made significantly earlier than by current DST. This allows for further improvements to patient outcomes. The implementation of the shortened MDR-TB regimen, and the laboratory reflex testing to support this, has been rolled out nationally. To assist with training at the MDR-TB initiation sites and the laboratories registering specimens to support the laboratory reflex testing, flyers have been developed as guides and reminders of the tests to request (treatment initiation sites) and the tests to load on the LIS. Training activities are being conducted as a joint venture between the Centre for Tuberculosis (CTB, NICD) and the NPP. Training activities began in the fourth quarter of the financial year covering the following provinces and training sites: North West (one facility and 10 HCWs), Northern Cape (three facilities and 50 HCWs), KwaZulu-Natal (four facilities and 78 HCWs), Limpopo (10 facilities and 36 HCWs), and Gauteng Province (55 facilities and 396 HCWs). In terms of the DCS, 34 centres were visited and 144 staff members trained. The training activities target the laboratory staff (specimen registration and selection of the DR-TB reflex superset), and the hospitals/clinics/treatment initiation sites/tbfocal points (requesting the correct test on the request form). Figure NPP21: Flyer to guide correct requests for reflex test at MDR-TB treatment initiation sites Figure NPP22: Flyer to guide correct loading of the reflex test superset on the LIS by the registering laboratory Urine Lipoarabinomannan Urine Assay Pilot Project The urine lipoarabinomannan test (LF-LAM), marketed as a point-of-care test, is a lateral flow assay designed for tests on urine samples collected from patients suspected of having tuberculosis disease. The lipoarabinomannan (LAM) antigen detected by the assay is a 84 National Health Laboratory Service

86 component of the mycobacterial cell wall and is released from metabolically active or degenerating bacterial cells. The LAM antigen is present in persons with active tuberculosis disease. Detection of LAM in urine is indicative of disseminated TB with renal involvement in patients living with HIV and advanced immunodeficiency. The WHO 2015 policy recommendations regarding use of the test are as follows: 1. The assay may be used to assist in the diagnosis of TB in HIV positive in- and out-patients with signs and symptoms of TB (pulmonary and/or extrapulmonary) who have a CD4 cell count 100 cells/μl, or HIV positive patients who are seriously ill regardless of CD4 count or with unknown CD4 count; and 2. The assay should not be used as a screening test for TB. Although LF-LAM is designed for POC testing, there are concerns regarding the QA aspects of POC testing. The pilot was proposed to guide a final decision on whether LF-LAM should be offered as true POC or as a laboratory-based test. The pilot will be conducted in two arms/ phases In the first, the LF-LAM will be offered as a laboratory-based test at four selected sites. In the second phase, the LF-LAM will be a clinician-based POC test with testing done at focal points such as the emergency department, medical casualty, and internal medicine departments. Both arms/phases will be compared in terms of the objectives: 1. Utilisation in terms of appropriateness of testing Inpatient versus outpatient and capturing CD4 and HIV VL parameters, other assessments of illness severity like respiratory rate, temperature, and heart rate, 2. Time to result (measured for the laboratory component), 3. Time to treatment initiation as determined by the proportion commencing treatment, 4. Test reproducibility Residual urine specimens from both the laboratory and POC arms will be retested for quality purposes at a centralised point, 5. Determine the utility and role of LF-LAM by testing residual urine specimens with the GeneXpert MTB/RIF and Xpert Ultra platforms (This will be highly beneficial as urine is currently a specimen-type not endorsed by WHO for Xpert testing), and 6. Test the yield of the LF-LAM in terms of positivity. Training of pilot sites and testing commencement is expected by the second quarter of 2017/18. Meeting of the African Society for Laboratory Medicine 2016, Cape Town 2016 Prof. Wendy Stevens was appointed conference co-chair and was tasked with organisation of the conference. Dr Da Silva served as lead rapporteur for the Global Health Security Track. Significant contributions were made by NPP staff to workshops, seminars, oral sessions, session convening/chairing, and poster presentations. Details of oral and poster presentations are provided below. Congress Presentations Berrie L. Laboratory management ensuring efficiency, quality testing, and timely return of results. In: CDC/ASLM Workshop Scaling up HIV VL testing and uptake of results through improving efficiencies of systems, Windhoek, Namibia, September Berrie L. National Xpert MTB/RIF roll out The South African experience. In: Meeting of the African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Berrie L. Improving access to viral load testing through coverage, linkage, and directed/targeted programme interventions. In: Meeting of the African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Berrie L : Lessons learnt and solutions for HIV viral load scale-up. In: Meeting of the African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Berrie L, Sarang S, Stevens W. Lessons learnt from national HIV viral load implementation and scale-up in South Africa. In: Meeting of the African Society of Laboratory Medicine (ASLM), Cape Town, South Africa, December Bor J, Brennan A, Fox MP, Maskew M, Stevens W, Carmona S, et al. District prevalence of unsuppressed HIV in South African women: Monitoring programme performance and progress towards In: 21 st International AIDS Conference, Durban, South Africa, Bor J, Nattey C, Maughan-Brown B, MacLeod W, Maskew M, Carmona S, et al. Rising CD4 counts at clinical presentation: Evidence from a novel national database in South Africa. In: 21 st International AIDS Conference, Durban, South Africa, Carmona S, Wedderburn C, MacLeod W, Hsaio M, Jani I, Kroon M, et al. Field performance of point-of-care HIV testing for early infant diagnosis: Pooled analysis from six countries from the EID Consortium. In: 21 st International AIDS Conference, Durban, South Africa, Cassim N, Coetzee LM, Glencross DK. HIV treatment guideline changes: Implications for predicting network restructuring needs and distribution of CD4 testing platforms to laboratories across South Africa. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Cassim N, Coetzee LM, Glencross DK. Review of CD4 data as a proxy for establishing disease burden for municipalities identified as national development nodes. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Cassim N, Coetzee LM, Glencross DK. HIV treatment guideline changes: Implications for predicting future national CD4 testing costs for South Africa. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Cassim N, Coetzee LM, Glencross DK. Retrospective analysis of aggregate laboratory CD4 data to assess changes in immunological status of HIV+ patients accessing HIV testing and care. In: Southern African HIV Clinicians Society Conference, Johannesburg, April Annual Report 2016/17 85

87 Cassim N, Lekalakala R, Coetzee L, Asmall S, Glencross DK. The Ideal Clinic Initiative and the need for mhealth solutions. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Chakezha T, De Gita G, Ballah NJ, Puren A, Takuva S, Carmona S, et al. Determinants of CD4 immune recovery among individuals on antiretroviral therapy in South Africa: A national analysis. In: 21 st International AIDS Conference, Durban, South Africa, Coetzee LM, Glencross DK. Site verification of the Aquios flow cytometer as replacement platform for outmoded XL-cytometer across a national testing network. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Coetzee LM, Drury S, Glencross DK. Comparison of the new fully automated volumetric Aquios flow cytometer PanLeucogate (PLG) platform for CD4 T-lymphocyte enumeration to existing predicate PLG technology in South Africa. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Coetzee LM, Cassim N, Glencross DK. District and sub-district analyses of CD4 counts <100cells/μl identify areas with higher rate of late presentation for ART initiation and risk for opportunistic infections. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Coetzee LM, Drury S, Glencross DK. Comparison of the new fully automated volumetric Aquios flow cytometer PanLeucogate (PLG) platform for CD4-T lymphocyte enumeration to existing predicate PLG technology in South Africa. In: Wits Research Day and Postgraduate EXPO, Johannesburg, South Africa, September Coetzee LM, Moodley K, Glencross DK. Comparative results of a novel flow cytometric assay (FA) for early detection of cryptococcal antigen (CrAg) against LFA and EIA in HIV-infected patients with a CD4 count <100 cells/µl. In: WITS Research Day and Postgraduate EXPO, Johannesburg, South Africa, September Coetzee LM, Moodley K, Glencross DK. Comparative results of a novel flow cytometric assay (FA) for early detection of Cryptococcal antigen (CrAg) against LFA and EIA in HIV-infected patients with a CD4 count <100 cells/µl. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Da Silva MP. Molecular TB diagnostics Clinical interpretation and lessons learnt from the field. Improving post-analytical quality. ACTGsponsored workshop: Quality needs for Molecular TB/HIV and HPV diagnostic assays applied in Clinical Laboratories. In: Meeting of the African Society of Laboratory Medicine, ASLM, Cape Town, South Africa, December David A. Experience from quality monitoring options for molecular TB diagnostics (verification and EQA). ACTG-sponsored workshop: Quality needs for molecular TB/HIV and HPV diagnostic assays applied in clinical laboratories. In: Meeting of the African Society of Laboratory Medicine, Cape Town, South Africa, December Farley JE, Seiguer S, Naicker M, McKenzie-White J, Chiasson G, Elmi M, Stevens W, Stewart-Isherwood l. Rapid diagnosis, linkage and treatment initiation of patients with drug-resistant tuberculosis in South Africa: The milinc Solution to improve access to care. In: 21 st International AIDS Conference, Durban, South Africa, July Fox MP, Bor J, MacLeod W, Maskew M, Brennan A, Stevens W, et al. Is retention on ART underestimated due to patient transfers? Estimating system-wide retention using a national labs database in South Africa. In: 21 st International AIDS Conference, Durban, South Africa, Fraser-Hurt N, MacLeod W, Bor J, Shubber Z, Carmona S, Pillay Y, et al. Fast-tracking of the HIV response: Do the metros lead the way to reaching in South Africa? In: 21 st International AIDS Conference, Durban, South Africa, Glencross DK, Moodley K, Coetzee LM. Introducing the new fully automated volumetric Aquios flow cytometer PanLeucoGate (PLG) platform for CD4-lymphocyte enumeration in South Africa: Establishing instrument precision and accuracy. 21 st International AIDS Conference, Durban, South Africa, July Gous N, Bethlehem L, Subramunian C, Coetzee J, Stevens W, Scott LE. New Options for HIV viral load testing: The Panther Aptima HIV-1 Quant Dx assay (Hologics, Inc). In: African Society for Laboratory Medicine, Cape Town, South Africa, December MacLeod W, Bor J, Fraser N, Shubber Z, Sanne I, Stevens W, et al. Measuring viral load suppression in South Africa using a novel, national database. In: Conference on Retroviruses and opportunistic infections, Boston, Massachusetts, USA, MacLeod W, Fraser N, Bor J, Shubber Z, Carmona S, Pillay Y, et al. Analysis of age- and sex-specific HIV care cascades in South Africa suggests unequal progress towards UNAIDS treatment targets. In: 21 st International AIDS Conference, Durban, South Africa, Mahlatsi O, Ndlovu S, Morokane P, Berrie L, da Silva MP, Cassim N. Analysis of Xpert MTB/RIF positivity for defined age ranges and gender between 2014 and In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Marokane P, Ntsimane S, Magida V, Scott LE, Berrie L. Improving the quality of a large-scale Xpert MTB/RIF programme in South Africa. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Marokane P, Ndlovu S, Mahlatsi O, Ntsimane S, Da Silva P, Berrie L. Analysis of Xpert MTB/RIF rejection rates using laboratory data , South Africa. In: African Society of Laboratory Medicine (ASLM), Cape Town, South Africa, December Maskew M, Bor J, Hendrickson CJ, MacLeod W, Bärnighausen T, Pillay D, et al. Imputing clinical records from routine laboratory data: Date of ART initiation. In: Conference on Retroviruses and Opportunistic Infections, Boston, Massachusetts, USA, National Health Laboratory Service

88 Maskew M, Bor J, MacLeod W, Carmona S, Sherman G, Fox MP. The youth treatment bulge in South Africa: Increasing numbers, inferior outcomes among adolescents on ART. In: 21 st International AIDS Conference, Durban, South Africa, Maskew M, Hendrickson CJ, MacLeod W, Sanne I, Carmona S, Stevens W, et al. Utilising laboratory data to impute ART start dates and monitor cohort treatment outcomes. In: 21 st International AIDS Conference, Durban, South Africa, Phaswana A, Skhosana N, Berrie L, Stevens W. Setting up of GeneXpert laboratories in Correctional Centres in South Africa The route travelled and lessons learnt. In: Meeting of the African Society of Laboratory Medicine (ASLM), Cape Town, South Africa, December Phaswana A, Skhosana N, Berrie L, Stevens W. Setting up of GeneXpert laboratories in Correctional Centres in South Africa The route travelled and lessons learnt. In: National Department of Correctional Services Conference, Gauteng, South Africa, March Phaswana A, Skhosana N, Berrie L, Stevens W. Health systems strengthening: Offering TB and HIV tests to the inmates in correctional facilities in South Africa. In: Free State, Northern Cape, and KwaZulu-Natal Regional DCS Conference, Drakensberg, March Sarang S, Berrie L, Stevens W. Reducing the error rates in HIV viral load testing and does training on a national level provide any positive outcomes? In: Meeting of the African Society of Laboratory Medicine (ASLM), Cape Town, South Africa, December Scott LE Xpert MTB/RIF Research and development experience from South Africa. In: Academic Conference of Anti-Tuberculosis, Zhuhai City of Guangzhou Province, China, April Scott LE How to measure TB programme success using Cepheid C360. In: Satellite symposium, International Union of Tuberculosis and Lund Disease (UNION) Conference, Liverpool, UK, October Scott LE GeneXpert connectivity, experience with a laboratory information system and remote dashboard Cepheid C360, Workshop sponsored by the SA National Priority Programme: Lessons learnt from a large-scale implementation of the Xpert MTB/RIF TB programme in South Africa. In: African Society for Laboratory Medicine, Cape Town, South Africa, December Scott LE, Barnard M. OMNIgene: TB diagnostic companion performance. In: Future Directions and Progress of the AIDS Clinical Trials Group (ACTG) Network Laboratory Centre session, ACTG Annual Meeting, Washington, USA, June Scott LE, da Silva P, Berrie L, Nicol M, Whitelaw A, Candy S, Stevens W. The spectrum of use of the Xpert MTB/RIF test in the South African National GeneXpert Programme. In: African Society for Laboratory Medicine, Cape Town, South Africa, December Scott LE, David A, Stevens W. Update on line probe assay external quality assessment. In: Future Directions and Progress of the ACTG Network Laboratory Centre session, ACTG Annual Meeting, Washington, USA, June Scott LE, Wallis C. Abbott Real Time MTB and INH/RIF assay: Prospective HIB/TB cohort evaluation in Johannesburg, South Africa. In: Future Directions and Progress of the ACTG Network Laboratory Centre session, ACTG Annual Meeting, Washington, USA, June Shearer K, Dowdy D, Scott LE, Berrie L, MacLeod W, Fox M, Golub J, Stevens W Has the threshold of case-detection with Xpert MTB/RIF been reached in South Africa? In: African Society for Laboratory Medicine, Cape Town, South Africa, December Sawry S, Moultrie H, Wadula J, Scott L, Rie AV Poor yield of Xpert MTB/RIF on routine pulmonary samples from HIV-infected children. In: 8 th International Workshop on HIV Paediatrics, Durban, South Africa, July Steegen K, Shoul E, Berhanu R, Evans D, Hans L, Papathanasopoulos MA, et al. Protease inhibitor resistance in patients failing 2 nd - line ART in two academic hospitals in Johannesburg, South Africa. In: South African HIV Clinicians Society 3 rd Biennial Conference, Johannesburg, South Africa, Stewart-Isherwood L, Madumo P, Olsen F, Berrie L, Stevens W. Laboratory-driven linkage-to-care: outcomes from the Treat-TB mhealth solution for MDR-TB patient care in South Africa. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Stewart-Isherwood L. Translating laboratory informatics in patient care: mhealth and Implementation science. In: African Society for Laboratory Medicine (ASLM), Cape Town, South Africa, December Journal Publications Boender TS, Kityo CM, Boerma RS, Hamers RL, Ondoa P, Wellington M, et al. Accumulation of HIV-1 drug resistance after continued virological failure on first-line ART in adults and children in sub-saharan Africa. J Antimicrob Chemother. 2016; 71: Carmona S, Peter T, Berrie L. HIV viral load scale-up: Multiple interventions to meet the HIV treatment cascade. Curr Opin HIV AIDS. 2017; 12: Cassim N, Coetzee L, Glencross D. Piloting a national laboratory electronic programme status reporting system in Ekurhuleni Health District, South Africa. SAMJ. 2016; 106(4): Cassim N, Coetzee LM and Glencross DK. Programmatic implications of implementing the relational algebraic capacitated location (RACL) algorithm outcomes on the allocation of laboratory sites, test volumes, platform distribution and space requirements. African Journal of Laboratory Medicine. 2017; 6(1), a545, Annual Report 2016/17 87

89 Cassim N, Coetzee LM and Glencross DK. Evaluating costs of laboratory-based, reflex cryptococcal antigenaemia screening for HIV patients using the Lateral Flow Assay (LFA) at a busy CD4 laboratory in South Africa. PLOS ONE. DOI: /journal.pone ecollection, Cassim N, Coetzee LM, Schnippel K, Glencross DK. Compliance to HIV treatment monitoring guidelines can reduce laboratory costs. Southern African Journal of HIV Medicine. 2016; 17(1): 1-5. Chikaonda T, Ketseoglou I, Nguluwe N, Krysiak R, Thengolose I, Nyakwawa F, Rosenberg NE, Stanley C, Mpunga J, Hoffman IF, Papathanasopoulos MA, Hosseinipour M, Scott L, Stevens W. Molecular characterisation of rifampicin-resistant Mycobacterium tuberculosis strains from Malawi. African Journal of Laboratory Medicine. 2017; 6(2): a Chikaonda T, Nguluwe N, Barnett B, Gokhale RH, Krysiak R, Thengolose I, Rosenberg NE, Stanley C, Mpunga J, Hoffman IF, Hosseinipour M, Scott L, Stevens W. Performance of Xpert MTB/RIF among tuberculosis outpatients in Lilongwe, Malawi. Afr J Lab Med. 2016; 6(2): a v6i Clouse K, Vermund SH, Maskew M, Lurie MN, MacLeod W, Malete G, et al. Mobility and clinic switching among postpartum women considered lost to HIV care in South Africa. J Acquir Immune Defic Syndr. 2017; 74: Coetzee L, Cassim N, Glencross D. Implementation of a new community laboratory CD4 service in a rural health district in South Africa extends laboratory services and substantially improves local reporting turnaround time. SAMJ. 2016; 106(1): Coetzee LM, Moodley K, Glencross DK. Performance Evaluation of the Becton Dickinson FACSPresto Near-Patient CD4 instrument in a laboratory and typical field clinic setting in South Africa. PLOS ONE. 2016; 11(5): e PubMed PMID: Pubmed Central PMCID: Cunnama L, Sinanovic E, Ramma L, Foster N, Berrie L, Stevens W, Molapo S, Marokane P, McCarthy K, Churchyard G, Vassall A. Using top-down and bottom-up costing approaches in LMICs: The case for using both to assess the incremental costs of new technologies at scale. Health Economics. 2016; DOI: /hec Daneau G, Gous N, Scott L, Potgieter J, Kestens L, Stevens W. Human Immunodeficiency Virus (HIV)-infected patients accept finger stick blood collection for point-of-care CD4 testing. PLOS ONE. 2016; 11:e Diallo K, Kim AA, Lecher S, Ellenberger D, Beard RS, Dale H, et al. Early diagnosis of HIV infection in infants - One Caribbean and six sub-saharan African countries, MMWR Morb Mortal Wkly Rep. 2016; 65: Fox MP, Berhanu R, Steegen K, Firnhaber C, Ive P, Spencer D, et al. Intensive adherence counselling for HIV-infected individuals failing second-line antiretroviral therapy in Johannesburg, South Africa. Trop Med Int Health. 2016; 21: Godfrey C, Andersen J, Mngqibisa R, Scott LE, Conradie F. Tuberculosis control. Lancet. 2016; 387: Godfrey C, Tauscher G, Hunsberger S, Austin M, Scott L, Schouten JT, Luetkemeyer AF, Benson C, Coombs R, Swindells S. A survey of tuberculosis infection control practices at the NIH/NIAID/DAIDS-supported clinical trial sites in low and middle income countries. BMC Infect Dis. 2016; 16:269. Gous N, Scott L, Berrie L, Stevens W. Options to expand HIV viral load testing in South Africa: Evaluation of the GeneXpert(R) HIV-1 viral load assay. PLOS ONE. 2016; 11(12):e Gous NM, Berrie L, Dabula P, Stevens W. South Africa s experience with provision of quality HIV diagnostic services. African Journal of Laboratory Medicine. 2016; 5(2). Jacobson KR, Barnard M, Kleinman MB, Streicher EM, Ragan EJ, White LF, Shapira O, Dolby T, Simpson J, Scott L, Stevens W, van Helden PD, Van Rie A, Warren RM. Implications of failure to routinely diagnose resistance to second-line drugs in patients with rifampicin-resistant tuberculosis on Xpert MTB/RIF: A multisite observational study. Clin Infect Dis. 2017; doi: /cid/cix128. Larson BA, Rockers PC, Bonawitz R, Sriruttan R, Glencross DK, Cassim N, et al. Screening HIV-infected patients with low CD4 counts for cryptococcal antigenemia prior to initiation of antiretroviral therapy: Cost effectiveness of alternative screening strategies in South Africa. PLOS ONE. 2016; 11(7): 24. Lebina L, Fuller N, Osoba T, Scott L, Motlhaoleng K, Rakgokong M, Abraham P, Variava E, Martinson NA. The use of Xpert MTB/Rif for active case finding among TB contacts in North West Province, South Africa. Tuberc Res Treat. 2016: Lecher S, Williams J, Fonjungo PN, Kim AA, Ellenberger D, Zhang G, et al. Progress with scale-up of HIV viral load monitoring - Seven sub-saharan African countries, January 2015-June MMWR Morb Mortal Wkly Rep. 2016; 65: Papasavvas E, Surrey LF, Glencross DK, Azzoni L, Joseph J, Omar T, Feldman MD, Williamson AL, Siminya M, Swarts A, Yin X, Liu Q, Firnhaber C, Montaner LJ. High-risk oncogenic HPV genotype infection associates with increased immune activation and T cell exhaustion in ART-suppressed HIV-1-infected women. Oncoimmunology Jan 19; 5(5): e doi: / X ecollection 2016 May. Scott L, da Silva P, Boehme CC, Stevens W, Gilpin CM. Diagnosis of opportunistic infections: HIV co-infections - tuberculosis. Curr Opin HIV AIDS. 2017; 12: National Health Laboratory Service

90 Smith H, Smith J, Glencross DK, Cassim N, Coetzee L, Carmona S, Stevens WS. A relational-algebraic algorithm for location of HIV/AIDS in South Africa. Intl. Trans. in Op. Res ; 1 18 DOI: /itor Steegen K, Bronze M, Papathanasopoulos MA, Van Zyl G, Goedhals D, Van Vuuren C, et al. Prevalence of antiretroviral drug resistance in patients who are not responding to protease inhibitor-based treatment: Results from the first national survey in South Africa. J Infect Dis. 2016; 214: Steegen K, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, Variava E, et al. HIV-1 antiretroviral drug resistance patterns in patients failing NNRTI-based treatment: Results from a national survey in South Africa. J Antimicrob Chemother. 2017; 72: Steegen K, Carmona S, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, et al. Moderate levels of pre-treatment HIV-1 antiretroviral drug resistance detected in the first South African national survey. PLOS ONE. 2016; 11: e Stevens WS, Scott LE, Noble LD, Gous NM, Keertan D. Impact of the GeneXpert MTB/RIF technology on tuberculosis control. Microbiol Spectrum. 2017; 5(1): TBTB DOI: /microbiolspec.TBTB Templer SP, Seiverth B, Baum P, Stevens W, Seguin-Devaux C, Carmona S. Improved sensitivity of a dual-target HIV-1 qualitative test for plasma and dried blood spots. J Clin Microbiol. 2016; 54: Wake RM, Glencross DK, Sriruttan C, Harrison TS, Govender NP. Cryptococcal antigen screening in HIV-infected adults: Let s get straight to the point. AIDS Jan 28; 30(3): PubMed PMID: Contributions to Policy Glencross D, Coetzee L, Cassim N, Sriruttan C and Govender N. DoH Cryptococcal antigen policy and national wide-scale implementation of screening services for all CD4 samples with counts < 100 cells/µl (official start date 01/10/2016). Stevens W, Gous N, Scott L, Berrie L, Cassim N, Glencross DK, Carmona S and the NHLS working group. Point-of-care policy document draft. Content development as well as document review (2015/16). Cassim N. DoH, Ideal clinic development (ongoing). Haeri Mazanderani A, Technau K-G, Hsiao N-y, Maritz J, Carmona S, Sherman GG. Recommendations for the management of indeterminate HIV PCR results within South Africa s early infant diagnosis programme (2016). South African National Strategic Plan on HIV, sexually transmitted infections, and tuberculosis (launched 31 March 2017). Awards Professor Glencross received an Honourable Mention for Lifetime Achievement awarded by the ASLM (December 2016) Professor Glencross received a Wits Faculty of Health Sciences Award for Dedication and Achievement in Research (August 2016) Professor Glencross was honoured with an Excellence Award by the International Lyceum for Greek Women (January 2017). Annual Report 2016/17 89

91 Performance Information by Province GAUTENG Introduction Gauteng is defined by two of the nation s largest cities, Pretoria, the administrative capital of South Africa, and Johannesburg, the provincial capital. While it is the country s smallest province, it has the largest population, and by far the highest population density. The NHLS Gauteng Region provides services to a network of academic, provincial tertiary, regional and district hospitals and primary healthcare facilities. These are distributed across five districts within the province. Area Manager Bahule Motlonye Table G1: Laboratories per district Tshwane Tshwane Academic Division Dr George Mukhari Academic Kalafong Provincial Tertiary Mamelodi Regional Jubilee District Odi District Ekurhuleni Tembisa Provincial Tertiary Tambo Memorial Regional Pholosong Regional Far East Rand Regional Thelle Mogoerane Regional Bertha Gxowa District City of Johannesburg Sedibeng West Rand Charlotte Maxeke Sebokeng Regional Leratong Regional Academic Chris Hani Baragwanath Academic Helen Joseph Provincial Tertiary Edenvale Regional South Rand District Braamfontein Complex Kopanong District Dr Yusuf Dadoo District Carletonville District The region is divided into six business units, with a footprint across all five health districts in the province, as outlined above. It is also a referral site for some of the other provinces, Southern African Development Community (SADC) countries and other African states. Diagnostic Services and New Developments Gauteng performed tests, representing an increase of 18% compared with the previous financial year. The region has laboratories on site in four Central hospitals, three provincial tertiary, eight regional, and seven district hospitals across the province. In addition, three depots are located in different districts. These all work closely in support of the Department of Health s (DoH) National Priority Programmes (NPP), covering tuberculosis, cervical screening and HIV and AIDS. The data below demonstrates the volumes dealt with by the NHLS Gauteng laboratories in 2016/17. Table G2: National Priority Programmes volumes Test 2015/ /17 Difference % Increase Comment Viral load % Increase HIV PCR (EID) % Increase CD % Increase GeneXpert % Increase Lateral Flow: Cryptococcal Antigen New Test 90 National Health Laboratory Service

92 Table G3: Cervical Screening Volumes Tests 2015/ /17 Difference % Increase Comment Gynaecological % Increase Non-Gynaecological % Decrease Fine Needle Aspiration (FNA) % Decrease General Tests (All Inclusive) % Increase New Tests Charlotte Maxeke introduced the following tests: Salivary cortisol, respiratory syncytial viral testing and bacterial identification through 16S rrna sequencing. Service Delivery and Coverage Services were delivered by a total staff complement of 2 021, which includes training staff, pathologists, scientists, medical technologists, medical technicians and other support functions. Clinic-Laboratory specimen collection was maintained at 100% coverage, and the optimisation of routes allowed for increased frequency of collection, especially from Community Health Centres. Improved interaction between the NHLS and the Gauteng Health facilities (Healthcare Workers) enhanced working relationships to address challenges identified. Collaboration with DoH partners took place in March 2017 to strengthen the Clinical Laboratory interface. Collaboration with partners and other departments has ensured that the negative impact of various policies on health outcomes is understood and mitigated, and promotes policies that result in positive health outcomes. Turnaround Time (TAT) The region continued to strive to attain the Key Performance Indicator (KPI) targets set for 2016/17. Strategies were developed during the period, resulting in the attainment of all targets by the end of the financial year. Regional TAT performance is demonstrated in Table G4. Table G4: Turnaround time for Gauteng Region Data Source CDW Annual Target 2016/17 Actual Performance 2016/17 Percentage TB microscopy tests performed within 48 hours 90% 97% Percentage TB GeneXpert tests performed within 48 hours 90% 98% Percentage CD4 tests performed within 48 hours 90% 97% Percentage viral load tests performed within 96 hours 60% 96% Percentage HIV PCR tests performed within 96 hours 70% 94% Percentage cervical smear tests performed within 5 weeks 65% 91% Percentage laboratory tests (FBC, U&E and LFT) performed within 8 hours 80% 78% It is befitting to indicate the business unit s contribution to this performance on TAT, as outlined in Table 5. Each business unit has its own dynamics, which are mitigated differently. Table G5: Turnaround time per business unit Business Unit Target TB Microscopy GeneXpert CD4 tests Viral Load HIV PCR Cervical 90% within 48 hours 90% within 48 hours 90% within 48 hours 60% within 96 hours 70% within 96 hours 65% within 5 weeks (FBC, U&E and LFT) 80% within 8 hours Chris Hani Baragwanath 94% 99% 99% n/a 99% n/a 70% Johannesburg, Sedibeng and 99% 98% n/a n/a n/a 98% 93% West Rand Dr George Mukhari Academic 97% 97% 97% 97% n/a 77% 94% Charlotte Maxeke Academic 96% 98% 96% 95% 95% n/a 56% Tshwane Academic Division 99% 99% 95% n/a 87% 99% 68% Ekurhuleni Tshwane 98% 99% 98% n/a n/a n/a 85% Regional Average 97% 98% 97% 96% 94% 91% 78% Annual Report 2016/17 91

93 Notable Achievements Accreditation The following laboratories maintained their ISO accreditation in all divisions: Charlotte Maxeke Academic, Dr George Mukhari Academic, Chris Hani Baragwanath, Tshwane Academic Division (Steve Biko) and Braamfontein Complex (TB Laboratory, Immunology and Cytology). Accreditation continues to be focus area for the region, striving to increase the number of accredited laboratories at provincial tertiary and regional levels. Laboratory Upgrades Charlotte Maxeke Academic upgraded to a new Roche platform, which is a fully automated system with a track system, and high throughput to improve TAT, efficiencies and productivity. Figure G1: Medical Technologists at Charlotte Maxeke Academic Laboratory, using the new automated platform Figure G2: Left to Right: N Hlwati, N Dlulane, J van Schalkwyk, D Lioma, H Ngema and P Ntuli The Dr George Mukhari Microbiology Laboratory was renovated in 2016, to replace work benches, cabinets and the ceiling. Helen Joseph and Sebokeng Laboratories were refurbished. Technical Skills and Staffing The total head count as at March 2017 was 2 021, of which 323 are training staff (registrars, intern medical technologists and medical technicians). The reporting period was encouraging for the region in terms of attracting and retaining staff. The only challenge remaining is in the histopathology discipline. A number of options have been pursued, as a result of which a number of intern medical technologists among the new intake have been encouraged to do histopathology. Histopathology will be the focus for the coming 2 3 years, as failure to capacitate this unit will compromise the service in the future. Table G6: Staffing breakdown Business Unit Vacancies Training Head Count Total Head Count Chris Hani Baragwanath Academic Johannesburg, Sedibeng and West Rand Dr George Mukhari Academic Charlotte Maxeke Academic Tshwane Academic Division Ekurhuleni Tshwane Finance Unit Human Resource (Learning Academy) Management Total National Health Laboratory Service

94 Table G7: Staff category breakdown Business Unit Pathologists Medical Technologists Medical Technicians Lab Clerks Other* Total Chris Hani Baragwanath Academic Joburg, Sedibeng & West Rand Dr George Mukhari Academic Charlotte Maxeke Academic Tshwane Academic Division Ekurhuleni Tshwane Total *Other denotes business managers, laboratory managers, quality assurance co-ordinators, phlebotomists, phlebotomy technicians, store clerks and assistants and laboratory assistants Skills Development Gauteng NHLS continues to develop and up-skill employees in different areas as an intervention strategy. A total of employees undertook various skills development courses in the reporting period. Because compliance with legislation is important, and employees need to understand, adhere to policy and maintain compliance, the following legislative (Occupational Health and Safety Act) courses were attended by 130 employees: First Aid, Fire Warden, Dangerous Goods Transportation and Health and Safety. To improve quality management systems and efficiencies, leadership skills and customer centric approaches, laboratory managers received training in customer service, the foundation of laboratory leadership and management, quality management system (ISO 15189) and inventory management. Stakeholder Relations The region has a very good relationship with its stakeholders, including its DoH partners. These relationships are strengthened through several committees and meetings that take place regularly: Provincial stakeholder meetings regarding the Service Level Agreement (SLA) and Quarterly Review meetings Monthly participation in Medical Advisory Committee meetings National Institute of Communicable Diseases (NICD) helping with the identification of complicated organisms that need further testing Infection Prevention and Control, Therapeutic Committee and Medical Advisory Committee meetings, where pathologists/registrars play a significant role Quarterly TB meetings with the DoH, and bimonthly visits to clinics Institutional Academic Pathology Committees (IAPC) meetings with the Deans of the universities (University of the Witwatersrand (Wits), University of Pretoria (UP), Sefako Makgatho Health Sciences University (SMU). NHLS Gauteng supports all the initiatives of the Gauteng DoH and participated in the following activities as part of NHLS visibility: Hospital open days World AIDS Commemoration Day a national event that was held in Daveyton on 1 December 2016 TB World day participated in the planning activities. Conclusion NHLS Gauteng will continue to offer a patient-orientated service and align with Gauteng DoH programmes. Although financial challenges restrain service delivery, the majority of staff is dedicated to providing the extra effort required to meet the mandate. New avenues will be pursued to add new test repertoires to existing profiles as well as new technology to reduce costs further while increasing efficiencies. Annual Report 2016/17 93

95 EASTERN CAPE Introduction The Eastern Cape Region supports the National and Provincial Departments of Health in the delivery of quality, accessible and affordable health services through a network of 38 laboratories and seven depots situated across the eight Health Districts of the province. The scope of testing in each laboratory is in line with the package of services required per level of care. The region consists of five business units, adequately resourced with competent staff and state-of-the-art equipment, to ensure delivery of a quality service. The region has centralised specialised testing at the only academic laboratory, Nelson Mandela Academic, and two tertiary laboratories, East London and Livingstone. Area Manager Tabita Makula Laboratories offer a 24-hour service to the central, tertiary and regional hospitals, and a call out system for district laboratories to improve service delivery. Table EC1: Laboratories per district Nelson Mandela Metropolitan Port Elizabeth Provincial Tertiary Livingstone Sarah Baartman Graaff Reinet Somerset East Buffalo City Metropolitan Amathole Chris Hani OR Tambo East London (Frere) Tertiary Cecilia Makiwane Regional Butterworth Queenstown Regional Nelson Mandela Academic Madwaleni Glen Grey St Elizabeth Regional Alfred Nzo Matatiele Mt Ayliff Joe Gqabi Empilisweni Aliwal North Dora Nginza Humansdorp Bisho Willowvale Hewu Holy Cross St Patricks Mt Fletcher Uitenhage Grahamstown SS Gida Cradock Zitulele Madzikane KaZulu Port Alfred Victoria Cofimvaba Canzibe All Saints St Barnabas Cala Dr Malizo Mpehle Memorial 4 Labs 5 Labs 3 Labs 5 Labs 7 Labs 7 Labs 4 Labs 3 Labs Table EC2: Depots per district OR Tambo Amathole Alfred Nzo Isilimela Tafalofefe Greenville Qumbu Health Centre Maluti Nessie Knight Bambisana Diagnostics Services The total number of tests performed increased by 2% year-on-year from in 2015/16 to in the year under review. The increase in workload can be attributed to an 11% increase in viral load tests and a 16% increase in HIV PCR, due to the introduction of policy guidelines on the use of viral load and Early Infant Diagnosis (EID) tests for the initiation and monitoring of Antiretroviral Therapy (ART). GeneXpert tests decreased markedly by 13%. 94 National Health Laboratory Service

96 Table EC3: National Priority Programme test percentage differences 2015/16 vs 2016/17 Test 2015/ /17 % Difference Viral load % CD % HIV PCR % GeneXpert % Cervical Smears % New Tests To improve service delivery and patient outcomes, the laboratories introduced new tests. Some of the tests had previously been referred to either Gauteng or the Western Cape, which greatly affected TAT. Table EC4: New tests introduced in 2016/17 Business Unit Laboratory New Test Nelson Mandela Academic Laboratory Chemistry Lithium, Folate, Vitamin B12, RF and ASOT Anatomical Pathology Special stains for CD4, CD8, CD15, CD30, GFAP and Myoglobin Microbiology E TEST Fluconazole antibiotic on Candida albicans, Candida species and Cryptococcus neoformans isolated from blood cultures Ibhayi TB Laboratory HAIN MTBDRs v2.0 assay Livingstone Urine Osmolality Border Cecilia Makiwane HIV ELISA; TSH; T4 and Quant β-hcg Southern Transkei Cofimvaba Calcium; Magnesium and Phosphate St Barnabas Blood Morphology The World Health Organization (WHO) recommended that Cryptococcal antigen (CrAg) should be used to screen HIV-infected persons with CD4 counts of less than 100 cells/µl. In support of the DoH s goal to reduce mortality of patients due to cryptococcal meningitis, the region successfully introduced CrAg as a reflex test for CD4 counts of less than 100 cells/µl, in all the CD4 testing laboratories. Service Delivery In response to customer demands and the changing environment, the Northern Transkei Business Unit extended the NHLS footprint by opening three depots to enhance accessibility of services. Access coverage remained 100% for clinic-to-clinic and hospitals with no laboratories on site, in line with the NHLS Strategy. Couriers collect more than once from the community health centres and gateways offering a 24-hour service in the metropolitan municipalities. The Health Level 7 (HL7) interface between Livingstone Laboratory and Livingstone Hospital went live in August This has significantly improved the accuracy of patients registrations on the laboratory information system (LIS) and reduced unnecessary repeat testing for Livingstone Hospital. TAT in the laboratory has improved due to reduced time spent on registration of patient demographics. Turnaround Time A great improvement was noted on TAT in the year under review compared to the previous year. Even though the volumes for some priority tests increased due to changes in the National Guidelines for Management of Tuberculosis (TB) and HIV, the region achieved and exceeded all the targets set. Annual Report 2016/17 95

97 Table EC5: TAT Business Unit TB Microscopy within 48 Hours GXP within 48 Hours CD4 within 48 Hours Viral Load within 96 Hours HIV PCR within 96 Hours Cervical Smear within 5 Weeks FBC; U&E and LFT within 8 Hours Target 90% 90% 90% 45% 67% 43% 80% NMAL 98.0% 93.2% 90.3% 85.7% 89.9% 88.2% 91.0% Ibhayi 82.2% 84.2% 96.8% 92.4% 80.2% 100.0% 91.6% Border 93.8% 99.4% 94.7% 75.9% N/A 99.9% 91.0% Northern 95.3% 97.0% 90% N/A N/A N/A 88.3% Transkei Southern 97.8% 98.6% 90.6% N/A N/A N/A 90.8% Transkei Region 93.4% 94.57% 92.5% 84.7% 85% 95.4% 90.5% Customer Education The increase in customer education and related interactions has played a pivotal role in advancing the NHLS as a brand and increasing visibility to customers: The Laboratory Manager at Dora Nginza was involved in the orientation of the internship doctors in January Port Elizabeth Provincial hosted a CPD accredited phlebotomy workshop in partnership with BD Trainers. A total of 51 healthcare workers and staff from the South African National Defence Force (SANDF) attended. The Border Business Unit trained 36 healthcare workers on specimen collection and phlebotomy techniques in the Buffalo City Municipality. In November 2016, the Northern Transkei Business Unit conducted training at OR Tambo, Qaukeni sub-district on TB specimen collection, handling and shipping, and minimising specimen rejections. More than 30 healthcare workers attended the training. Notable Achievements To mitigate the shortage of pathologists in the region, Nelson Mandela Academic Laboratories (NMAL), together with Walter Sisulu University (WSU), achieved Health Professions Council of South Africa (HPCSA) accreditation for MMed in Anatomical Pathology and Chemical Pathology. Two registrars were subsequently appointed from 1 February 2017, one in each department. HPCSA accreditation for the training of medical technologists and technicians at NMAL, in microbiology; histology; chemical pathology and clinical pathology was also achieved. The region continued to strive for the accreditation of its laboratories, with a major focus on central, tertiary and regional laboratories. The Cytology Department at NMAL/WSU was the only department not accredited. It is worth noting that following the initial accreditation of Cytology in November 2016, the business unit achieved 100% accreditation (all departments accredited). Port Elizabeth Provincial, Livingstone and Dora Nginza laboratories successfully maintained their South African National Accreditation System (SANAS) accreditation status. Accreditation of the Virology and Serology laboratories was postponed to the new financial year due to the relocation of the Virology Laboratory from Dora Nginza to Port Elizabeth Serology. East London Tertiary Laboratory maintained its accreditation status after a SANAS assessment of five departments; however, histology could not be assessed due to the unavailability of a pathologist. The department is nevertheless ready for accreditation, and will be assessed as soon as a pathologist has been successfully recruited. Diagnostic Media Products (DMP) in Port Elizabeth once again received ISO 9001:2015 certification, with no non-conformances reported. Three regional laboratories (Queenstown, Cecilia Makiwane, and St Elizabeth), were enrolled in the Stepwise Laboratory Quality Improvement Process towards Accreditation (SLIPTA) Programme, in preparation for SANAS accreditation in the new financial year: Queenstown achieved 3 stars in its first assessment Cecilia Makiwane achieved 2 stars in its second assessment St Elizabeth achieved 2 stars in its initial assessment. 96 National Health Laboratory Service

98 The district laboratories that are not SANAS accredited were subjected to quality compliance audits to assess compliance with ISO All the laboratories performed well and as a result the region achieved 92% on average. New Laboratories and Laboratory Upgrades To ensure that the organisational strategic goal for state-of-the-art laboratories is achieved, the region installed high throughput viral load testing analysers at its Nelson Mandela Academic Laboratory and Port Elizabeth Virology Laboratory, and upgraded laboratories. The region prides itself in these high throughput viral load testing sites as they contribute significantly to the use of viral load and EID testing for the initiation and monitoring of ART. The Virology Laboratory was relocated from Dora Nginza to Port Elizabeth Provincial Laboratory in an attempt to centralise the specialised tests at the tertiary laboratories and improve the workflow of specimens. Major renovations were done to upgrade both the Virology and Serology laboratories at Port Elizabeth Provincial. It must be noted that the region has one of the most highly automated microbiology laboratories in the country in Port Elizabeth. The laboratory received a PREVI-ISOLA instrument in February 2016, in addition to a VITEK Mass Spectrometer, which was installed in 2015/16. The resultant reduction in manual intervention has improved TAT significantly. Madwaleni Laboratory in the Amathole District was upgraded in the year under review and is now a state-of-the-art laboratory. The commissioning was honoured by DoH representatives from the district. Figure EC 1: The commissioning of Madwaleni Laboratory Area Manager and Business Manager Ms Bukiwe Makaba cutting the ribbon, with acting CEO of Madwaleni Hospital, Mr Mawande Mtalana St Patricks Laboratory was allocated space in the newly constructed hospital building and the laboratory was relocated from a park home in November Technical Skills and Staffing The total headcount increased from 660 in the previous year to 701 in the year under review. Although the region experienced challenges in attracting pathologists in all disciplines, two pathologists were successfully recruited, a chemical pathologist and an anatomical pathologist at Nelson Mandela Academic Laboratory and Port Elizabeth Provincial Tertiary, respectively. All laboratories were adequately staffed, especially after the implementation of the reward and remuneration policy. This has proven to be the best strategy to attract and retain scarce skills as well as to boost the morale of existing employees. Annual Report 2016/17 97

99 To support the laboratories in quality improvement, the region appointed Quality Assurance Co-ordinators in three business units that had never had this category of staff. Training NMAL appointed two registrars in Anatomical Pathology and Chemical Pathology in February A nurse from Nelson Mandela Academic was trained on Fine Needle Aspiration in order to improve the adequacy rate and also received Prothrombin Index training to provide comprehensive support to the Haemophilia Clinic at Nelson Mandela Academic Hospital. Intake for medical technologist and medical technician students in training was higher than any previous year. The Region attracted students for all categories in the three HPCSA-accredited training facilities, namely Nelson Mandela Academic; East London; and Port Elizabeth laboratories. Table EC6: Student intake Category Discipline Nelson Mandela Academic Laboratory Port Elizabeth Provincial Tertiary East London Laboratory Region Medical Technologist Clinical Pathology Haematology 1 1 Chemical Pathology 1 1 Microbiology Histology Cytology 1 1 Medical Technician Clinical Pathology Chemical Pathology 1 1 Microbiology Total Skills Development Skills development remained a priority for the region in order to build a skilled workforce. In total 545 employees were trained in the year under review. Table EC7: Skills development training Type of Training Number of Attendees Legislative 103 Business Continuity 130 Management 70 Quality 29 Technical 22 Other 191 Total 545 In an attempt to increase the skilled workforce, the region assisted six medical technicians from three different business units to register for the National Diploma in Biomedical Technology. Three technicians attend part-time lectures at Mangosuthu University of Technology and three at Tshwane University of Technology. To improve recruitment of medical technologists, the region has tied the bursaries to recruitment, with the aim of attracting the bursary holders to the needy areas when they are qualified. 98 National Health Laboratory Service

100 Table EC8: External bursaries offered per district Health District Year of Study Number of Students Alfred Nzo Third 1 First 1 Chris Hani Second 1 First 1 OR Tambo Third 4 First 1 Amathole Third 1 Second 3 Buffalo City Third 2 Second 1 First 1 Nelson Mandela Bay Third 7 Sarah Baartman Third 1 Total 25 Stakeholder Relations The business units attended District Management as well as Blood and Laboratory User s Committee (BLUC) meetings to improve communication and relations. Meetings aimed at strengthening academic relations and interfacing diagnostic services, research and academic training, such as Pathology Management Committee and IAPC were held as scheduled throughout the 2016/17 financial year. In collaboration with the Dean of the Faculty of Health Sciences, the Area Manager of the Eastern Cape and the AARQA Executive held a major stakeholder initiative referred to as the Pathology Indaba in Mthatha. The purpose of the indaba was to deliberate on how to deliver on the academic mandate, hence achieving academic excellence jointly as Walter Sisulu University and Nelson Mandela Academic Laboratory. Figure EC2: Pathology Indaba From left to right are Tabita Makula (Area Manager, Eastern Cape); Dr Johan van Heerden (Executive Manager, AARQA); Dr Wezile Chitha (Dean of Health Sciences, WSU); and Prince Mdlalose (Business Manager, NMAL) Annual Report 2016/17 99

101 To increase NHLS visibility and improve stakeholder relations, the region participated in World TB and World AIDS day provincial events. The region participated in the World AIDS day provincial event on 1 December 2016, held in Joe Gqabi District in the Elundini Sub-district. To discuss service challenges and improvement strategies, scheduled quarterly bilateral meetings were held between the DoH and the NHLS. The region also participated in a Science and Technology career guidance and awareness programme held by Umhlobo Wenene FM. The aim was to introduce biomedical technology as a profession and assist the youth to make informed career choices. The Northern Transkei Business Unit and Nelson Mandela Academic Laboratory visited a number of schools in the OR Tambo and Alfred Nzo districts to assist in career guidance. Southern Transkei participated in a career guidance programme organised by Amathole Health district. Conclusion The region prioritised service delivery in the year under review and through team effort and allegiance, clients received a quality, reliable service. 100 National Health Laboratory Service

102 WESTERN CAPE Introduction The Western Cape has two national central laboratories and one tertiary laboratory that link to and have a co-operative agreement with the Universities of Cape Town, Western Cape and Stellenbosch. The region includes 40 laboratories in three business units, which are spread across six health districts within the province. The business units provide diagnostic laboratory services to the DoH and the City of Cape Town, which includes two national central hospitals; one tertiary hospital (Red Cross War Memorial Children s Hospital), five regional hospitals, 33 district hospitals and 274 primary healthcare facilities, including nine community healthcare centres. Coverage is also extended to the Department of Correctional Services, Department of Home Affairs, SANDF and private laboratories in the Western Cape. Pathology services are provided not only to the Western Cape, but also to Northern Cape and Eastern Cape. The total staff complement is 933 staff members. The laboratories are well resourced with state-of-theart equipment and dedicated and highly competent staff to deliver quality and patient-focused service. Western Cape Business Units Western Cape Business Units consist of the following laboratories: Area Manager Nasima Mohamed Groote Schuur Hospital (GSH) Tygerberg Hospital (TBH) Green Point Complex (GPC). Table WC1: Western Cape laboratories National Central Academic Laboratories Tertiary Laboratories Regional Laboratories District Laboratories GSH Chemical RXH Chemical GPC Chemical Vredendal Pathology pathology Pathology GSH Haematology RXH Haematology GPC Haematology West Coast District GSH Microbiology RXH Anatomical GPC TB Lab Karl Bremer Pathology GSH Virology GPC Media Lab Mitchell s Plain GSH Cytology GPC-Satellite Helderberg Emergency Lab GSH Anatomical George Mossel Bay Pathology GSH Immunology Paarl Oudtshoorn GSH Tissue Immunology Worcester Knysna GSH Genetics Beaufort West TBH Chemical Pathology Khayelitsha TBH Haematology Hermanus TBH Microbiology Pollsmoor TBH Virology TBH Immunology TBH Cytology TBH Anatomical Pathology TBH Genetics 17 Laboratories 3 Laboratories 8 Laboratories 12 Laboratories As part of the NPP, GeneXpert (GXP) and Auramine smears as well as viral load (VL), CD4 and HIV Polymerase Chain Reaction (PCR) are performed at several laboratory sites in the Western Cape. Annual Report 2016/17 101

103 Table WC2: 14 Laboratories perform GXP analysis Laboratory Paarl Worcester Green Point GSH Tygerberg Karl Bremer Khayelitsha Mitchells Plain Pollsmoor George Oudtshoorn Knysna Beaufort West Vredendal District Cape Winelands Cape Winelands City Metro City Metro City Metro City Metro City Metro City Metro City Metro Eden Eden Eden Karoo West Coast GXP sites use a total of 15 GX4 analysers, 13 GX16 analysers and one Infinity analyser (Green Point Laboratory). More than GXP tests were performed in the period 1 April 2016 to 31 March Two laboratories (Table WC 3) use Roche Cobas/Ampliprep analysers to process HIV and VL testing. These sites processed a total of VL tests over the reporting period. Table WC3: HIV and VL testing sites Lab Groote Schuur Tygerberg District Cape Metro Cape Metro Table WC4: CD4 analysis laboratory sites Lab Name George Green Point Groote Schuur Tygerberg District Eden Cape Metro Cape Metro Cape Metro George Laboratory has now been running the new Aquios analyser for more than 12 months, with very few breakdowns and hence TATs have improved. Diagnostic Services and New Developments The Western Cape achieved a 2.3% increase year-on-year from tests performed in 2015/16 to tests in the year under review. Anatomical pathology volumes increased by 12% with the province assisting the Eastern Cape and Northern Cape. The focus in 2016/17 was on improving the quality of specialised services. In November 2016 the NPP launched the VL and CD4 Monitoring Dashboard. This will allow users access to various data sets with regard to VL and CD4. A new pilot project will see GX4 analysers installed in three laboratories (Beaufort West, George and Vredendal) to perform VL as point-of-care. Cryptococcus antigen reflex testing was introduced at the CD4 laboratories. The reflex is based on all CD4 values of < 100 for those HIV positive patients who are susceptible to developing meningitis. A new way of capturing Club ART patients is currently being piloted in some of the metro laboratories. This assists the clerks to sort the results before filing them and adds considerably to the efficiency of filing. The Hain second line (SL) lipoprotein(a) (LPA) was introduced in January 2017 after the WHO sanctioned the use of the second line PCR/ LPA directly on clinical samples, irrespective of smear status. An excellent TAT, within 5 days, for SL results can now be offered, especially on clinical samples where the GXP was positive and rifampicin resistant. The GXP test allows for testing of gastric washings in children as well as cerebrospinal fluids (CSFs), fine needle aspiration (FNA) and purulent fluids in adults. This is in line with provincial guidelines. 102 National Health Laboratory Service

104 The Human Genetics Laboratory at the Groote Schuur Academic NHLS Business Unit comprises a molecular and cytogenetics component and is the only SANAS (ISO 15198:2012) accredited genetics laboratory within the NHLS and the second largest NHLS genetic service in the country. The diagnostic genetics service at GSH has been expanding since 2010, with the introduction of new tests to improve the quality of results; keep up with international trends and standards; as well as respond to demands by referring clinicians. The rapid growth of genomic technologies, the improvement in detection rate of disease-causing variants and the drop in price of these technologies, together with the close relationship with the University of Cape Town s Division of Human Genetics, places the NHLS Western Cape in an excellent position to develop as a national Centre of Excellence for Genetic and Genomic Diagnostics. An important area of development in the diagnostic human genetics laboratory pertains to the use of genome-wide technologies e.g. cytogenomic microarray analysis (CMA) for copy number variation (CNV) detection and whole exome sequencing for specific mutation identification. Internationally, the use of CMA leads to a detection of pathogenic CNVs in 15 25% of cases of intellectual disability/ developmental delay compared to only 1 5% of these patients showing gross chromosome abnormalities with the technologies currently used in our laboratories. In keeping with international standards and in an effort to improve the quality of service in response to the needs of our clients, we now therefore offer our clients genomic testing with CMA. The NHLS has entered into a contract with the Department of Home Affairs (DHA), as the sole service provider of DNA-based paternity testing of all late registrations of birth and foreign parent/s. The genetics laboratory procured an ABI genetic analyser 3500, which is used for both sequencing and fragment analysis applications using capillary electrophoresis. In line with the directive from the DHA, Human Identification (HID) testing will be performed. The GSH Laboratory will assist the other NHLS laboratories with the paternity testing workload from the DHA. The Groote Schuur Tissue Immunology Laboratory is the only European Federation of Immunology (EFI) accredited laboratory in Africa. This enables the laboratory to provide the donor/recipient human leukocyte antigen (HLA) matching screening for bone marrow transplant patients to the international community. The laboratory assists the Sunflower Fund South African Bone Marrow Registry donor drives by providing the phlebotomy service. The Tygerberg Microbiology Laboratory expanded its test repertoire to include Legionella antigen testing on urines (February 2017). The Western Province Blood Transfusion Service made use of the laboratory, requesting blood tests for possible bacteriological cause for transfusion reactions (August 2016). The Tygerberg Virology Laboratory is the only unit performing routine cell culture, virus isolation and Coxsackie Virus neutralisation assays. It remains one of only a few NHLS laboratories performing HIV drug resistance testing for routine diagnostic purposes. A number of new assays was accredited in 2016 including Epstein Barr Virus (EBV) viral load; Hepatitis B Virus (HBV) PCR, viral load and genotyping; Hepatitis E Virus (HEV) PCR as well as Immunoglobulin G (IgG) and Immunoglobulin M (IgM) antibody testing; and qualitative PCR assays for parvovirus B19, a panel of 16 respiratory viruses, and polyomaviruses JC and BK. The Tygerberg Laboratory initiated the phased implementation of a new Roche automated analyser track and pre-analytical automation system from July This significant change to the laboratory has brought in state-of-the-art technology to enable the consolidation of testing platforms, improve use of resources, improve workflow and enhance efficiency in the unit. Figure WC1: The new Somerset Hospital Emergency (STAT) Laboratory was opened in April 2017 Annual Report 2016/17 103

105 Figure WC2: Opening of the Somerset Hospital STAT laboratory, Ms Faith Koopa (Lab Manager - NHLS GPC Chem Path), Nicolene van der Westhuizen (Support Services - DoH), Nanette Spencer (Acting NHLS Area Manager - WNC), Dr Donna Stokes (CEO - Somerset Hospital), Mr Francois Barton (Business Manager - NHLS GPC and Regional Laboratories) and Dr Jacques Hendricks (Medical Manager - Somerset Hospital) Service Delivery and Coverage Health facilities in the Western Cape have 100% coverage of specimen collections with a large number of facilities having more than one collection per day. Expansion of weekend courier services to some districts was implemented to improve service delivery and TAT. The TB/HIV co-ordinator, laboratory manager and the pathologists continue to be involved in regular training and teaching programmes for healthcare workers. Western Cape pathologists play a pivotal role in pathology coverage within the NHLS. Quarterly lectures are presented four times a year to the nurses at the Nurses Training College. Lectures relate to diagnosing TB (presented by a laboratory manager) and drug resistant TB (presented by a pathologist). The division of Anatomical Pathology GSH and TBH continue to provide support to the Port Elizabeth and East London laboratories respectively, due to a shortage of pathologists in the Eastern Cape. GSH Anatomical and Chemical Pathology departments also provide support to the Northern Cape. The TBH Immunology Department continues to provide a consultancy service for Primary Immune Deficiency (PID) throughout South Africa and Africa. The addition of two GXP4 machines in June 2016 expanded the capacity of the TBH Microbiology Laboratory for additional GeneXpert MTB/RIF testing and vastly improved TAT. The TBH Microbiology Laboratory provided key testing to Tygerberg Hospital during the Carbapenem-resistant Enterobacteriaceae outbreak in Tygerberg during July 2016 and suspected C.diphtheria outbreak in December A special Occupational Health and Safety service is provided to the SANDF for the testing of water and food samples for Parliament. Additional service is provided to 2 Military Hospital when they are short-staffed due to deployments. Phlebotomy services are provided in support of the Area Military Health (substructure of the SANDF), which monitors Occupational Health and Safety for the military. Pathologists, registrars and Heads of Department (HODs) participate in various clinical meetings and forums contributing to and guiding patient management. Pathologists as well as a number of senior technologists and managers serve on among others the Medical Technologist Scientific Advisory committees; National Education Committee; and the NHLS Expert committees. There is also participation in setting and moderation of Board examinations. Turnaround Times (TATs) 2016/17 Table WC5: Average TATs for priority programme tests by Western Cape Laboratories Priority Test Volume % within TAT Percentage of GeneXpert tests with TAT within 24 hours % Percentage of TB microscopy tests with TAT within 40 hours % Percentage of CD4 tests with TAT within 40 hours % Percentage of viral load tests with TAT within 96 hours % Percentage of HIV PCR tests with TAT within 96 hours % Percentage of Cervical Smears tests with TAT within 5 weeks % 104 National Health Laboratory Service

106 It should be noted that lengthy breakdown periods on the VL analysers have affected TAT. Since analyser breakdowns are now more carefully monitored, new workflows at TBH Virology Laboratory improved their TAT in the final quarter of the reporting period. A decrease in CD4 volumes compared to 2015/16 has been noted, with a concomitant increase in VL testing. Stakeholder Relations On a monthly basis, a TB pathologist from the Green Point TB Laboratory attends the TB Forum at TBH. The forum is a monthly meeting of all the stakeholders in the TB environment, from the DoH and the City of Cape Town to Non-Governmental Organisations (NGOs). Presentations are given and cases are presented with the laboratory answering queries from attendees. DoH sub-district meetings are attended monthly. These provide the opportunity to interact with health facility management and staff. World Aids Day was supported at various sites with the DoH. Support was provided to the Phelophepe Train when it moved through the Worcester area on its way to George. Consumables requested were supplied and laboratory results were made easily accessible. TB in prisons remains a high priority. Continuum of care meetings were attended with the Department of Correctional Services in various management areas to listen to some of their challenges regarding laboratory work. The NHLS Western Cape fully supported the African Society for Laboratory Medicine when it held its conference at the CTICC during December Western Cape laboratories participated in the hospital intern doctor s orientation for 2017 and laboratory support services managers participated in training hosted by Becton Dickenson for hospital and clinic nursing staff. The TBH Laboratory support staff visited some of the children s wards at Tygerberg on Monday, 17 July, as a 67 Minutes event for Nelson Mandela Day. This event was very successful in that the children really enjoyed the visit and were so excited to receive their packages (consisting of a colouring booklet, balloon, packet of chips and a few sweets). Notable Achievements including Accreditation In total, 25 laboratories (specific disciplines) in the Western Cape maintained SANAS ISO 15189:2012 accreditation status. These specific discipline laboratories are based at the George Laboratory, Green Point Complex (GPC), GSH and TBH laboratories. GPC Haematology and Chemical Pathology Laboratory also maintained its College of American Pathologists accreditation. The DMP Laboratory at Green Point maintained its SABS ISO 9001:2008 certification for a consecutive year without any non-conformances raised. This laboratory will in future be assessed on the ISO 9001:2015 standard. All divisions achieved an average of % for external proficiency testing schemes. International Pathology Day was celebrated on 16 November The GSH RXH/UCT Unit took this opportunity to showcase the pathology laboratories work on E floor of the Groote Schuur Hospital. The event (themed What happens to your blood sample? ) attracted extensive public interest. Figure WC3: International Pathology Day event Annual Report 2016/17 105

107 The Cytology staff had an exhibition table at the Mitchell s Plain Day Hospital Breast Clinic during the Pink drive on 30 August Technical Skills and Staffing The appointment of an expert in flow cytometry at Tygerberg has enabled the Cape Peninsula University of Technology (CPUT) to offer training to Bachelor of Health Science (BHSc) students in Immunology, which is a first for the discipline. Training Training programmes were held during the financial year and were well attended. Journal clubs and Continuing Professional Development (CPD) talks continued in the various divisions. The laboratory training programme includes BHSc and diploma technologist students, technicians, intern scientists and registrars. Figure WC6: Courses attended by Western Cape Laboratory technologists Course Attendees Output Advanced GeneXpert Training Medical Technicians and Medical Technologists Understanding the GeneXpert in order to train other staff members Finance for Non-Financial Managers Laboratory Managers Improved management skills Leadership & Management Performance Management Systems Internal Quality Management Systems (QMS) Advanced Quality Control (QC) Workshop Internal Audit Medical Technicians, Medical Technologists and Laboratory Managers Improved approach to QC in the laboratories Overview of QMS Health Technology Assessment (HTA) and ISO 15189:2012 training Diversity Management Medical Technicians, Medical Technologists and Laboratory Managers Preparation for changes to SANAS auditing standards and training of internal auditors Excel 1-3 and Power Point All levels of staff Increased skills in preparing spreadsheets and presentations Lean Management Laboratory Managers and Improved workflow in laboratories and reduced bottlenecks Business Ethics Supervisors to improve service delivery HR training Typing skills Laboratory Clerks Improved accuracy and speed of data capturing in order to reduce errors in sample registration Dangerous goods, Fire Warden and First Aid All levels of staff Legislated courses for staff with those responsibilities EP15 for validation and verification of instruments and tests New Laboratories and Upgrading of Facilities Medical Technologists and Laboratory Managers Improved the quality of the overall test system to ensure a quality result The University of Stellenbosch undertook the upgrading of the NHLS Virology Division, housed on the 8 th floor of its Faculty of Health Sciences, as part of its Catch-up Maintenance programme, to bring the building in line with safety regulations and improve the facilities. This included the complete replacement of electrical and communication systems, network points and telephone and fire protection systems. Refurbishment of passage floors, and the provision of dedicated rooms for fridges and freezers with extraction units for CO 2 gas and air-conditioners were included in the project. The TBH Laboratory underwent extensive upgrades during Improvements included renovation of the receiving office to create additional space and improve workflow; replacement of flooring to improve safety; and painting to create a more acceptable working environment. The Core Laboratory at Tygerberg was upgraded to incorporate the new Roche automated analyser, track and pre-analytical automation (MPA). Further upgrades included the air-conditioning system and one combined walk-in fridge and freezer. Numerous rooms and facilities on the 10 th floor Anatomical Pathology were improved for the benefit of both academic and service areas. Conclusion The Western Cape NHLS continues to provide a high quality diagnostic service to stakeholders in the Western Cape. Western Cape Laboratories have improved their services to clients and 25 laboratories continued to maintain SANAS accreditation. Work will continue towards the NHLS Strategy of accrediting all laboratories in the region. 106 National Health Laboratory Service

108 NORTHERN CAPE Introduction The Northern Cape is the largest and most sparsely populated province in South Africa. It has a surface area of km² with a population of approximately (2015) and comprises five districts, Frances Baard, John Taolo Gaetsewe, ZF Mgcawu, Pixley ka Seme (NHI site) and Namaqua. There is one NHLS laboratory in each district. In line with the NHLS Strategy, an effort is being made to increase accessibility to services by increasing the number of laboratories in the business unit. This will be achieved by having a laboratory in each district hospital. The initial focus is on Kuruman and Hartswater (Connie Vorster) hospitals. The total staff complement in the business unit at the end of March 2017 was 83. The business unit continues to support and align services with the mandate of the DoH, and is committed to contributing to government s vision of A long and healthy life for all South Africans. All laboratories perform TB microscopy and GeneXpert tests. There are three CD4 testing sites, namely Kimberley, Upington and De Aar laboratories. Specialised tests are referred to Universitas, Tygerberg, Green Point and Charlotte Maxeke Johannesburg Academic hospitals. Area Manager Nasima Mohamed Table NC1: NHLS laboratories per district District Laboratory After-hour service Frances Baard Kimberley Night shift John Taolo Gaetsewe Tshwaragano On call ZF Mgcawu Upington Night shift/on call weekends Pixley ka Seme De Aar On call Namaqua Springbok On call Diagnostic Services, Test Volumes and New Developments The Northern Cape achieved a 4.0% year-on-year increase from tests performed in 2014/15 to tests in 2015/16 and tests in 2016/17. CD4 volumes increased 1.6% and 9.2% for GeneXpert tests. This increase is attributed to the implementation of and adherence to the TB/ART guidelines and training provided by NPP. Four mines, namely Beeshoek, Black Rock, AfriSam and Khumani are currently serviced and Kolomela and Petra Finsch mines are in the process of being registered. Priority Programmes CD4 test volumes increased by 1.6% from in 2014/15 to in 2015/16 and in 2016/17. However a decrease in volumes was noted from October 2016 due to the removal of CD4 count as an eligibility criterion for ARV treatment from 1 September, as announced by the Minister of Health on 10 May TB microscopy analysis decreased by 24% from in 2014/15 to in 2015/16 and in 2016/17. The decrease is attributable to implementation and training on the GeneXpert algorithm conducted by the NPP Department as well training on minimum clinical data sets (MCDS). GeneXpert analysis decreased by 5.8% from in 2014/15 to in 2015/16 and in 2016/17. The decrease is attributable to continuous training and support provided by the NPP Department on GeneXpert algorithm implementation; cost containment measures on laboratory testing implemented by the DoH; and a decrease in TB infection, as announced by the Minister. Table NC2: New laboratory tests introduced in 2016/17 Laboratory Kimberley New Tests Automated D-Dimer Innovance FSH, Progesterone, LH, Oestrogen, Ferritin, Amikacin, Vitamin B12, Folate, Testosterone, CA15-5, CA15-3, CA19-9 validation in progress. Annual Report 2016/17 107

109 Cryptococcal antigen reflex testing for CD4 counts <100 was implemented in September 2016 at the CD4 testing sites, namely Kimberley, De Aar and Upington. Upington, De Aar, Springbok and Tshwaragano laboratories were identified as pilot sites for viral load testing. They were assessed for availability of resources and infrastructure. The GX4 analysers for the purpose were installed at Upington, Springbok; Tshwaragano and De Aar. Service Delivery Daily collection from healthcare facilities is maintained at 100% by Hartmann Emergency Care. In total, 240 facilities are serviced. Additional new bidirectional SMS Printers were installed in the Namaqua District facilities to improve turnaround times of priority programmes. Figure NC1: Bidirectional SMS printer The pathologists continue to provide advisory support to clinicians, train staff and improve service delivery. Advisory services are provided for microbiology, chemistry and haematology by Universitas and Groote Schuur hospitals. They are also involved in the Continuing Professional Development (CPD) programme and advise on technical issues. This has a positive impact on the business unit as the clinicians also consult as and when needed, resulting in improved morphology and histology turnaround times. Table NC3: Daily clinic coverage per laboratory/district District Laboratory Number of Clinics 2016/17 Daily Collection Frances Baard Kimberley % Pixley Ka Seme De Aar % ZF Mgcawu Upington % John Taolo Gaetsewe Tshwaragano % Namaqua Springbok % Turnaround Times The business unit continued to perform well in both diagnostic and priority programme TATs. Table NC4: Priority Programmes Turnaround Times Test 2014/15 % within TAT 2015/16 % within TAT 2016/17 % within TAT Target (%) TB microscopy (40 hours) CD4 (40 hours) GeneXpert MTB/RIF (24 hours) FBC N/A N/A U&E N/A N/A LFT N/A N/A Average National Health Laboratory Service

110 Client Interaction Management The presence of the Client Liaison Officer has improved stakeholder relationships in the business unit, resulting in a reduction in the number of complaints received. This has been achieved by spending more time in the districts and the laboratories, assisting with service improvement issues and training. District meetings were also attended to ensure that issues are addressed at district level. Visits were undertaken to 161 facilities, and 854 healthcare workers were trained on MCDS, WebView access, stock control, Pap smears, PCR, GeneXpert, blood collection and SMS Printers. Fig NC2: Blood collection, SMS printer and GXP training in Francis Baard district The business unit has collaborated with the Northern Cape DoH in extending laboratory services to the mines. The service to the four mines previously mentioned commenced in November 2014 and monthly partnership meetings are held with these parties. Courier services are also provided for the mines. Stakeholder relationships have significantly improved through regular district and provincial meetings, resulting in turn in improved services. The business unit was actively involved in the provincial World TB Day commemoration, which was held at Upington and in World AIDS Day, which was held at Masilo Maria Leu Community Hall, in Deben, Khatu. Figure NC3: From left to right: World TB Day in Uppington, Pinky Moipolai, Motsamai Mofekeng, Busisiwe Ngubeni In an effort to address skills shortages in the province, an initiative to recruit learners from the two districts, Namaqua (Springbok) and John Taolo Gaetsewe districts high schools, was pursued, in collaboration with a learning academy. The first learner has been awarded a bursary and has commenced her studies at Central University of Technology. Annual Report 2016/17 109

111 Figure NC4 : High school learners recruitment drive at John Taolo Gaetsewe district in Tshwaragano Technical Skills and Training Over the years, considerable effort has been put into ensuring that training takes place at all levels. A total of 854 healthcare workers and 214 staff have received training. The following courses were provided. Table NC5: Courses provided Course New NCE, CA.PA procedure and Risk management Trackare refresher Fire Fighting training First Aid Level 1 training Customer Service Finance for Non-finance Management Conflict Management Presentation Skills Stress Management Time Management Laboratory Management in Practice Ethics workshop Morphology Attendees All internal auditors, laboratory managers and supervisors LSS staff, technologists, technicians Fire wardens and deputies First aider and deputies LSS staff, technologists, CLO, technicians Managers and supervisors All staff Managers and supervisors Managers, supervisors, IT, CLO Managers and supervisors Laboratory managers All staff Technicians and technologists Technical staff acquisition and retention remains a challenge. Posts are advertised and either no response is received, or applicants are unsuited to the positions. To ensure that staff members are kept abreast of new developments in the pathology sector, four staff members attended the ASLM Congress in Cape Town. Training of Students Kimberley Laboratory is the only training laboratory in the business unit. Of the two student technologists who wrote the examinations in September 2016, only one passed and has been appointed to Kimberley Laboratory. Two wrote their board exams in March 2017 and one passed. Seven student medical technologists were appointed in February The students are continuously assessed, and gaps and challenging areas are identified and actioned timeously. These students also attend the refresher courses offered by the Training Department. Retention of students in the rural/outlying areas remains a challenge. 110 National Health Laboratory Service

112 Accreditation Kimberley Laboratory had a successful pre-sanas audit in August 2016 after which a full SANAS audit was conducted from February 2017 and the laboratory was recommended for SANAS accreditation. This was a great achievement for the Northern Cape as this is the only tertiary laboratory in the province. The appointment of a Quality Assurance Co-ordinator in September 2016 has had a positive impact. The Co-ordinator has provided support to all the laboratories in the business unit and played an important role in the accreditation process. Figure NC5: Kimberley laboratory team De Aar Laboratory has been identified as the National Health Insurance (NHI) pilot site. It is being prepared for accreditation and in the review period achieved 95.7% in its quality compliance audit and 99.1% in its safety audit. The Quality Assurance Department is working closely with all the laboratories to ensure that they perform at an accredited laboratory level. The Northern Cape achieved an overall outcome of 88% for compliance audits and 97% for safety audits. New Laboratories and Laboratory Upgrades The new hospital has been completed at De Aar, with the proposed occupation date being May Kimberley Laboratory has been recommended for pre-analytical automation and the tender process is underway. This will improve workflow tremendously. Renovations are also in the pipeline. Conclusion Generally, the business unit s performance has improved. Great improvement was noted in the compliance and safety audits. Tshwaragano Laboratory continues to perform well despite regular power outages due to insufficient electricity at Batlhlaros Village. Attracting staff to the province, especially the rural areas remains a challenge. However, as a team the staff members are committed to making the best with what is available to improve patient care and service delivery in the province. We are positive that the new high school learner retention strategy will address this challenge. Annual Report 2016/17 111

113 KWAZULU-NATAL Introduction The KwaZulu-Natal (KZN) Region of the National Health Laboratory Service (NHLS) is one of six NHLS regions that supports the KZN DoH; other government departments, including but not limited to the Department of Agriculture Forestry and Fishery (DAFF), Department of Correctional Service (DCS); Non-Governmental Organisations; and Non-Profit Organisations (NPOs). The region supports all eleven health districts, with 100% access coverage to laboratories at National Central Hospitals, Regional Hospital, District hospitals and Primary Health Clinics (PHC) through a daily specimen collection courier service, which is outsourced by NHLS. The region prides itself in having 100% provincial pathologist coverage through the availability of Laboratory Medicine Specialists (Pathologists) in all Clinical Pathology disciplines, either telephonically to give advice to clinicians throughout the province or through physical interactions where required and possible. Area Manager Sibulele Bandezi One of the key successes for the region was the alignment of the six Business Units with the DoH district boundaries and the renaming of all business units to reflect the name of the district the business unit is servicing. The aim was to ensure that the NHLS in the region is aligned with DoH nomenclature in order to be more responsive to their needs; improve efficiency; and improve communication, reporting and accountability. This prevents the confusion experienced previously, where business units cut across different health districts. Previously ethekwini District, for example, was service by three different NHLS business units i.e. Academic Complex Business Unit, ethekwini North Business Unit and ethekwini South Business Unit. This arrangement made effective communication and reporting difficult and almost impossible to hold NHLS managers accountable. The region consist of 65 laboratories of which two are at community healthcare centres (CHCs); and nine TB Microscopy Sites, of which eight are in CHCs, and one is at a Specialised TB Hospital. This means that the region has a more decentralised service than any other region within the NHLS. Service Delivery The introduction of Cryptococcal Antigen (CrAg) reflex testing (Cd4 count below 100) was initiated in October 2016 for early detection and treatment of Cryptococcal meningitis before it is symptomatic, to reduce morbidity and death due to meningitis infection. Table K1: Cases tested in the region Total CD4 Count Tested Number of CD4 Count Below 100 (tested for CrAg) CD4 Count % Positive Crptococcal Antigen (CrAg) Positive CrAg Positivity Rate % % The region focuses on customer centricity, improved quality of service and improving efficiencies to provide cost-effective services, as mandated by the NHSL Act. The region envisages achieving these goals by leveraging existing and new technology. This includes implementing pre-analytics automation, for which requisitions and approval have already been obtained, for implementation at the higher throughput laboratories, such as Addington and Prince Mshiyeni Memorial Hospital (PMMH). In January 2017, a project plan was drawn up for the automation of the microbiology space, of which PMMH has been identified as the pilot site. The project plan is currently being refined for implementation in 2018/19. KZN is moving with unprecedented speed towards SANAS accreditation of its laboratories. IALCH- Microbiology achieved SANAS accreditation in the review period; and IALCH-Cytology, Greys Hospital, Edendale and PMMH passed pre-sanas audits and are confident of achieving SANAS Accreditation in the first quarter of 2017/18. The Academic Complex Business Unit The unit provides specialised and routine diagnostic pathology services to the two National Central Hospitals, which are IALCH and King Edward VIII Hospital (KEH), and their clinics and serves also as a referral for all laboratories for specialised tests for the KwaZulu-Natal Province as a whole. The 112 National Health Laboratory Service

114 Academic Complex laboratories play a pivotal role in the training of registrars, in collaboration with University of KwaZulu-Natal (UKZN), as the only training platform for training of Laboratory Medicine Specialists (Pathologists) in various disciplines, and the training of medical scientists and medical technologists collaborating with Universities of Technology (UoTs). Academic Complex laboratories also collaborate with other government and non-governmental organisations and perform testing on request for research units such as UKZN Laboratory Medicine and Medical Sciences; the Medical Research Council; KwaZulu-Natal Research Institute for Tuberculosis and HIV; and the private sector. Pathologists provide coverage to the province through various clinico-pathological consultative services, which are offered to clinicians and NHLS laboratories. Diagnostic Services and New Developments During the 2016/17 financial year, tests were performed and billed, reflecting an 11.6% increase over the previous financial year. This increase was mainly due to an aligned response to changes in the guidelines for the Comprehensive Care, Management and Treatment of HIV and AIDS (CCMT) Programme, which affected all the diagnostic laboratories, despite renewed efforts at manual and clinical gatekeeping. Continued interventions and strategies to reduce rejections resulted in an average rejection rate for the period of 2.3% (test set) and 5.1% (episodes). In the face of cost containment and efficiency measures, the introduction of new tests and technology was limited and efforts were focused primarily on ensuring sustainability as a business unit and eliciting maximum productivity from the existing skilled staff. An average of 32% of total revenue was spent on the procurement of direct materials up until the end of the financial year, which was within the 34% budgeted ratio. Labour comprised 47% of revenue and exceeded the 46% budget target due to organisation-wide salary adjustments made by the Reward and Remuneration Project, which aim was to improve lagging salary scales within the organisation. The Academic Complex exceeded its expenditure budget by 7.8%, mainly as a result of external testing expenses to the value of R24,422,039 (112% variance from budget) for the outsourcing of histopathology, cytogenetics, certain haematology molecular and some specialised chemical pathology tests due to national skills shortages of health professionals in certain fields. Income from the Training, Teaching and Research Grant was received to the value of R which does not fully cover the training, teaching and research mandate of the NHLS, however the business unit managed to post a net surplus of R at year-end. The Virology Laboratory introduced the cytomegalovirus (CMV) viral load test in February 2017 and an average of 182 samples were tested monthly. Cryptococcal Antigen (CrAg) reflex testing was implemented at KEH Haematology for CD4 levels <100. The CrAg positivity rate was 10%. New chemical pathology and haematology analysers were installed at KEH over a period of six months in Coagulation analysers in the IALCH Haematology Laboratory were replaced and upgraded in August 2016 by the Impilo Consortium, as part of the KZN DoH Private Public Partnership (PPP) arrangement with Impilo Consortium. Aging analysers in the IALCH Haematology Laboratory could not be repaired successfully nor replaced due to the Impilo Consortium s budgetary restrictions and the testing of Vitamin B12 and Folate was ultimately transferred to the IALCH Chemical Pathology Laboratory in March 2017 to be performed on another platform. However, whilst the validation was under way, extended downtimes at the only other site in KwaZulu-Natal necessitated the referral of Vitamin B12 and Folate samples to a private laboratory, in order to maintain service delivery. The laboratory, which continued to be plagued by a shortage of highly specialised skill sets, increased its outsourcing of Cytogenetics and molecular testing to private laboratories in 2016/17. The Anatomical Pathology Department was able to reduce its outsourcing from 50% to 32% by the end of the financial year because of the placement of newly qualified pathologists in February and March In total, histopathology specimens i.e. 10% of the total workload, were outsourced privately during 2016/17. Service Delivery and Coverage The IALCH laboratories perform specialised referral tests. Shifts were optimised to ensure that service delivery continued in the 24-hour and priority programme laboratories, despite a critical staffing shortage in certain laboratories. However, this could not be implemented for HIV DNA PCR testing due to the specialised nature of the testing and a shortage of medical technologists qualified in the discipline. This had a negative impact on the turnaround times for this test (63.94%). Overtime was approved for laboratories with inadequate staffing to ensure optimal staffing during shifts; however, a full shift system could not be implemented since all vacant positions had not yet been filled. A workforce model and an adequate operational budget are critical to determine the optimal staffing needs and it is anticipated that these will be in place by 2017/18. Clinics were visited on a quarterly basis and issues were addressed regularly. Specimen tracking has been discontinued at the three clinics covered by KEH (Cato Manor, SACTWU and Chesterville clinics) as the functionality has been disabled due to procurement issues with the contract. SMS Printers have been functional and operational in all clinics during 2016/17. The academic pathologists ensure consultative service delivery coverage to the laboratories in the province, and perform regular visits to specific sites in the area. Regional expert groups advise on and provide assistance on service delivery platforms in the region. Annual Report 2016/17 113

115 Turnaround Times The TAT for CD4 testing was 95.9% and was within the expected target. For viral load testing, the TAT was met (96.5%), however for HIV PCR the target was not met (63.9%) due to a critical shortage of medical technologists in the Department of Virology. Instrument downtime also played a role. Targets were met for TB microscopy TAT (97.8% at IALCH and 98.4% at KEH). GeneXpert testing TAT was 89.6% at IALCH for extrapulmonary TB and 99.6% at KEH for pulmonary TB. The average cervical screening turnaround time for Pap smears was 99.7%. Targets for FBC, U&E and LFT were also met at both hospitals; IALCH 99.8%; 99.6%; 92.5% respectively and KEH 99.7%; 98.3%; 91.2% respectively. For the laboratories performing tests for the National Priority Programmes, the average TAT was as follows: Table K2: TAT targets and performance 2016/17 April 2016 May June July August September October November December January 2017 February March Ave IALCH HIV PCR 52.79% 86.05% 75.69% 95.48% 76.70% 76.99% 80.65% 93.43% 66.35% 17.97% 44.20% 6.80% 64.43% VL 98.72% 98.66% 97.93% 99.55% 97.48% 98.69% 94.91% 99.63% 92.22% 97.88% 90.30% 89.50% 96.29% LFT 85.53% 85.04% 85.20% 85.28% 96.14% 97.54% 98.02% 97.76% 98.18% 98.27% 97.49% 93.43% U&E 99.94% 99.84% 99.56% 99.73% 99.59% 99.80% 99.86% 99.63% 99.80% 99.76% 99.10% 99.69% CervSm 97.81% 99.01% 99.85% % 99.99% 99.98% 99.97% 99.99% 99.99% 99.62% 99.85% 99.75% 99.65% FBC 99.88% 99.82% 99.93% 99.82% 99.89% 99.74% 99.83% 99.74% 99.87% 99.83% 99.88% 99.84% Gxp 79.46% 92.48% 89.93% 82.85% 90.98% 92.28% 87.99% 91.15% 84.97% 95.50% 92.49% 90.90% 89.25% TBM 91.12% 99.08% 97.15% 99.84% 99.86% 99.25% 99.59% 99.13% 98.36% 96.52% 98.34% 96.60% 97.90% KEH CD % 99.20% 98.97% 92.94% 97.88% 98.96% 98.18% 99.01% 97.33% 99.03% 99.05% 71.04% 95.88% LFT 85.13% 85.45% 85.12% 85.29% 97.91% 99.39% 97.45% 91.66% 94.15% 93.89% 96.20% 91.97% U+E 99.64% 99.88% 99.59% 99.59% 99.73% 99.59% 98.76% 96.38% 95.12% 94.69% 97.23% 98.20% FBC 99.87% 99.87% 99.85% 99.90% 99.84% 99.94% 99.74% 99.92% 99.69% 99.55% 99.33% 99.77% GXP % 99.77% 99.77% 99.68% 99.54% 99.80% 99.90% % % 99.77% 99.46% 99.89% 99.80% TBM 98.10% 96.06% 98.47% 98.22% 99.44% 96.56% 95.38% 99.75% 99.07% % 99.72% 99.74% 98.29% Figure K1 depicts the changes in Priority Programme workload from 2015/16 to 2016/ CD4 VL HIV PCR TBM GXP CX Figure K1: Priority Programme performance Comparison of test volumes National Health Laboratory Service

116 The KEH Haematology Laboratory performed CD4 tests during the year for the CCMT Programme, a 6% increase over the previous year. As a result of guideline changes viral load and HIV DNA PCR tests done, demonstrating a 15.7% and 15.1% increase respectively. In total, cervical Pap tests were screened by the Cytology Unit, which equated to a 16.8% increase over the previous year. For both the KEH and IALCH TB laboratories, TB microscopy was performed on samples, reflecting a 2.8% decrease. At the IALCH and KEH TB Culture laboratories, specimens were cultured for TB during the financial year, reflecting a 38% decrease since the previous financial year. Molecular TB Line probe assays at IALCH TB Laboratory numbered , demonstrating a 1.7% decrease during this period. A 6% increase in volumes to was noted in GeneXpert testing for both pulmonary and extrapulmonary sites at KEH and IALCH TB laboratories. HIV drug resistance tests numbering 587 were performed during 2016/17, demonstrating a 127.5% increase over the previous year. Notable Achievements including Accreditation Two laboratories at IALCH, namely Chemical Pathology and Microbiology, attained SANAS accreditation for the first time. Further, the Virology and all KEH laboratories at the Academic Complex were successful in the SANAS surveillance audits during The three other IALCH laboratories are involved in various stages of preparation for the accreditation process and were severely impacted by discipline-specific skills shortages, failure to fill vacancies, and continued staff attrition. The Cytopathology Unit passed the pre-sanas audit in February 2017 was subsequently recommended for a full SANAS audit in Anatomical Pathology (Histopathology) and IALCH Haematology are earmarked for accreditation by the end of 2017/18. All laboratories are now aligned with the standards set out in ISO 15189:2012. IALCH Chemical Pathology and Virology laboratories participated in an internal audit by the NHLS and KEH Chemical Pathology and Virology underwent an External audit. Both the NHLS laboratories at IALCH and KEH hospitals attained 100% in the National Core Standards audits during the year, carried out by the National Office of Health Standards Compliance. All laboratories in the business unit underwent Health and Safety audits and Risk Assessments and the average audit score for the business unit was 95%. Good external quality assurance/assessment (EQA) performance continued. For the 75% Proficiency Testing Scheme (PTS) EQA, the business unit attained an average of 96% and for the 90% PTS EQA, an average score of 93% was achieved. New Laboratories and Laboratory Upgrades Preparation for the IALCH Pathology Laboratory Floor Repair Project in 2017 is under way. The DoH has received approval of the budget from Treasury to commence with roof and floor structural repairs and reinforcements for the building in 2017/18. The Coagulation Section in IALCH Haematology underwent structural repairs to accommodate new analysers placed by the Impilo Consortium. Infrastructural challenges still exist at KEH laboratories. Floor repairs were budgeted for and are now pending. The matter of the KEH non-functional lift has been escalated to the DoH and may be addressed in F2017/18, pending budget approval. Technical Skills and Staffing The Academic Complex has five academic departments that span nine laboratories at both hospitals. The staff members of the unit are mandated to teach and train, perform research and ensure service delivery requirements are met. During the period, the unit was challenged by attrition and the inability to recruit suitably qualified and experienced candidates in specific job categories. Despite this, there was a net increase of five employees by the end of the period. The HOD position for Haematology remained vacant despite being advertised several times. The Haematology Laboratory Manager post was filled in May The QA Co-ordinator and HOD Chemical Pathology posts were filled in November and December 2016, respectively. Currently, the business unit has four HODs and one acting HOD, nine laboratory managers, two laboratory supervisors, 27 pathologists, three medical officers, 110 medical technologists, 69 medical technicians and seven medical scientists among its 390 employees. The professional staff members are involved in continuous professional development programmes. Table K3: Academic staff HR Job Category Chemical Pathology Haematology Microbiology Virology Anatomical Pathology HOD Pathologist Medical Officers Registrars Med Scientist Med Scientist Intern Total: Annual Report 2016/17 115

117 Table K4: Technical staff HR Job Category Chemical Pathology Cytology Haematology Lab Assistants Lab Supervisors Med Scientists Med Technicians Med Technologists Total: Skills Development and Training Microbiology The business unit is HPCSA-accredited for the training of registrars, medical technologists, medical technicians and intern medical scientists, with the exception of Haematology, whose training status for registrars was withdrawn in The unit is currently training 78 students (29 pathology registrars, two intern medical scientists, 33 student medical technologists and four student technicians. Six postgraduates are registered as PhD students and three academic staff members already hold PhD degrees. Virology Anatomical Pathology Chemical Pathology Haematology Microbiology Lab Support The Haematology Department s accreditation for registrar training status was withdrawn in 2016 because of the lack of a permanent HOD and training programme. Five haematology registrars who are currently on the training platform are being trained by Wits. Six registrars participated in the Histopathology FCPath College of Medicine of South Africa (CMSA) Part II examinations during the financial year. One registrar wrote and passed Part I Anatomical Pathology; two anatomical pathology registrars were retained as newly qualified pathologists; one supernumerary registrar returned to Malawi after qualifying; and four registrars are currently completing their MMED dissertations in anatomical pathology. In chemical pathology, one registrar participated in and passed Part I CMSA examinations and two registrars passed Part I (a 100% pass rate). There was a 100% pass rate for medical technicians in cytology and virology and a 78% pass rate for medical technologists in clinical pathology in the March 2016 examinations. Training was provided to senior management on the Quality Manual v11 Performance Management System, Risk Management, and Enterprise Content Management (ECM) Scanning, amongst others. Laboratory staff attended various training courses in line with the Workplace Skills Plan (WSP) 2016/17. Within the business unit, training was conducted by the Quality Assurance Co-ordinator and other designated employees. Stakeholder Relations Several meetings and workshops formed part of continual stakeholder engagement. Client relations meetings and training sessions with the Primary Healthcare (PHC) and Community Healthcare (CHC) clinics that drain to KEH were held. WebView access for the clinics and hospitals was enabled for new doctors and clinic sisters to view results. Training was conducted on the new barcoded request forms and ECM project, which was implemented during the year. Currently there are challenges with the ECM scanning licences at KEH. Numerous DoH-NHLS meetings at IALCH and KEH were held to discuss cost efficiencies, the top 10 expensive tests, rejection rate monitoring, clinical gatekeeping, electronic gatekeeping, specimen taking practices and Laboratory Information System-Hospital Information System challenges, etc. Additional meetings were convened with the NHLS to discuss the Global Green Healthy Hospital Initiative, IALCH Pathology Laboratory Floor Repair Project, the Soarian-Trak and MediTech-Trak challenges, the crisis in clinical haematology and haematopathology, specialised reflex testing, the mortuary services, and various other issues. An intern orientation workshop was held at King Edward Hospital on 4 January 2017 to orientate incoming medical interns on good laboratory practice and protocols. The medical interns were also given web access to enable the viewing of laboratory results via the internet. On a quarterly basis, the NHLS laboratories were invited to participate in the induction workshops for new employees at King Edward VIII Hospital. KEH Intern Committee meetings with medical interns and supervisors were attended and customer complaints were addressed to ensure optimal access to laboratory results at KEH. The monthly KEH Extended Management and Quality Assurance Committee meetings were attended by the business manager and laboratory managers. The business manager attended several meetings with medical management to foster good client relations, attend to operational efficiency matters, optimise clinical gatekeeping and minimise costs. Peer review audits were also conducted to ensure compliance with NHI standards. 116 National Health Laboratory Service

118 At IALH the Maternal and Child Health Domain, Perioperative and Surgical Domain, and Medical Domain meetings were attended by the business manager and designated laboratory managers/hods, where relevant. Test statistics were provided to the clinical HODs to assist them with electronic and clinical gatekeeping, rejections, contamination, TAT, pre-ordering, future orders and to enforce compliance with the MCDS. Meetings between the NHLS and AME Afrika focussed on the optimisation of the newly introduced MediTech Health Information System (HIS) and its interface with TrakCare LAB. The placing of future orders was deactivated on the new HIS to prevent the erroneous reporting of prolonged TATs. Initially there were several challenges during the migration such as missing orders, duplication, unscheduled downtimes, etc. and these have been sequentially resolved over the course of the year. Meetings between the NHLS and Impilo Consortium focussed on day-to-day operational issues, which involved ensuring compliance with the regulations of the Department of Labour, municipality and the Private Public Partnership (PPP) regarding equipment placement cycle, infrastructural changes, security, waste disposal and health and safety amongst others. To this end, the NHLS also met with relevant subcontractors with respect to various operational/infrastructural changes. The UKZN School of Laboratory Medicine and Medical Sciences Board meetings were attended by HODs, Acting HODs, the Business Manager and other jointly appointed staff. College of Health Sciences meetings with the NHLS academic staff were held and chaired by the Deputy Vice-Chancellor and the Dean and Head of School of the college. Discussions revolved around motivating academics to pursue postgraduate studies, in particular, PhD degrees, key performance areas, the undergraduate curriculum, postgraduate support, the visual learning project and the ROBOT system, etc. Institutional Academic Pathology Committees (IAPC) meetings were held to address operational and academic matters not resolved at Pathology Management Committee (PMC) level, as per the Umbrella Agreement and to finalise the local Bilateral Agreement between UKZN and NHLS KZN Academic Complex. The Dean/Head of School and the School s Operational Manager also attended the PMC meeting (on invitation) to ensure that academic challenges are highlighted and resolved and that teaching, training and research platforms are optimised for delivery. Academic Performance The academic business unit produced 52 publications during the year, a 15% increase over the previous year. There were also 23 conference presentations during the year. Departmental Academic Reports tabling teaching, training and research outputs were submitted by each Academic Head to the Academic Affairs, Research and QA (AARQA) Department. These are included in this NHLS Annual Report under the AARQA section. Conclusion Overall, the business unit demonstrated excellent performance against set targets with marked improvements noted since the previous year in the areas of academic output, service delivery and financial sustainability, despite continued challenges on the training and service platforms. The business unit demonstrated a surplus compared to past years deficits. Lessons learned during the year will add value to operational activities and performance in the year ahead. umgungundlovu- uthukela Business Unit Introduction The Mgungundlovu-Thukela Business Unit supports two health districts i.e. umgundundlovu district and uthukela district, via seven laboratories and three TB microscopy centres. The business unit caters for the diagnostic needs of 10 hospitals one provincial tertiary hospital (Greys), two regional hospitals (Edendale and Ladysmith), seven district hospitals, 123 clinics and four prisons, and deals with referrals from another nine peripheral hospitals in the western part of KwaZulu-Natal for anatomical pathology testing and other specialised testing. Diagnostic Services Diagnostic services are pivotal to the success of the DoH s initiatives to improve the general health of the population. These initiatives are dynamic and include complex and specialised clinical interventions, hence the need to respond from a diagnostic laboratory perspective, with 24-hour and call out laboratories, to enable optimum patient care. Mgungundlovu-Thukela performed billed tests during the year under review, compared with in the previous period, an increase of tests (3.6%). Sales increased by 1.5 % year-on-year while staffing reduced by 7.7%. The increase in sales was mainly driven by increased numbers in the priority programmes and changes in the guidelines. The rationalisation of certain tests did not affect the diagnostic services. Annual Report 2016/17 117

119 Continuous training of pre-analytical staff, both internally and externally, ensured a more effective and efficient diagnostic service in the period under review. Service Delivery PHC coverage There was 100% PHC coverage for the 123 facilities via 27 outsourced and two NHLS vehicles. Routes were optimised and reviewed to ensure effectiveness and cost efficiencies. Shift systems were introduced where possible to counter the financial environment and were aligned to peak workflow of specimens into laboratories. Turnaround times New automation contributed to viral load TAT being met and to countering increasing demand. The replacement of human resources during the year under review was a major challenge with increasing work volumes. Table K5: TAT performance Test Performance Target Comment GXP 97% 90% within 48 hours Target achieved TB 96% 90% within 48 hours Target achieved CD4 90% 90% within 48 hours Target achieved Viral load 67% 65% within 96 hours Target achieved Cervical Smears 99% 50% within 13 days Target achieved FBC 89% 80% within 8 hours Target achieved U&E 86% 80% within 8 hours Target achieved LFT 80% 80% within 8 hours Target achieved Client interaction Client relationships were strengthened via regular scheduled meetings between the District Manager, Provincial Co-ordinator and implementing partners and the formation of task teams in collaboration with the DoH. Laboratory managers attended scheduled DHC meetings, clinic visits and hospital management meetings. Feedback was obtained and incorporated in continuous improvement plans. Customer Satisfaction Index The annual Customer Satisfaction Index was performed and a 3.5% improvement was noted resulting from intervention actions after the previous Index. An increased responsiveness by customers year-on-year was also noted, with an overall response rate of 90%. All laboratories achieved response rates above the 70% target. 120% 100% 80% 60% % 20% 0% Estcourt Emmaus Ladysmith Greys Edendale Northdale Appelbosch Average Responses 2016 Responses 2017 Figure K2: Customer Satisfaction Index response rates per laboratory 118 National Health Laboratory Service

120 90% 85 80% 70% 60% 50% 40% 30% 20% 13 10% 1 1 0% Satisfied Dissatisfied N/A No Response Figure K3: Overall customer satisfaction rate Appelbosch Edendale Emmaus Estcourt Greys Ladysmith Northdale Average Satisfaction Rate 2016 Satisfaction Rate 2017 Figure K4: Year-on-year satisfaction by laboratory Notable Achievements Edendale and Greys achieved pre-sanas recommendations Northdale Laboratory maintained SANAS accreditation Edendale Laboratory achieved 94% in the African Society for Laboratory Medicine (ASLM) external audits second highest in South Africa An intern orientation programme for new doctors was established within the GEN complex (Greys, Edendale and Northdale Laboratories) The business unit was complemented in the year under review by five different clients Three CEO awards were received for excellent performance. Annual Report 2016/17 119

121 Figure K5: CEO Award for Excellent Performance Laboratory Upgrades Northdale and Edendale laboratories were upgraded in line with the NHLS Strategic Plan. Technical Skills Training programmes were developed to improve technical skills as a continuous improvement project. This was supported by in-house training and competency workshops. Outreach support and training by a business unit pathologist had a further positive impact. Accreditation As per the accreditation plan, Northdale Laboratory maintained SANAS accreditation status during 2016/17. Edendale Laboratory underwent a SLIPTA external audit, achieving 94% in February. An internal pre-sanas audit was undertaken in November, and the laboratory was recommended for a full external SANAS audit. Greys Laboratory also had a successful pre-sanas audit resulting in recommendation for an external SANAS audit. Ladysmith Laboratory is on the SLIPTA Programme as part of the preparation for a pre-sanas audit. The lack of human resources appointments affected the pace of progression for accreditation during the 4 th Quarter of the year. Project plans have been drawn up and implemented to ensure that the target of achieving SANAS accreditation for Greys and Edendale is realised. The business unit averaged 92% during the safety audits performed in the reporting period. Training Ongoing training in all facets of laboratory medicine was a focus area in the year under review. Training programmes were implemented for internal and external customers and were well attended. The impact of the training is now visible in most laboratories. The primary training and competency drive focused on pre- analytic activities to ensure that an effective and efficient service was offered. Northdale Laboratory is a certified HPCSA training laboratory. Information Technology Challenges were experienced with connectivity and downtimes, mainly in two laboratories (Appelsbosch and Emmaus). This created major service delivery interruptions and affected TAT. Duel broadband connectivity was installed at Edendale and Greys laboratories to mitigate the risk of LIS downtime. New computers were received which assisted with improved work efficiencies, however delays in the replacement/upgrading of all computers is of concern. Business was also affected by poor response times from the Information Technology (IT) Department and this lack of effective and timeous support from IT is a serious concern, both regionally and nationally. 120 National Health Laboratory Service

122 Ethekwini Business Unit Introduction The re-alignment of business units within the KZN Region to the KZN DoH s District Health boundaries, makes it impossible to do year-onyear comparisons between the 2016/17 and 2015/16 performance. During 2015/16, ethekwini Health District was split into ethekwini North and ethekwini South, which included parts of ilembe, ugu and uthungulu health districts. Currently the ethekwini Business Unit shares the same boundaries as ethekwini Health District. This alignment with the health district makes it easy to report statistics and information for ethekwini District, which is the largest district by population. The throughput for the business unit is more than 7 million tests per year, making it making it the largest in the region by test volumes and laboratory coverage. It has 10 laboratories i.e. four regional, seven district, one Public Health Laboratory and three microscopy sites. Therefore, it has the highest number of regional hospitals and by implication has specialised testing in support of regional hospital services level of care. Diagnostics Services The unit continues to provide efficient services to the majority of the population of over 3 million in the ethekwini Health District. In total, million billed tests were recorded with a revenue of R452 million. The Public Health Laboratory (PHL), based at Prince Street Durban, plays a pivotal role in the testing of imported meat from other countries to South Africa. It performs testing on water for human consumption and does food poisoning testing. The PHL is therefore a strategic asset from a public health perspective for the KZN Province and the country as a whole. Service Delivery Turnaround Times (TATs) The business unit is proud to report that target TATs for National Priority Tests were all achieved, with an average of 99% for CD4, 99% for GeneXpert, 96% for TB smears, and 76% for viral load testing. The TATs for routine tests indicate an average of 97% for Urea & Electrolytes, 81% for Liver Function tests and 87% for Full Blood Count tests. Stakeholder Relations Constant interaction with clients strengthened relationships between partners, including the DoH; Department of Agriculture, Forestry and Fisheries; SANDF; Correctional Services Centres; municipalities; and Department of Health partners. This interaction happens at all levels, e.g. Laboratory managers attending hospital management meetings, PHC meetings and clinic visits; and the Business Manager attending hospital meetings, district health meetings, and district visits etc. HPCSA Training Mahatma Gandhi Laboratory was accredited for the training of medical technologists; however, RK Khan lost its training status. The business unit has two training laboratories, with the capacity to train medical technologists, medical technicians and phlebotomy technicians. SANAS Accreditation Three accredited laboratories (Addington, Mahatma Gandhi and Public Health) maintained their accreditation status during the SANAS surveillance process. RK Khan Laboratory also achieved WHO SLIPTA 4-Star accreditation. Staffing and Technical Skills The total number of employees at the end of the financial year was 312, with two critical positions vacant, namely Business Manager and Addington Laboratory Supervisor. In line with the WSP and Personal Development Plans (PDP), employees continue to attend capacity-building courses, including ISO training, provided by internal and external service providers Facility Upgrades Renovations were done at Wentworth Laboratory, Pinetown Laboratory training room, the TB Department at RK Khan, and Receiving Department at King DinuZulu. Annual Report 2016/17 121

123 Conclusion The business unit continues to strive for excellence in the region and in the NHLS as a whole and will, in the year ahead, endeavour to ensure that all regional laboratories are SANAS accredited and that PHL is accredited to the ISO standard to ensure a high quality service and boost stakeholder confidence. The business unit s next step is a focus on improving efficiency and quality of service by leveraging technology such as pre-analytics automation for the regional laboratories and microbiology automation as test case for a public laboratory setting. Maju-Mzinyathi Business Unit Introduction This inland business unit consists of six laboratories and one microscopy centre. The unit supports two districts, namely Amajuba and umzinyathi. There is an NHLS laboratory at each general hospital within the districts. NHLS laboratories also support three community health centres in Dannhauser, Pomeroy and St Chads. There are two regional laboratories and four district laboratories. The regional laboratories provide a 24-hour service, while district laboratories provide call-out services to ensure uninterrupted client service. The business unit serves a predominantly rural population. Diagnostic Services The business unit continues to provide diagnostic and monitoring services to clients, and performed tests during the financial year, an increase of 2.9% year-on-year. The TB workload increased by 28.5% due to the introduction of the DoH Strategy, an increase from to tests. GeneXpert tests decreased in number by 12.4% from to , also associated with the revised ART guidelines. In total CD4 tests were done showing a decrease of 4.2% year-on-year. The analysis of viral load samples at Madadeni Laboratory increased by 96% from to This is attributable to the fact that during the previous reporting period, Madadeni Laboratory underwent renovations. The laboratory was automated with a Vitek system to identify and ascertain the susceptibility of microorganisms, which improved turnaround time and quality of service by reducing manual testing. The acquisition of an automated blood culture analyser during the reporting period also improved the quality of microbiology testing at Madadeni Laboratory. Service Delivery Continuous process and quality improvements were initiated in 2016/17. A shift system was introduced, aligned with the flow of samples from the clinics to laboratories, and the collection of samples from 24-hour clinics was introduced to improve turnaround times. Strengthening the tracking of specimens also improved turnaround times. The challenge of accommodating staff in rural areas remains. A solution lies in accommodating staff within hospital premises and this will be pursued with hospital management. The current reporting period was characterised by periods of downtime on TrakCare, thus negatively affecting TAT. Rationalising of CD4 at Madadeni and Church of Scotland Hospital laboratories improved TAT and reduced the need for staff recruitment within the business unit. TAT targets were met for the following tests: TB microscopy at 98%, GeneXpert at 98%, CD4 at 97% and viral load at 85%. The Majuba Mzinyathi Business Unit is participating in the Proficiency Testing Scheme (PTS) to improve quality in laboratory processes. On the PTS, 75% and 90% levels, the business unit achieved 91% and 91% respectively. Notable Achievements Achievements of note include: The successful achievement of all turnaround targets Successful Proficiency Testing Scheme results The placement of the Aquios CL for CD4 testing at the Church of Scotland Laboratory The placement of the blood culture analyser at Madadeni to improve quality of blood culture processing. Technical Skills and Staffing The headcount at 31 March 2017 was 89, an increase of 10.1% compared to 80 in March The support outreach pathologists from IALCH laboratory contributed positively to the operations of the Microbiology Department at Madadeni Laboratory. This has also resulted in improved communication between the clinicians and staff members. 122 National Health Laboratory Service

124 Training A number of training initiatives was achieved in this reporting period. In total, 109 courses were conducted and 26 staff members trained. The courses included introduction to QMS, travel booking, TrakCare super user, i-procurement, risk assessment, customer and internal audit. The business unit is training medical technologist and medical technician students at Madadeni. Two medical technician students passed their examinations a 100% success rate. One Medical Technologist has written his examination and is awaiting his result. Accreditation Preparation for accreditation is on track and the activities were given to the staff members for preparation. Two laboratories in the business unit are participating in the SLIPTA programme. Madadeni Laboratory obtained 3 stars, which is a marginal improvement from the 2 stars obtained in the previous cycle and Dundee posted no improvement on the SLIPTA project. Other Laboratories that are not on the SLIPTA project are using FMQ0001 to monitor accreditation progress. Information Technology A number of IT challenges were experienced in the period, with laboratories being severely affected. Dundee Laboratory experienced downtime and TrakCare was very slow in the Dundee and Madadeni laboratories. The implementation of Web View, however, has increased accessibility of results for doctors. There was also some positive improvement on the retrieving of results from TrakCare compared to the previous year. Stakeholder Relations Stakeholder relations are vital to improve the image of NHLS and identify gaps that should be addressed. Laboratory managers attend extended management meeting at the facility level. The Business Manager attended district management meetings and hospital management meetings to interact with hospital management and improve service delivery. Laboratory managers and the Business Manager support campaigns initiated by the DoH and other departments such as Correctional Services. Clinic visits were conducted and gaps identified, following which, action plans were introduced to address the gaps. Harry Gwala - Ugu Business Unit Introduction Harry Gwala-Ugu is a new business unit resulting from the alignment of all business units within the KZN province with the KZN DoH District Health boundaries. It encompasses two health districts, namely Harry Gwala (formerly Sisonke) and ugu District Health. The business unit supports one regional hospital (Port Shepstone) and seven district hospitals. It therefore has eight laboratories and two TB Microscopy sites (one based at a Community Health Centre and one located at a specialised TB hospital. It is mainly deep rural with three laboratories in peri-urban settings. Diagnostics Services The total test revenue for the financial year was R million, which is 15% below the budget of R million. It is important to highlight that it is impossible to do a year-on-year comparison because of the new configuration of the business unit. Service Delivery PHC Coverage The focus has been on improving transport logistics to the clinics, turnaround times for all tests including clinical pathology, and the quality of the service. The business unit maintained 100% coverage of clinic-to-laboratory specimen collection. To ensure that 100% specimen coverage is maintained, an extension to the existing route was made to cater for a clinic previously covered by the DoH. Turnaround Times All the target TATs for tests were achieved, including routine tests like U&E, LFT and FBC which wre not previously monitored. TB Auramine achieved 96.82%, TB GXP (98.66%) and CD4 (93.76%). This has been attained through the introduction of different shift systems in all the laboratories. Stakeholder Relations Constant interaction with clients has strengthened relationships with partners and the DoH. This interaction happens at all levels i.e. Laboratory managers attend Hospital management meetings, PHC meetings and clinic visits; the Business Manager attends hospital and district health meetings and makes district visits. The Business Manager attends events that are planned by the DoH e.g. World Aids and TB Day. The business unit arranged blood collection training for clients, which has resulted in a decrease in the specimen rejection rate. Annual Report 2016/17 123

125 Technical Skills, Staffing, Training and Accreditation Technical Skills Peripheral blood smear testing skills training was offered to the relevant employees in order to develop skills and improve the quality of tests. A noticeable improvement has been seen in the laboratories. Staffing Recruitment and retention of technical staff has been a challenge, especially at St Apollinaris Laboratory, resulting in high overtime hours. The matter of out of scope medical technologists will be addressed through skills development and natural attrition in the next financial year. Training The business unit has no laboratory with the capacity to train medical technologists and medical technicians, but plans to develop the capacity are at an advanced stage. Training status will be achieved in the next financial year. Quality Assurance and Accreditation The business unit achieved 86% in the Quality Compliance Audit and 97% in the Health and Safety Audit. Accreditation was not achieved in identified laboratories but preparations for Port Shepstone and Scottburgh are at an advanced stage. Information Technology The Laboratory Information System has improved TAT in the business unit following the upgrade of bandwidth, especially at Rietvlei Laboratory. A backup network has also been installed at Port Shepstone laboratory. The ECM project was completed in the latter part of the financial year and all laboratories are storing forms through scanning. The business unit is awaiting delivery of laptops for laboratory managers, which will assist with service delivery. Mkhanya-Zulu Business Unit Introduction The Mkhanya-Zulu Business Unit is composed of two health districts, namely Mkhanyakude and Zululand, which were re-aligned with the DoH health districts in 2016/17. It is situated in the deep rural part of northern KwaZulu-Natal. The alignment enabled the business unit to support and service five district hospitals in umkhanyakude and six district hospital situated in the Zululand district. Table K6: Laboratories per district Zululand District Laboratories Vryheid Itshelejuba Dumbe Ceza Nkonjeni Benedictine UMkhanyakude District Laboratories Hlabisa Bethesda Mosvold Manguzi Mseleni Diagnostics Services The total test revenue for the business unit was R million which is 9% below budget and a decrease of R million when compared to the R million of the last financial year. This is due to improved gatekeeping by DoH facilities. CD4 volumes decreased from to due to adherence to a revised ARV guideline that promoted the viral load monitoring test instead of the CD4 count. TB Auramines decreased from to due to the use of GXP tests for TB diagnosis in all the laboratories. Again, it is not easy to make comparisons with the previous reporting period due to the new business unit configuration. New Developments The acquisition of 57 new computers made a noticeable difference in IT performance. Requisitions were submitted for 10 laptops for the laboratory managers and delivery is awaited. This will benefit the laboratories during LIS down times and will enable laboratory managers to remotely authorise results using 3G, even when they are away from the laboratories. 124 National Health Laboratory Service

126 Service Delivery and Coverage The focus has been on improving transport logistics to the clinics, turnaround times for all tests and the quality of service. The business unit has maintained 100% clinic-to-laboratory specimen collection coverage. Turnaround Times The business unit achieved the target TATs for Auramines: 97%, TB GXP: 98% and CD4 96%. These were achieved through the introduction of different shift systems in all the laboratories. TAT targets for U&E, LFT and FBC were not met due to network downtimes and challenges with result verification. Measures have been put in place to mitigate this and are yielding positive results, as the TAT targets for Quarter 3 and Quarter 4 were achieved. The improvement of NHLS IT performance is very critical, failing which, all other efforts that were put in place may fail. Notable Achievements Quality Assurance and Accreditation: The business unit achieved 91.4% compared to 85% in the last financial year in the Quality Compliance Audit and 96% compared to 94% in the last financial year in the Health and Safety Audits. No laboratory achieved accreditation with Hlabisa and Vryheid earmarked for accreditation in the 2017/18 financial year. New Laboratories and Laboratory Upgrades The infrastructure upgrade for laboratories affected by drought, to install galvanised water tanks, is still outstanding due to slow response from the DoH in providing authorisation for the NHLS to erect the tanks. The planned upgrades in Bethesda and Ceza could not be executed due insufficient funds. The project to acquire two new park homes for Mseleni and Nkonjeni could also not be completed in total due to insufficient funds for Mseleni. Nkonjeni is awaiting delivery of the park home. Technical Skills and Staffing Technical skills Peripheral blood smear and supplier training for instruments in use was offered to the relevant employees in order to develop employee skills and improve the quality of tests. A noticeable improvement has been seen in the laboratories. Other training, related to health and safety, was offered to ensure compliance, and quality management system training was offered to the relevant staff to improve quality in the laboratory. Staffing Recruitment of technical staff improved, especially at Hlabisa Laboratory, which had trouble in recruitment and retention of suitably qualified technical staff. All laboratories within the business unit are now well staffed in terms of technical staff members. Training The Business unit has two training laboratories, with a capacity to train medical technicians and phlebotomy technician students. Three medical technicians, recruited in the previous financial year, passed their medical technician examinations. Stakeholder Relations Constant interaction with clients has strengthened relationships with partners, namely the DoH, SANDF and the Correctional Centres. This interaction happens at all levels i.e. Laboratory managers attend hospital management meetings, PHC meetings and clinic visits; the Business Manager attends hospital, district health meetings and district visits. In addition, the Business Manager attends events that are planned by the DoH e.g. World Aids and TB day. The business unit arranged blood collection training for clients in the review period, which resulted in a decrease in the specimen rejection rate. Lembe-Thungulu Business Unit Introduction The KwaZulu-Natal Region realigned itself with the DoH district health facilities in order to ensure effective and efficient service delivery in the region. This realignment led to a name change for some business units. Lembe-Thungulu Business Unit is one of them. The business unit has one provincial tertiary, two regional and nine district laboratories and one microscopy site. National Priority Programmes are supported at all levels of care in each district, either on site, or off site with the assurance of the same TAT that is within target. Annual Report 2016/17 125

127 SANAS accreditation has been the focus in this financial year. Ngwelezane (a provincial laboratory) and Stanger (a regional laboratory) went through the pre-sanas programme as well as the SLIPTA/SLMTA programme. Ngwelezane Laboratory achieved 4 Stars and Stanger achieved 3 Stars. Business Unit Laboratories Table K7: Laboratories and level of care Laboratory Name Ngwelezane Stanger Empangeni Montebello UMphumulo Untunjambili Catherine Booth Eshowe St Mary s Mbongolwane Nkandla Sundumbili microscopy site Level of care Provincial Tertiary Regional Regional District District District District District District District District CHC Diagnostic Services and New Developments All laboratories provide testing for routine clinical pathology tests. There are two CD4 testing sites, one HIV VL testing site that provides an overnight service for all hospitals in ILembe and UThungulu District and nine TB sites, which do TB microscopy and TB GXP testing. The total number of routine tests and NPP tests performed in the period was of which 91% of the test results were made available to clients within the expected TAT for each category. Two new viral load Roche analysers were commissioned at Ngwelezane and have assisted the laboratory to maintain its TAT at above 90%, with less staff members than in previous years. The impact of the strategy was particularly noticed in the last quarter through an increase in all NPP tests. Service Delivery and Coverage Accessibility and improved service delivery are achieved through the provision of daily specimen collections and deliveries of results (100% coverage); the use of SMS Printers at PHC level; and the use of WebView at clinic and hospital levels. In order to streamline service delivery, the business unit has maximised routes, by doubling collections in clinics with high workloads. The DoH is reviving the specimen-tracking project that seeks to increase visibility to clinics and improve specimen loss. In an endeavour to ensure quality, e.g. reduced rejection rate and improved TAT, ILembe-UThungulu has collaborated with MSF and Broad Reach (NGOs) and suppliers. The support given by these NGOs and suppliers seeks to address phlebotomy technical challenges and adherence to SOPs related to specimen collection. The average TAT achieved for NPP tests was 95.6% and 91% for routine tests. Constant interaction with clients has strengthened the relationship with the KwaZulu-Natal DoH. This interaction happens at all levels. Laboratory Managers attend hospital management meetings and the Business Manager attends hospital and district health meetings. A remarkable impact has been made with the pathology service coverage that is provided to provincial tertiary hospitals, regional hospitals as well as district hospitals. Turnaround Times Despite challenges experienced from month to month, ranging from TrakCare network downtime due to cable theft, and instrument downtime, ILembe-UThungulu Business Unit managed to achieve the following turnaround times: 126 National Health Laboratory Service

128 Table K8: Turnaround times Test TAT Comment TB microscopy 97% Target was achieved TB-GXP 97% Target was achieved CD4 count 96% Target was achieved HIV VL 92.8% Target was achieved U&E 93.5% Target was achieved FBC 93.5 Target was achieved LFT 86% Target was achieved The TAT for LFTs was not achieved due to instrument downtime at St Mary s Laboratory and the closure of Catherine Booth Hospital, which meant that this test had to be referred to another laboratory. Notable Achievements Pre-SANAS audits were conducted at Ngwelezane and Stanger. Three departments at Ngwelezane and two departments at Stanger were recommended, and these are due for full SANAS audits in 2017/18. SLIPTA audits were conducted at Ngwelezane, which achieved 4 Stars and at Stanger, which achieved 3 Stars. The business unit achieved 94% in the Health and Safety Audit. All laboratories have scored above 80% in proficiency testing with the overall annual performance result for the business unit being 94.5%. Two students passed their examinations with distinction. New Laboratories and Laboratory Upgrades Minor renovations were done at Ngwelezane and this has improved the image of the laboratory. Untunjambili Laboratory moved to new Park Home premises, which are closer to the hospital. These premises were provided by the hospital at no cost to the NHLS; however, the NHLS has equipped the laboratory with furniture, electricity and a network etc. Technical Skills and Staffing The Training Department constantly provides training support to enhance the skills and knowledge of the current work force. The total head count at the end of 2016/17 was 149 comprising technical and non-technical staff with the vacancy rate at nine. Due to financial constraints towards year-end, it was difficult to recruit technical staff to replace those who had exited the organisation. Training The focus in 2016/17 was to ensure quality service. As such, a number of technical and non-technical staff members underwent QMS training. Training interventions were conducted at regional level and in-house with the assistance of suppliers, to ensure staff competence. In total, 47 staff members undertook training in various courses. The business unit has two HPCSA accredited training laboratories for medical technicians. The pass rate for the period was 75%, with two distinctions. Stakeholder Relations Constant interaction with clients has strengthened the relationship with the KwaZulu-Natal DoH. This interaction happens at all levels. Laboratory managers attend hospital management meetings and the Business Manager attends hospital and district health meetings. A remarkable impact has been made on the pathology service coverage that is provided to provincial tertiary, regional, and district hospitals. Conclusion Overall performance for the business unit has been generally acceptable, with remarkable and constant performance in achieving set TAT targets for NPP tests and PTS schemes. Annual Report 2016/17 127

129 KwaZulu-Natal Cytology Laboratories Introduction Cervical cancer is the one of the most common causes of cancer deaths in South African women, yet it is a preventable disease. South Africa has a National Cervical Cancer Control Policy (CCCP), with one of the management objectives outlined in this policy being to reduce the incidence of cervical cancer using secondary prevention methods i.e. by offering Pap smear screening tests, and detecting and treating patients with pre-cancerous abnormalities. The National Guidelines for a Cervical Screening Programme was launched by the DoH in This programme allows for all asymptomatic women of 30 years and older to have three free Pap smears in their lifetime (at 10 year intervals between every adequate Pap smear that is negative). The aim of the programme is to achieve an outreach where 70% of women within this target population are screened. In April 2011, the DoH launched its HIV Counselling and Testing (HCT) Programme, which requires that all females who are diagnosed as HIV positive and have a CD4 count less than or equal to 250/uL should have a Pap smear taken. The HCT Programme takes into consideration the need to screen more frequently in patients that are HIV positive, since the rate of progression of an abnormality from a low-grade lesion to cancer is quicker in HIV positive women than in HIV negative women with a low-grade lesion. In September 2016, the HCT Programme was replaced by the Universal Test and Treat (UTT) Strategy, which indicates that in women who test positive for HIV, regardless of the CD4 count, a Pap smear must be taken and the patient must receive antiretroviral treatment (ART). It must be noted that these national programmes do not include the Pap smears taken from all symptomatic ladies, which is another target group indicated in the CCCP and contributes significantly to the coverage and uptake of this important testing platform. In the Kwazulu-Natal region, there are two NHLS Cytology laboratories. One is situated at Greys Hospital and services the Midlands region and parts of Inland and Northern Natal, and the other is situated at Inkosi Albert Luthuli Central Hospital (IALCH) and services the North and South coast regions and parts of the Inland and Northern Natal. Diagnostic Services The cytopathology discipline is divided into three test categories: Gynaecological Testing Non-Gynaecological Testing/General Cytology Fine Needle Aspiration Cytology (FNA) Testing. Cytology Workload Volumes Table K9: Total number of slides tested Category 2015/ /17 Actual Variance % variance Comment Gynaecological % Increase Non-Gynaecological % Increase FNA % Decrease Total % Increase In 2016/17, the province tested gynaecological slides, the highest uptake experienced nationally. The province also experienced an increased uptake for non-gynaecological testing. This equates to a positive variance of 4% for gynaecological testing and a 14% increase for non-gynaecological testing year-on-year, whilst with FNA testing there was a decrease/negative variance noted. The total number of slides tested in cytology overall showed a positive increase of 4%. Service Delivery Table K10: Gynaecological testing turnaround time (TAT) Period Target Actual % Comment 2015/16 70% within 13 days 55.36% Target not achieved 2016/17 50% within 5 weeks 99.79% Target achieved KwaZulu-Natal achieved the Balanced Scorecard TAT for cervical (Pap) smear testing, with 99.79% achieved within 5 weeks. Greys Cytology achieved 99.93% and IALCH Cytology 99.65% 128 National Health Laboratory Service

130 Table K11: Pap smear adequacy rate Period Target Actual % Comment 2015/16 80% 56.1% Not achieved 2016/17 80% 60% Not achieved, but an improvement of approximately 4% achieved The Pap smear adequacy rate improved from a baseline of 56.1% in 2015/16 to 60% in 2016/17, an improvement of almost 4%. KwaZulu- Natal is above the national average of 57% and currently is the third best performing province when it comes to Pap smear adequacy rate. Table K12: Pre-Cancerous pick up rate on gynaecological cytology testing Fiscal Actual % Comment 2015/ % 2016/ % Variance % Increased pick up rate Cervical cancer can be prevented with early detection of abnormalities of the cervix and treatment thereof. The treatment is most effective and the prognosis is better when the abnormality is detected and treated at a pre-cancerous stage (High Grade Squamous Intraepithelial Lesion HGSIL) as opposed to when it is at a cancerous stage. With the significant improvement in the Pap smear adequacy rate, the precancerous pick up rate also increased by 0.9%. Table K13: Cancer pick up rate on gynaecological cytology testing Period Actual % Comment 2015/ % 2016/ % Variance % Increased pick up rate The cancer pick up rate on gynaecological cytology for 2016/17 was 0.28%, an increase of 0.04% when compared to 2015/16. Table K14: Cytology unsatisfactory rate Period Actual % Comment 2015/ % 2016/ % Variance % Decreased unsatisfactory rate The Pap smear unsatisfactory rate for 2016/17 was 2.87%, representing a 0.34% decrease when compared to 2015/16. Table K15: Cytology rejection rate Fiscal % Comment 2015/ % 2016/ % Variance 0.46% Decreased rejection rate The cytology rejection rate for 2016/17 was 1.4%, representing a 0.46% decrease from 2015/16. The major reason for rejection is the mismatch of information between the specimen and the cytology request form. This reason is addressed in the quality training and raised in quality meetings with the DoH. Annual Report 2016/17 129

131 Stakeholder Relations Month Total Training Sessions Conducted Total Number of Meetings Attended Apr-16 One training session King Cetshwayo One DoH provincial meeting Four training sessions ethekwini May-16 Three training sessions Ugu One DoH meeting - Umzinyathi District Jun-16 Three training sessions ethekwini Three DoH provincial meetings Three training sessions umzinyathi One training session King Cetshwayo Jul-16 Three training sessions Ilembe One DoH provincial meeting One training session Zululand One training session ethekwini One training session umzinyathi Aug-16 Three training sessions uthukela One DoH provincial meeting Two training sessions umgungundlovu Two training sessions Zululand Sep-16 Three training sessions Zululand One DoH provincial meeting Two training sessions umgungundlovu One training sessions Ugu Oct-16 One training session ethekwini None Nov-16 One training session ethekwini None One training session Amajuba Jan-17 None Five DoH meetings Feb-17 One training session umkhanyakude One DoH provincial meeting One training session Zululand One training session Ilembe One training session umzinyathi One training session DUT Mar-17 Five training sessions Zululand Total 47 DoH training sessions conducted 14 DoH meetings Ongoing quarterly meetings and ad hoc meetings were held with the DoH (provincial managers and various district managers/co-ordinators). In these meetings, Pap smear screening performance according to the quality indicators stipulated in the CCCP are discussed. Assistance in the form of quality training by the NHLS is ongoing to improve the quality of Pap smear screening in the province. Ad hoc meetings were also held with NGOs like Match and Beyond Zero. The NHLS also collaborated with the NGOs in conducting quality training sessions. It must be highlighted that the improvement in the quality of service delivery can be attributed directly to the strengthening of relationships between the NHLS and the various stakeholders. The improvement has also contributed significantly to a financial saving for the DoH. Notable Achievements The province received and completely tested the highest Pap smear uptake/coverage nationally i.e Pap smear slides tested The Pap smear adequacy rate improved by almost 4% from 56.1% to 60%, 3% above the national Pap smear average, due to focused training by the Regional Cytology Co-ordinator The Pap smear rejection rate decreased by 0.46% from 1.86% to 1.4% The Pap smear unsatisfactory rate decreased by 0.34% from 3.21% to 2.87% The province achieved the BSC TAT for gynaecological testing 99.79% within 5 weeks Both Greys and IALCH Cytology laboratories passed pre-sanas assessments. 130 National Health Laboratory Service

132 FREE STATE AND NORTH WEST Introduction The Free State and North West Region delivers laboratory services at various levels, from primary health clinics to tertiary level care to all districts within the two provinces. The region operates a wide specimen pickup and results delivery service to a large number of primary healthcare clinics in all the districts, thus assisting the Provincial DoH in providing health services to all communities. The diagnostic pathology services rendered for the region range from basic clinical pathology tests to highly specialised tests. These include chemical pathology, haematology, microbiology, virology, anatomical pathology (histopathology and cytopathology), genetics, and tissue typing. The region has three business units, namely Free State, Universitas Academic and North West. As at 31 March 2017, the region had 613 staff members. Performance per province is outlined below. North West Province The North West Business Unit is responsible for providing laboratory services to all the provincial districts through its 14 laboratories and depots. Tshepong and Rustenburg are provincial tertiary laboratories linked to the Wits and Sefako Makgatho Academic centres respectively. As a result, the two laboratories are the main referral centres in the business unit and the province, providing tests that are more complex. The distribution of the laboratories per district is indicated in Table F1. Area Manager Jone Mofokeng Table F1: Laboratories per district North West Province Bojanala Dr Kenneth Kaunda Ngaka Modiri Molema Ruth S Mompati Rustenburg Tshepong Mafikeng/Bophelong Joe Morolong Moses Kotane Potchefstroom Lehurutshe Taung Brits Wolmaransstad (depot) Gelukspan Ganyesa (depot) Swartruggens Thusong (depot) Total Diagnostic Services and New Developments As indicated, Tshepong and Rustenburg are the referral laboratories in the province, with Tshepong being the main centre. In addition to routine testing, Tshepong does LPA, TB Culture, CD4 and viral load testing. However, due to proximity and by association, the laboratories in Bojanala district refer their specialised tests to Sefako Makgatho Academic Unit. The North West Business Unit undertook tests in 11 laboratories in 2016/17. This reflects an increase of 4.4% year-on-year. In total, tests were referred for specialised testing. Two percent of manual tests were automated within the Business Unit in the reporting period in an effort to improve turnaround time. Volume changes are indicated in Table F2, in line with testing protocol changes. Table F2: Comparison of NPP volumes between 2015/16 and 2016/17 Test Volumes 2015/16 Volumes 2016/17 % Difference CD % HIV viral load % TB GeneXpert % Service Delivery The North West NHLS laboratories provide services to 19 hospitals, 331 clinics, 3 SANDF Area Health Military Units and 15 Correctional Centres. Four of the laboratories, Tshepong, Mafikeng, Potchefstroom and Rustenburg, operate a 24-hour service, and the remainder provide call-out services. All the routes to the facilities for transportation of specimens, delivery of consumables and hardcopy results are 100% covered by NHLS outsourced courier services. TATs were achieved and exceeded as indicated in Table F3. Annual Report 2016/17 131

133 Table F3: TAT performance for NPP tests 2016/2017 Test Target Actual CD4 (within 48 hours) 90% 95% HIV PCR (within 96 hours) 70% 87% HIV Viral load (within 96 hours) 65% 90% Cervical smear (within 5 weeks) 50% 76% GeneXpert (within 48 hours) 90% 98% TB Microscopy (within 48 hours) 90% 97% U&E (within 8 hours) 80% 92% LFT (within 8 hours) 80% 86% FBC (within 8 hours) 80% 93% Notable Achievements Tshepong Laboratory was recommended for SANAS accreditation and this was confirmed in August New Laboratories and Laboratory Upgrades Gelukspan Laboratory was renovated in a move by the NHLS towards state-of-the-art laboratories. Renovations addressed a number of challenges including health and safety matters to making the facilities appealing, user-friendly and ergonomically safe. Technical Skills and Staffing The North West business unit had 205 staff members as at the end of March A Quality Assurance Co-ordinator was appointed to support all laboratories in maintaining excellent total quality assurance and work towards attaining SANAS accreditation. The staff categories are indicated in Table F4. Table F4: Staff Complement Job Category Number of Staff Medical Technologists 36 Medical Technicians 48 Pathologists 0 Laboratory Managers and Supervisors 18 Laboratory Clerks 63 Other 40 Total 205 Three laboratories in the North West are accredited by the HPCSA for the training of medical technologists and technicians, namely Mafikeng, Tshepong and Rustenburg. Students who qualified were all absorbed into permanent positions in the various North West laboratories and other business units. In January 2017, nine new technologist interns were placed, three in each training laboratory. Training Training was conducted in line with the WSP and attendance is indicated in Table F5. Table F5: WSP Training 2016/17 Training Intervention Number of Employees Training Intervention Number of Employees Bacteriology Workshop (Gauteng South) 4 Inventory Management 19 Customer Service Training 14 ISO Systems and Internal Audit ISO Diversity in the Workplace 2 Laboratory Systems and Internal Audit Course ISO :2012 Effective Communication 1 Minutes-Taking Skills 2 Ethics 8 PLG/CD4 Training 3 Ethics in the Workplace 9 SDF and Skills Planning 10 Excel Level 1 2 Total: National Health Laboratory Service

134 Stakeholder Relations The SLA between the NHLS and the North West provincial DoH is in place and current. However, it is expected to be reviewed on an annual basis and updated accordingly, should it be necessary. The prescribed meetings were held during the period between the two parties, as was a scheduled meeting between the CEO of the NHLS and the HOD of the provincial DoH in October 2016 in line with stakeholder engagement. The NHLS was well represented at health commemoration ceremonies such as World AIDS Day and TB World Day and fully participated in relevant health campaigns, including Cervical Cancer campaigns during the month of September. The region operates the Mobile Laboratories attached to Rustenburg and Potchefstroom laboratories. These are used largely to reach the peri-mining communities for on the spot testing for TB, and during HIV/AIDS, Sexually Transmitted Diseases and TB (HAST) campaigns. Free State Province Free State Province is serviced by two NHLS Business Units, namely Universitas Academic Unit and the Free State Business Unit. Universitas services the academic hospital, including the national district hospital, while the Free State BU services the Pelonomi provincial tertiary hospital and the rest of the hospitals in the province. Both laboratories are associated with the University of Free State Medical School. Pelonomi and Universitas laboratories are the main referral centres, with the latter providing full pathology services, including paternity testing. The distribution of the laboratories per district is indicated in the Table F6. Table F6: FS Laboratories per district Free State Province Fezile Dabi Lejweleputswa Motheo Thabo Mofutsanyane Sasolburg Welkom (Bongani) Universitas Bethlehem Kroonstad National District Manapo Pelonomi Botshabelo Total Diagnostic Services and New Developments Universitas, as the tertiary laboratory in the province, does almost all the specialised tests except for CD4 testing which is done at Pelonomi Laboratory. However, CD4 testing is also done at the Welkom and Manapo regional laboratories. The total provincial statistics are in line with the Policy and are as indicated in Table F7. Table F7: Comparison of NPP volumes between 2015/16 and 2016/2017 Test Volumes 2015/16 Volumes 2016/17 % Difference Cytology % CD % HIV DNA PCR % HIV viral load % TB GeneXpert % Service Delivery The Free State Business Unit has seven laboratories that provide services to 225 primary health care facilities and 10 community health centres. These laboratories also service 15 district hospitals and 18 Correctional Services centres. Universitas Laboratory services and is responsible for the national district hospital as well as 3-Military hospital. Outsourced transport services are responsible for the collection of specimens and the delivery of results and consumables. The routes are covered 100% and collection is undertaken daily on weekdays. TATs were achieved and exceeded as indicated in Table F8. Annual Report 2016/17 133

135 Table F8: Percentage TAT performance for NPP tests 2016/2017 Test Target Actual CD4 (within 48 hours) 90% 93% HIV PCR (within 96 hours) 70% 75% HIV Viral load (within 96 hours) 65% 77% Cervical smear (within 5 weeks) 50% 98% GeneXpert (within 48 hours) 90% 99% TB Microscopy (within 48 hours) 90% 96% U&E (within 8 hours) 80% 96% LFT (within 8 hours) 80% 94% FBC (within 8 hours) 80% 91% Notable Achievements Kroonstad Laboratory received a 5-Star rating by SLIPTA and is one of only two laboratories in the country with this rating. Welkom and Pelonomi laboratories achieved 4-Star ratings. The three laboratories are ready to apply for SANAS accreditation. Universitas maintained its SANAS accreditation during the annual assessment for all but one department, Genetics. The department applied for voluntary suspension due to severe staff shortages. Both the Universitas and Pelonomi laboratories achieved a 100% pass rate for their intern medical technologists in this reporting period. New Laboratories and Laboratory Upgrades The planning and procurement process was initiated to upgrade the TB laboratory at Universitas and completion of the project is expected in the next financial year. Histopathology received a state-of-the-art automated histology block marking system during the last quarter of the financial year. Technical Skills and Staffing The Free State Province had 325 staff members as at the end of March Two Quality Assurance Co-ordinators were appointed to support all laboratories in maintaining excellent total quality assurance and work towards maintaining and attaining SANAS accreditation. The staff complement is indicated in Table F9. Table F9: Free State Staff Complement Job Category Number of Staff Free State BU Universitas BU Medical Technologists Medical Technicians Pathologists and HODs 0 15 Laboratory Managers and Supervisors Laboratory Clerks Other Total Universitas, Pelonomi, Welkom and Kroonstad laboratories are accredited by the HPCSA for the training of medical technicians and technologists. Universitas is also accredited for the training of pathologists (registrars) and scientists. Training Training was conducted in line with the WSP and attendance is indicated in Table F National Health Laboratory Service

136 Table F10: Free State WSP training 2016/17 Training Intervention Number of Employees Training Intervention Number of Employees Au480 Training 1 HIV Drug Resistance Workshop 2 Bacteriology Workshop (Gauteng South) 3 Inventory Management 3 Biosafety and Biosecurity Training 5 ISO Customer Service Training 14 PLG/CD4 Training 1 Diversity in the Workplace 18 SDF Course 1 Effective Communication 13 First Aid 10 Emotional Intelligence 20 Health and Safety Representative 16 Ethics 1 Fire Warden 10 Ethics in the Workplace 18 Finance for Non-Financial Managers 15 Excel Level 1 12 Total: 164 Stakeholder Relations The NHLS was well represented and supported health commemoration ceremonies such as World AIDS Day and TB World Day and fully participated in relevant health campaigns, including Cervical Cancer campaigns during the month of September. The province operates the Mobile Laboratory attached to Welkom Laboratory. This is used mainly to reach the peri-mining communities for on the spot testing of TB, and during HAST campaigns. The relationship with the University of the Free State is governed by an Umbrella Agreement and mandatory meetings and engagements such as the IAPC took place during the reporting period. An SLA between the NHLS and the Free State DoH is in place and current. The recently amended SLA was signed by the NHLS CEO, Ms Joyce Mogale, and the Free State DoH HOD, Dr David Motau in October The prescribed meetings were held during this period between the two parties. The relationship with the Free State DoH, the BU s major stakeholder, remained strong and positive, with BLUC meetings assisting in the management of the laboratory-clinician interface. Figure F1: Signing of the Free State SLA by Dr D Motau and Ms J Mogale Annual Report 2016/17 135

137 LIMPOPO Introduction The NHLS in Limpopo provides laboratory services across all five districts in all general hospitals. The service is provided on a 24-hour/seven days a week basis. This is achieved using multiple shifts, a call-out system, and 24-hour availability of the laboratory. Table L1 represents the Limpopo health districts and laboratories attached to each general hospital in the district. This model of service provision aims to bring the service closer to the patient. Table L1: NHLS laboratories in each of the five districts Area Manager Jacob Lebudi NHLS Business Unit Laboratory Name Health District Capricorn Business Unit Botlokwa Capricorn Helen Franz Capricorn Lebowakgomo Capricorn Mankweng Capricorn Polokwane Capricorn Seshego Capricorn WF Knobel Capricorn Zebediela Capricorn Sekhukhune-Waterberg Dilokong Sekhukhune Business Unit Mecklenburg Sekhukhune Jane Furse Sekhukhune St Ritas Sekhukhune Matlala Sekhukhune Groblersdal Sekhukhune Philadelphia Sekhukhune Bela Bela (Warmbaths) Waterberg Nylstroom Waterberg Potgietersrus Waterberg Mokopane Waterberg George Masebe Waterberg Witpoort Waterberg Ellisras Waterberg Thabazimbi Waterberg Vhembe Mopani Business Tshilidzini Vhembe Unit Elim Vhembe Donald Fraser Vhembe Malamulele Vhembe Siloam Vhembe Louis Trichardt Vhembe Musina Vhembe Letaba Mopani Giyani Mopani Namakgale Mopani Tzaneen Mopani Kgapane Mopani CN Phatudi Mopani Sekororo Mopani The NHLS in Limpopo underwent restructuring to ensure that it becomes more responsive to the needs of clients, and maintains a close and positive relationship with all stakeholders. To this end, the number of business units was increased from two to three to reduce the span of control for business managers. Furthermore, the NHLS had to respond to the development of the University of Limpopo s (UL) new Medical School by ensuring that the Polokwane Laboratory is gearing up to become an Academic Laboratory. The restructuring of the business units through the creation of the third unit, as well as the creation of the HOD and pathologist positions were some of the immediate steps taken to migrate towards academic status in support of the UL Medical School. 136 National Health Laboratory Service

138 The total staff complement increased from 262 in 2015/16 to 268 in 2016/17. Sixty percent of these are technical staff. Diagnostic Services and New Developments In total, the number of tests performed increased by 8 % from tests in 2015/16 to tests in 2016/17. These tests were performed in the network of 37 NHLS laboratories in the province, of which 30 are in the 30 district hospitals, five are regional laboratories and two are provincial tertiary laboratories in the same category as level of care hospitals. Continued support was given to the National Priority Programmes, with test volumes achieved as reflected in Table L2. Table L2: NPP test volumes Test Type Volumes 2015/16 Volumes 2016/17 % Difference CD % HIV viral load % Cervical cancer screening % TB GeneXpert % Viral load tests show an increase of 45% when compared to 2015/16. This increase was expected due to a change in the national guidelines for HIV management and for the same reason CD4 count tests declined in the period. The following new developments were achieved as part of service delivery improvement initiatives: Mankweng Laboratory A new analyser was installed in the Chemical Pathology Laboratory, resulting in improved service delivery to deal with the increasing and changing demands of clients. Notably, internal quality control and total turnaround time for the Chemical Pathology tests improved. The laboratory was able to increase the scope of tests offered to match the level of service provided by the hospital as a tertiary level service. The new tests offered through this analyser are: Hepatitis studies HIV Enzyme-Linked Immunosorbent Assay (ELISA) Iron profiles Thyroid function tests Beta-Human Chorionic Gonadotropin (BhCG) Furthermore, the laboratory was successful in validating the Rapid Plasma Reagin (RPR) test, which is a labour intensive manual test that often results in the need for employees to work extended hours. Automation of this test will reduce overtime and improve the quality and TAT of the results. Figure L1: New Cobas 6000 in the Mankweng Laboratory Annual Report 2016/17 137

139 Polokwane Laboratory In this Provincial Tertiary Laboratory, service delivery in haematology was improved through the installation of a second haematology analyser. This enabled the provision of uninterrupted service and better TATs to the hospital and 97 clinics that refer to the laboratory. Furthermore, the laboratory introduced Factor VIII and Factor IX testing, which brought much-needed service improvement to haemophilia patients in the clinic though improved TAT of results. Figure L2: Polokwane Laboratory s haematology analyser Figure L3: Analyser testing for haemophilia Letaba Laboratory At this regional laboratory, a new chemistry analyser was installed, resulting in the following improvements: Improved efficiencies Improved TAT The ability to introduction new tests e.g. RPR, Prostate Specific Antigen test (PSA), lipids studies and calcium, magnesium and phosphate. Tshilidzini Laboratory At Tshilidzini Regional Laboratory, a complete refresh of analysers was done to replace aged equipment that often failed, leading to customer complaints. New equipment included a new chemistry analyser; Cobas Integra and Cobas c411 for immunology; as well as a Beckman Coulter Aquios for CD4 testing. This ensured that TAT and the quality of associated tests improved leading to improved client satisfaction. 138 National Health Laboratory Service

140 Figure L4: Cobas c411 at Tshilidzini Cryptococcal Antigen Reflex Test In response to the NPP protocol on the management of HIV patients with CD4 counts of less than 100 cells/µl, Tshilidzini, Polokwane, Letaba, and Mokopane laboratories were prepared and trained to perform the cryptococcal antigen reflex test. Service Delivery and Coverage As reported above, all general hospitals in Limpopo Province have an NHLS laboratory on-site that provides a 24-hour laboratory service. The primary healthcare facilities are covered through a daily specimen collection network that moves from clinic to laboratory and from laboratory to laboratory for specimen referral, according to the upward referral model. This courier service extends beyond the Limpopo Province to ensure that specimens referred to laboratories in the national central hospitals are transported on time. The courier service also caters for emergency specimen deliveries to the NICD and other specialist laboratories in the event of outbreaks or the suspicion of highly infectious diseases. Table L3: Clinics per district where daily specimen collection service is provided District Number of clinics serviced daily Vhembe 128 Mopani 107 Capricorn 97 Sekhukhune 102 Waterberg 83 Total clinics 517 Over kilometres are travelled per day which equates to just over 4 million kilometres travelled for specimen collection in about 27 routes in the province per year. Turnaround Times All Business Units met all TAT targets for all tests except the CD4 count in the Capricorn Business Unit. The unit was affected by constant analyser breakdowns, which were ultimately resolved through persistent interaction with the supplier of the analyser. It should be noted that the total number of tests done in the Capricorn Business Unit is the highest in the province. Over 100 clinics and 21 hospitals refer their CD4 tests to this business unit. Annual Report 2016/17 139

141 Table L4: TATs per business unit Business Unit Test Group Test Method Test Count Volume within Target TAT % Within TAT ARV CD % VL % LFT % CHEM U&E % Limpopo Capricorn CYTO Cervical smear % HAEM FBC % TB GeneXpert % Microscopy % ARV CD % LFT % CHEM U&E % Limpopo Sekhukhune - Waterberg HAEM FBC % TB GeneXpert % Microscopy % ARV CD % LFT % CHEM U&E % Limpopo Vhembe - Mopani HAEM FBC % TB GeneXpert % Microscopy % Table L5: Target TATs Test Method Target % CD4 85% VL 65% LFT 80% U&E 80% Cervical smear 50% FBC 80% GeneXpert 90% Microscopy 90% Notable Achievements Accreditation South African National Accreditation System (SANAS) Mankweng Provincial Tertiary Laboratory maintained full accreditation status. All tests offered in the laboratory are fully SANAS accredited. Stepwise Laboratory Quality Improvement Process towards Accreditation (SLIPTA) Cohort 3 SLIPTA audits were conducted in the laboratories using the WHO checklist 2015 version with the aim of ensuring continuous improvement of the QMS. Table L6: Results of the SLIPTA follow-up audits Laboratory Previous Star rating Audit period Score Percentage Star rating Polokwane 2 in July % 3 Letaba 3 in July % 4 Lebowakgomo 3 in November % 3 Tshilidzini 2 in November % 3 Strengthening Laboratory Management Towards Accreditation (SLMTA) SLMTA is a mentoring programme aimed at improving laboratory staff QMS skills to prepare effectively for SANAS accreditation. The programme consists of a series of three workshops and laboratory visits by the mentors after every workshop. The programme runs for 140 National Health Laboratory Service

142 a period of 18 months. The following laboratories are enrolled in the SLMTA Programme which began in October 2016: Polokwane with four participants and Letaba with six participants. Other Achievements The appointment of Dr Lekalakala as Head of the Microbiology Department in Polokwane this laboratory is the only laboratory performing microbiology tests (such as TB Culture, 1 st line TB drug susceptibility tests, LPA etc.) in the province, and is the referral site for all other laboratories The appointment of the Provincial Cytology Co-ordinator who applies specialist technical expertise to ensure implementation of policy on the cervical screening programme, and ensures that NHLS and DoH programme-specific milestones and performance matrices are met Marked improvement in viral load test TAT through the installation of a high throughput analyser in early 2016 TAT improved from 32% of tests results within 96 hours to 81% of total test results within 96 hours No incidents of occupational disease (Tuberculosis) were reported in the financial year Health and safety compliance with NHLS policies and procedures improved, which may be attributed to commitment by the Area Manager, business unit managers and laboratory managers towards compliance with OHS legislations as well as the active support and guidance provided by the regional Occupational Health and Safety Team The NHLS Laboratory Manager at Donald Fraser Hospital was awarded a certificate for Innovation for the Public Service for his contribution to the hospital Health and Safety Committee. New Laboratories and Laboratory Upgrades Upgrades were undertaken in the following laboratories: Tzaneen Laboratory General maintenance to ensure compliance with Occupational Health and Safety requirements and improve working conditions in the laboratory Mecklenburg Laboratory Expansion of the laboratory workspace to improve workflow and working conditions and revamp of resting and ablution facilities to improve staff morale Giyani Laboratory Upgrade to create a call room to enable staff to respond quicker to after-hour service calls Malamulele Laboratory Upgrade to create a call room to enable staff to respond quicker to after-hour service calls and installation of blinds to ensure optimal working environment in the laboratory Kgapane Laboratory Repair to structural cracks in the building and repainting of the entire laboratory. Technical Skills and Staffing Subsequent to the creation and filling of 10 laboratory supervisor posts, a combined induction session was organised. This led to improved teamwork, uniformity and a clear understanding of their roles, not only as technical staff, but also as supervisors in their respective laboratories. Skills gaps were then identified and the required courses for the supervisors were added to the WSP. Thus far, they have attended the emotional intelligence course, which is essential in their roles in managing interpersonal matters. The ultimate goal is to have fully equipped, competent and motivated staff in the region with the first targeted group being the supervisors/managers. To ensure that there is proper oversight and segregation of duties in the asset stores, well as to ensure compliance with internal policy prescripts, a position for a procurement officer was created and filled. The asset store in Polokwane now operates within policy guidelines. A Cytology Co-ordinator was appointed to ensure the implementation of policy on the cervical screening programme and oversee appropriate co-ordination between the NHLS and the DoH in this regard. Table L7: Technical/core staff 31 March 2017 Job Title Number Laboratory Manager 19 Laboratory Supervisor 14 Medical Technologist 38 Medical Technician 89 HOD Microbiology 1 Pathologist 1 Total 162 Annual Report 2016/17 141

143 Skills Development and Training In line with the Regional WSP, a number of skills courses were implemented and attended by a total of 247 staff members. Many of these courses were in response to the skills gap identified during performance management as well as improving quality, service delivery and compliance with legislation. Table L8: courses were offered and attended Intervention Peripheral Blood Morphology QMS Parasitology Basic Fire Training OSH Act First Aid OSH Act Telephone Etiquette Customer Service Emotional Intelligence Foundations of Laboratory Leadership and Management Lean Laboratory Management Ethics Course Description Effective and accurate analysis and interpretation of blood smears The course covers all aspects of the QMS and provides an overview of the individual elements that constitute a QMS This course provides practical laboratory training in the diagnosis of common stool and urine parasites Identification and prevention of fire hazards and the effective use of firefighting equipment Assessment of an emergency medical situation and providing basic life support and basic first aid in order to stabilise patients prior to transfer to emergency services Telephone communication skills for internal and external customers Skills to enhance service delivery by understanding customer needs Self-awareness skills and enhancement of inter- and extra-personal relationships The course offers basic laboratory management tools The course offers skills to achieve maximum and optimal outputs with minimal inputs The course offers professional ethics, conduct and case studies Other skills development interventions, which were geared at improving the technical skills of employees, were held across the province, including: Training on the lateral flow assay for testing of cryptococcal antigen in laboratories performing CD4 testing Enterprise content management for electronic filing of laboratory request forms, attended by laboratory managers Advanced TB GeneXpert, attended by medical technologists and technicians Measurement of uncertainty, to comply with ISO 15189, attended by laboratory managers and medical technologists Phlebotomy training to improve the quality of specimens collected and reduce the rate of rejection, attended by phlebotomists Training on newly installed analysers e.g. Cobas Integra, Cobas 6000 and Cobas c411 Refresher course on DXc/DXi, CS200i and Advia 120 at the Polokwane Laboratory. Continuing Professional Development The Regional Office of the Learning Academy is an HPCSA Accredited Service Provider for CPD. Polokwane Laboratory and the Quality Department applied for an activity number and offered activities that earned participants continuing educational units that allowed them to be compliant with legislation. Stakeholder Relations A variety of stakeholder engagement initiatives were undertaken with a view to understanding and responding to customer needs, information sharing and relationship strengthening. Quarterly district SLA Review meetings were held. In attendance were the senior clinical managers of hospitals, finance managers as well as the provincial laboratory co-ordinator. The meetings include: A report by the NHLS on services delivered during the period under review A report by the department on the perceived quality, efficiency, effectiveness and economy of the laboratory service delivery A review of the timeliness of payments made by the department to the NHLS, qualification for any discounts or levying of penalties (as the case may be) in terms of the PFMA where applicable and the details mutually agreed. 142 National Health Laboratory Service

144 The Area Manager attended the National World Aids Day Commemoration that was held in Lephalale as well as the provincial TB Day commemoration, held in Vhembe district. The NHLS pathologist in the province engaged in a number of stakeholder engagements (Table L9). Table L9: Stakeholder engagements at local facilities Hospital Audience/Clients Objective/Topic Letaba Hospital Doctors and nurses Neonatal Quarterly Review Meeting George Masebe Hospital Local CPD accredited Doctors and nurses and TB diagnosis and management laboratory personnel Mankweng Doctors and nurses Antimicrobial resistance in the unit Warmbaths Hospital Local CPD accredited Doctors and nurses and laboratory personnel Approach to management and control of typhoid fever outbreak Provincial outbreak response team Outbreak response team all district Epidemic preparedness and response training workshop Voortrekker Hospital Clinicians Malaria overview Mankweng Hospital Internal medicine Clinical cases Morphology Province Provincial committee Pharmacy and therapeutic committee monthly meetings Province Clinicians Electronic gate-keeping (EGK) Clinician Consultation Workshop on rational laboratory usage and the proposed rules for electronic gatekeeping Training of Stakeholders Mopani District facilities were trained in the proper collection of dried blood spots for HIV PCR Testing. Training on correct usage of blood collection materials was conducted in collaboration with blood collection materials supplier. Training on collection of Pap smears and the use of the cytology consumables was done to improve the quality of smears. In addition, reports and statistics on the cervical cancer programme were shared with programme managers on monthly basis. All five districts in the province were trained. Engagement with the University of Limpopo Monthly school management meeting UL Lecturing to Medical students UL Co-ordinating micro component of the module Essentials of diseases UL MBChB curriculum review for HPCSA submission. Engagement with Non-Governmental Organisations A meeting was held with the Anova Health Clinical Advisor on the prevention of mother-to-child transmission (PMTCT) to discuss the causes of rejections of HIV DNA PCR in the Mopani and Vhembe districts. The meeting resolved to re-train healthcare workers on the proper process and techniques of sample collection for Dried Blood Spot (DBS) tests for HIV in babies younger than 18 months. Right to Care (Cervical Cancer Programme) held a pilot engagement on cervical brushes in an effort to improve collection of transformation zone cells on Pap smears. The NHLS was invited to give induction and orientation on the collection material and filling in of forms to healthcare workers associated with the Phelophepa Train (Transnet), in Polokwane. Conclusion The NHLS in Limpopo maintained good performance throughout the reporting period. The turnaround times for most measured tests and NPP tests were achieved. Exceptions were noted and strategies implemented to address shortcomings. Engagement with, and training of stakeholders at different levels and forums was achieved to improve customer relations and service delivery. Employees attended skills courses to maintain high standards of performance in the execution of their duties and improve the quality of results. Annual Report 2016/17 143

145 MPUMALANGA Introduction The NHLS in Mpumalanga provides a laboratory service to all general and specialised hospitals in all three districts of the province. The laboratory service is provided on a 24-hour/seven-day a week basis. This is achieved through a combination of different shifts and a call-out system with 24-hour continuous availability of the laboratory. The service is provided through 21 NHLS laboratories spread throughout the province. This model of service provision aims to bring the service, as far as possible, closer to the patient. Plans are under way to establish depots in all hospitals without an NHLS laboratory on site. This will ensure accountability in the handling of laboratory test requests and the results associated with the requests. Area Manager Jacob Lebudi The NHLS strategy to enable accessibility of services to its clients led to the splitting of the province into two business units. The Gert Sibande-Nkangala Business Unit offers laboratory services to about 10 general hospitals, including two sites that are currently operating as depots, 161 primary/ community healthcare facilities and three Correctional Services sites within the Gert Sibande and Nkangala Health Districts. The Ehlanzeni Business Unit offers a service through nine NHLS laboratories spread throughout five sub-districts, namely Mbombela, Nkomazi, Umjindi, Bushbuckridge and Thaba Chweu. The nine laboratories are made up of one provincial tertiary laboratory, two regional laboratories and six district laboratories. All hospitals in the Ehlanzeni Business Unit have laboratories, with the exception of two district hospitals, Matibidi and Sabie. Two laboratories, Rob Ferreira and Themba, render a 24-hour service; one laboratory, Lydenburg, operates an 8-hour service; and the remaining six laboratories operate an 8-hour service together with a call-out service. There are plans for Matibidi Hospital to have a depot in 2017/18 and provide a blood gas analyser for Sabie Hospital. Table M1: NHLS laboratories in the province per each of the three health districts NHLS Business Unit Laboratory Name Health District Ehlanzeni Rob Ferreira Ehlanzeni Themba Ehlanzeni Mapulaneng Ehlanzeni Matikwana Ehlanzeni Tintswalo Ehlanzeni Shongwe Ehlanzeni Tonga Ehlanzeni Lydenburg Ehlanzeni Gert Sibande- Nkangala Witbank Nkangala Delmas Nkangala Middleburg Nkangala Kwa Mhlanga Nkangala Mmametlhake Nkangala Piet Retief Gert Sibande Evander Gert Sibande Ermelo Gert Sibande Standerton Gert Sibande Embhuleni Gert Sibande Bethal Gert Sibande Volksrust Gert Sibande 144 National Health Laboratory Service

146 Diagnostic Services and New Developments The total number of tests performed by the NHLS in Mpumalanga increased by approximately 5%, from tests in 2015/16 to Continued support was given to the NPP, with test volumes for the programmes as reflected in Table M2. Table M2: Test volumes per test type Test Type Volume 2015/16 Volume 2016/17 % Difference CD % HIV viral load % Cervical cancer screening % TB GeneXpert % Viral load testing shows an increase of 16% when compared to 2015/16, while the CD4 count tests declined. These changes were expected due to the change in the national guidelines for HIV management. As part of a new development, all Rapid Plasma Reagin (RPR) test requests from clinics will be referred to Rob Ferreira Laboratory as of 1 March 2017, since the automated Roche Syphilis test has been validated there. This will reduce the number of manual tests done in the business unit, as well as the manual labour and ultimately the cost of overtime hours. Ermelo Laboratory is validating the automated RPR test with the aim of rationalising the test in the new financial year for Gert Sibande-Nkangala Business Unit. The cryptococcal antigen (CrAg) test, as a reflex test for CD4 results below 100 cells per cubic millimetre, has been introduced in all laboratories performing CD4 counts on site. These laboratories are, Rob Ferreira, Tintswalo, Shongwe, Ermelo and Witbank. The detection of CrAg will help in the early diagnosis of cryptococcal infections in HIV-infected patients who are on ARV treatment, and prevent deaths from cryptococcal infections. A new, fully automated haematology analyser was installed at Rob Ferreira Laboratory, to replace the old analyser that was unable to cope with the volumes required. This resulted in better service delivery to the hospital and Primary Health Care facilities referring to this laboratory, especially the antenatal clinic services. The minimum sample volume is 200ul, which caters very well for most of the paediatric samples received from the hospital and the clinics around. Figure M1: Beckman Coulter LH750 haematology analyser at Rob Ferreira All medium laboratories providing CD4 count testing services were equipped with new analysers to replace the old and often problematic ones. The following laboratories received new analysers, namely Shongwe, Witbank and Tintswalo. Annual Report 2016/17 145

147 Figure M2: The new Beckman Coulter Aquios CD4 Analyser at Shongwe Laboratory Service Delivery and Coverage The NHLS Mpumalanga ensured accessibility to pathology services by maintaining 100% daily coverage of primary/community healthcare facilities through its specimen collection service. Some small district hospitals without on-site NHLS services are covered through specimen collection twice daily. Matibidi Hospital has been identified as a site for a depot and equipment and human resources have been budgeted for and approved. Volksrust and Bethal are the two sites that are currently operating as depots within the two hospitals. Both sites have been identified for potential migration from depot to fully functional laboratories in order to perform routine testing in the new financial period. The appropriate equipment and human resources have been budgeted for and approved. This will increase the NHLS footprint in the Gert Sibande-Nkangala Business Unit and improve service delivery and turnaround times, which will result to improved patient care. A sophisticated logistics model is maintained to ensure clinic-to-laboratory specimen collection, laboratory-to-laboratory specimen referral, and out of province specimen referral each weekday. This includes emergency courier services as and when needed to respond to events such as disease outbreaks or highly infectious disease incidents, which require testing at the National Laboratories of the NHLS. Through this courier network, NHLS Mpumalanga courier service travels over 2.5 million kilometres per year. Table M3: Number of clinics per district where daily specimen collection is provided District Number of Clinics Serviced Daily Ehlanzeni 121 Gert Sibande 76 Nkangala 88 Total Clinics 285 Turnaround Times Table M4: Test turnaround times for the tests done in each business unit Business Unit Test Group Test Method Target Test Count Volume within Target TAT % Within TAT Ehlanzeni CD4 85% % ARV VL 65% % Chem LFT 80% % U&E 80% % Haem FBC 80% % TB GeneXpert 90% % Microscopy 90% % Gert Sibande- Nkangala ARV CD4 85% % Chem LFT 80% % U&E 80% % Haem FBC 80% % TB GeneXpert 90% % Microscopy 90% % 146 National Health Laboratory Service

148 It is noted from Table M4 that all business units met all TAT targets for all tests except LFT in Gert Sibande- Nkangala Business Unit. The main cause of this was staff shortages, which led to some shifts not being fully catered for in terms of the technologists needed to issue final results. This matter is receiving attention and interventions like off-site review have already been implemented. The recruitment of qualified technologists in this business unit is ongoing. Notable Achievements Accreditation South African National Accreditation System (SANAS) Witbank Laboratory in the Gert Sibande-Nkangala Business Unit maintained its SANAS accreditation. Ermelo, also in the Gert Sibande- Nkangala Business Unit, was recognised for SANAS Accreditation in October This laboratory was in SLIPTA Cohort 1, which aided its SANAS achievement. All the tests performed in the laboratory were accredited, including TB Culture, TB PCR and GeneXpert. This makes Ermelo Laboratory the third regional laboratory in the NHLS to attain full scope SANAS accreditation. Stepwise Laboratory Quality Improvement Process towards Accreditation (SLIPTA) Rob Ferreira Laboratory participated in a Cohort 3 SLIPTA audit. This was conducted using the WHO checklist 2015 version, with the aim of ensuring continuous improvement of QMS. This was a follow- up audit. Table M5: Outcome of the Rob Ferreira Laboratory audit Previous Star Rating Current Audit Period Score Percentage Star rating 2 in August % 3 in 2016 This improvement in laboratory performance augurs well for future SANAS Accreditation. Strengthening Laboratory Management towards Accreditation (SLMTA) SLMTA is a mentoring programme to improve laboratory staff skills on the Quality Management System, thus enabling effective preparation towards SANAS accreditation. The programme consists of a series of three workshops and laboratory visits by the mentors after every workshop. The programme runs for a period of 18 months. Rob Ferreira Laboratory was enrolled in the SLMTA Programme, which began in October 2016 with four participants. Rob Ferreira Laboratory underwent a pre-sanas audit from 7 8 March The results of the audit suggest that the laboratory is almost ready for its SANAS audit. Other Achievements The appointment of the Provincial Cytology Co-ordinator who applies specialist technical expertise to ensure implementation of policy on the cervical screening programme and ensure that the NHLS and DoH programme-specific milestones and performance matrices are met Marked improvement in viral load TAT, through the introduction of a high throughput analyser in early 2016 TAT improved from 32% of test results within 96 hours to 95.5% of total test results within 96 hours No incidents of occupational disease (Tuberculosis) were reported in the financial year Health and safety compliance with NHLS policies and procedures improved, which may be attributed to commitment by the Area Manager, business unit managers and laboratory managers towards compliance with OHS legislation, as well as the active support and guidance provided by the regional Occupational Health and Safety team. New Laboratories and Laboratory Upgrades Most of the Laboratories in Mpumalanga meet the required safety standards, thus not many upgrades were done in the reporting year. Delmas Laboratory A prefabricated extension was provided to improve laboratory space and workflow, create a better environment for testing patient samples, and improve working conditions for employees. Annual Report 2016/17 147

149 Figure M3: Delmas pre-fabricated laboratory Themba Laboratory The laboratory was renovated to improve accessibility for clients. Wall cabinets were provided for storage and internal painting was completed. Technical Skills and Staffing The total staff complement for the NHLS Mpumalanga Province was 186 as at 31 March This reflects a 3% drop in numbers when compared to the same period in 2015/16 (192 staff members). Table M6: Core staff makes up 46% of the staff complement Job Title Number Laboratory Manager 17 Laboratory Supervisor 5 Medical Technologist 24 Medical Technician 40 Pathologist 0 Total 86 Three positions are vacant in the Gert Sibande-Nkangala Business Unit, and have proved difficult to fill. Ehlanzeni Business Unit managed to fill the vacant supervisor post at Lydenburg Laboratory, which had been vacant for a long time. Thus all laboratories have managers to fulfil leadership roles and improve customer, financial, business process, and people and knowledge management interfaces. An induction session was organised for all laboratory managers and supervisors appointed in the year. This led to improved teamwork, uniformity and a clear understanding of roles, not only as technical staff but as supervisors in their respective laboratories. Subsequently, skills gaps were identified and the required courses were included in the WSP. Thus far, they have attended the emotional intelligence course, which is essential in their roles in managing interpersonal matters. The ultimate goal is to have fully equipped, competent and motivated staff in the region. Skills Development and Training In line with the Regional WSP, a number of skills courses were presented with 145 staff members attending. Many of these courses were offered in response to the skills gaps identified during performance management evaluations and others were geared towards improving quality, service delivery and compliance with legislation. Table M7: Courses attended by staff members Intervention Peripheral Blood Morphology QMS Parasitology Basic Fire Training OSH Act Course Description Effective and accurate analysis and interpretation of blood smears The course covers all aspects of QMS and provides an overview of the individual elements that constitute a QMS This course provides practical laboratory training in the diagnosis of common stool and urine parasites Identification and prevention of fire hazards and the effective use of firefighting equipment 148 National Health Laboratory Service

150 Intervention First Aid OSH Act Telephone Etiquette Customer Service Emotional Intelligence Foundations of Laboratory Leadership and Management Lean Laboratory Management Ethics Course Description Assessment of an emergency medical situation and provision of basic Life support and basic first aid in order to stabilise patients prior to transfer to emergency services Telephone communication skills for internal and external customers Skills to enhance service delivery by understanding customer needs Self-awareness skills and enhancement of inter- and extra-personal relationships The course offers basic laboratory management tools The course offers skills to achieve maximum and optimal outputs with minimal inputs The course offers professional ethics, conduct and case studies Other skills development interventions, geared to improving the technical skills of employees, were held across the province. These included: Training on the lateral flow assay for testing of cryptococcal antigen in laboratories performing CD4 testing Enterprise content management for electronic filing of laboratory request forms attended by laboratory managers Training on newly installed analysers e.g. Beckman Coulter Aquios and the Beckman Coulter LH500 Thistle EQA interpretation SMS Printer management training to ensure uninterrupted delivery of priority programmed results. Stakeholder Relations Stakeholder relations in Mpumalanga are continuously managed through engagements at different levels and through different programmes. SLA review meetings were held on a quarterly basis, where the following were addressed: Services delivered during the period under review Perceived quality, efficiency, effectiveness and economy of laboratory service delivery Timeliness of payments made by the department to the NHLS Cost of utilities arising from municipality services Other management and administrative matters as deemed necessary. In addition, engagements were held with the following stakeholders: Mpumalanga Department of Health Healthcare workers were trained on how to operate and troubleshoot SMS Printers to ensure uninterrupted service delivery and the improvement of TATs for NPP tests Training on the collection of Pap smears and the use of the cytology consumables was done to improve the quality of smears, and reports and statistics on the cervical cancer programme are shared with programme managers on monthly basis Thusano training for CEOs and clinical managers continues to be rolled out in the Ehlanzeni Business Unit so that the costs in hospitals can be managed A provincial EGK consultation workshop for clinicians was held at Themba Hospital to sensitise clinicians to rational laboratory usage Participation in provincial and district World TB Day as well as World AIDS day. Non-Governmental Organisations Right to Care on service delivery issues in partnership with the Mpumalanga Department of Health. Conclusion During the reporting period, the NHLS in Mpumalanga was able to fulfil its mandate in ensuring that quality service is timeously delivered to its clients. This was achieved through dedicated and competent employees, the acquisition of instrument platforms that are advanced in technology, an efficiently running courier service, and regular communication with the clients in order to address their needs. Annual Report 2016/17 149

151 Performance Information by Subsidiary SOUTH AFRICAN VACCINE PRODUCERS (SAVP) Director Megan Saffer The South African Vaccine Producers (SAVP) proudly continues to provide the country with products of national significance. The total number of antivenom units sold during the financial year was , an increase of 4.5% since the previous year. Scorpion antivenom sales showed a marked increase to units, an increase of 80% since the previous year. Director Megan Saffer The demand for antivenom is cyclical and is dependent on seasonal and environmental conditions. The breakdown of sales is 28% to the Department of Health, 44% to the South African private market and the balance to export. There has been uncertainty for the Médecins Sans Frontiers (MSF) regarding antivenom availability, due to the cessation of the production of Fav Afrique antivenom by Sanofi. The SAVP has reassured MSF that it can continue to assist and satisfy their requirements. In addition to supplying antivenom for human envenomation, the SAVP also supplies to the veterinary market. In the financial year, lifesaving antivenom was given to two anti-poaching dogs, one of which was bitten by a Puff Adder and the other by a Boomslang. Both dogs recovered fully following antivenom treatment. These dogs, both Belgian Malinois, undergo extensive training over several years. Each trained dog, once ready for field duty, has an approximate value of R In addition, the life of a Jack Russel, which was bitten by a Boomslang on two separate occasions, was saved twice in the same month. Stables SAVP Bags of horse blood totalling x 500 ml, were supplied by the SAVP, of which 40% was for use by the National Health Laboratory Service (NHLS) laboratories, and the balance for use by private laboratories for diagnostic purposes. A total of 189 x 500 ml bags of sheep blood was also supplied, of which 7 % was supplied to the NHLS laboratories and the balance to private laboratories. Small Animals The SAVP continues to supply various universities with animals; including the University of the Witwatersrand (Wits), the University of KwaZulu-Natal, Sefako Makgatho Health Sciences University, University of the Free State, University of Johannesburg, University of Cape Town, University of Pretoria, North West University, Nelson Mandela Metropolitan University and Walter Sisulu University. The SAVP also supplies large quantities of guinea pigs to both the National Control Laboratories in Bloemfontein, for safety testing of drugs being imported into South Africa, as well as to the University of Pretoria s Retrasol, which provides tuberculosis research in Witbank. In the 2016/17 financial year, the SAVP continued to export animals twice a month to Namibia. Animal Ethics Committee No animal ethics issues were discussed by the NHLS Animal Ethics Committee in the reporting period. 150 National Health Laboratory Service

152 Performance Information by Institute NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES In this age of precision medicine, the availability of robust data is pivotal to making informed decisions to inform public health policy. The National Institute for Communicable Diseases (NICD) has served, and continues to serve as a publicly-trusted source of data on communicable diseases, both during outbreak threats and as part of its routine surveillance of priority infectious diseases, which affect South Africans. In 2016/17, the NICD further expanded on its mandate of setting up a robust surveillance system on public-health priority diseases, following on from a mandate by the Department of Health (DoH) on re-engineering the South African Notifiable Medical Conditions notification system. This system, whose transition from an outdated paper-based system to a stateof-art electronic system was piloted during 2016, will be launched in July 2017 across South Africa. This re-engineered system will provide the backbone with which to monitor and timeously respond to infectious disease outbreaks, as well as serve as a barometer in tracking the progress being made in the prevention of morbidity and mortality associated with notifiable illnesses. Executive Director Prof. Shabir A Madhi The burden and threat of infectious diseases and progress made in reducing the impact of these diseases in South Africa, were continuously highlighted by ongoing laboratory-based and active field surveillance, undertaken by the NICD during 2016/17. Included among these was the support given by the NICD Outbreak Response Unit, augmented by the Centre for Respiratory and Meningitis Diseases, in assisting the Kwazulu-Natal DoH to investigate and control an outbreak of diphtheria. The NICD was also at the forefront in using Whole Genome Sequencing, to show that an increase in numbers of Salmonella enterica serotype Typhi, identified in Gauteng Province in 2016, was related to a contemporaneous outbreak of typhoid fever in Zimbabwe. This emphasises the need for communicable disease surveillance in South Africa to be linked to similar surveillance in neighbouring countries. The inter-relationship of South Africa with its neighbours is well characterised by the finding that the majority of malaria cases in South Africa are imported from neighbouring countries. However, in 2016/17 South Africa also noted an increase in local transmission and acquisition of malaria, possibly due to abnormally high rainfall patterns in Mpumalanga. This poses a setback in terms of South Africa s target to eliminate malaria in the near future. The NICD remains engaged with the DoH on surveillance and control of the malaria vector, including testing of new compounds to address the challenge of insecticide resistance in malaria vector mosquitoes, which is critical in terms of disease epidemiology and vector control. On the antimicrobial resistance (AMR) front, which is increasingly being recognised as a global threat to public health, drug resistance was highlighted at the United Nations General Assembly as a global priority. To address the threat, the NICD established a national surveillance data dashboard to identify and support efforts at combatting morbidity and mortality resulting from AMR bacterial disease. In acknowledgement of its expertise, the NICD became a Collaborating Centre for AMR for the WHO-AFRO region in In terms of antibiotic resistance, the Centre for Tuberculosis (CTB) at the NICD released results of the largest ever study on the prevalence of tuberculosis (TB) drug resistance, globally. This study identified the emergence of rifampicin mono-resistant TB, which has occurred primarily among new cases, resulting in an almost doubling of the prevalence of rifampicin resistant TB from 1 8 % (95%CI: 1 3%-2 3%) in 2001/02 to 3 4% (95%CI: 2 5%-4 3%) in the latest survey of Additionally, high levels of resistance to second line agents among multidrug-resistant-tb (MDR-TB) cases were identified. These findings supported two key policy shifts, implemented by the National TB Programme. The first was the rollout of reflex second-line drug susceptibility testing, using the WHO-endorsed line probe assay for detection of rifampicin-resistant TB cases for early initiation of treatment, and the second was the introduction of a shortened treatment regimen for MDR-TB patients. To better assist the DoH in dealing with this most important public health threat in South Africa, the NICD launched an online TB Surveillance Dashboard that is now accessible at This was accompanied by a surveillance report on microbiologically confirmed pulmonary TB (mptb) for the period 2004 to Annual Report 2016/17 151

153 2015, which shows consistent annual declines in mptb since The report has also identified geospatial hotspots to sub-district level and highlights considerable heterogeneity in prevalence, requiring a targeted response. In addition to supporting the DoH in its TB control programme, the NICD s Centre for HIV and Sexually Transmitted Infections (STIs), is a partner to the DoH National Strategic Plan for HIV, STIs and TB. The report on the sentinel surveillance of sexually transmitted infection syndrome aetiologies and human papillomavirus (HPV) genotypes among patients attending public health facilities in South Africa ( ), provided important aetiological data for STI management, as well as baseline HPV genotype prevalence data for monitoring the effects of HPV vaccine implementation. These data have been used to inform policy formulation in STI syndromic management guidelines (Standard Treatment Guidelines and Essential Medicines List for both primary and adult hospital levels of care). For monitoring HIV infections in the paediatric setting, the paediatric HIV viral load and CD4 dashboard and paediatric HIV VL and CD4 results for action reports were launched in November The DoH and its partners are now able to monitor the HIV programme nationally to improve patient outcomes. The antiretroviral (ARV) treatment programme in South Africa is the largest worldwide, with 3.2 million persons on treatment. Monitoring for drug resistance to inform treatment policy is an important activity for the CTB, which has established a clinicbased surveillance system for HIV drug-resistance among persons initiating antiretroviral therapy (ART) in five provinces that showed 13% resistance to ARTs used in first-line regimens. The drug resistance level amongst participants with prior antiretroviral (ARV) exposure was 38%. Effective and continued monitoring of drug resistance is thus crucial. The CTB remains involved in two key HIV prevention studies viz., the HVTN 702, the first HIV vaccine efficacy trial in seven years, and the HVTN 703 or antibody-mediated prevention (AMP) study; providing much of the specialised laboratory immunology services required for these studies. Also on the HIV front, the NICD led reflex screening and testing for Cryptococcus jirovecii in immunocompromised HIVinfected people; and is currently leading an evaluation of the effectiveness of this national intervention on patient outcomes. Globally, Cryptococcus infection was estimated to be responsible for 15% of AIDS-related mortality (95% CI 10% to 19%). During 2016/17, the NICD Outbreak Response Unit (ORU), in close collaboration with the DoH and other stakeholders, constituting a multisectoral national outbreak response team, continued to function as a source of technical expertise for outbreak detection, investigation and response activities. This included responding to outbreak verification calls, 97% of which were responded to within 24 hours. The public was kept informed of such outbreaks and other communicable disease threats through 12 editions of the NICD Communicable Diseases Communiqué, which circulates to a wide audience including general practitioners, specialists, infectious disease and travel medicine societies, and national and provincial public health personnel. Over the course of 2016/17, the ORU finalised the development and implementation of an infrastructural, policy and management framework for the Public Health Emergency Operations Centre, in fulfilment of a memorandum of agreement signed with the DoH in This will serve as a vital resource in the event of a major communicable disease outbreak occurring in South Africa. The continual growth of the NICD and its support to the DoH and the South African public at large is very much dependent on training of adequately qualified epidemiologists. The NICD is now the single largest employer of epidemiologists in the country, and continues its training of epidemiologists through its South Africa Field Epidemiology Training Programme (SAFETP), which celebrated its 10 th anniversary in Initially established in collaboration with the DoH and the Centres for Disease Control and Prevention (CDC) of the United States of America, the programme is now fully funded by the NICD. SAFETP has trained more than 80 health professionals since its inception, 88% of whom remain employed in the public service in South Africa. The team continues to work with the DoH in establishing epidemiology as a professional discipline in the Human Resource for Health Strategy, and is defining the epidemiology core competencies required for existing staff at the DoH. During the review period, the National Cancer Registry was moved to the newly established Centre for Cancer at the NICD as South Africa moves toward the establishment of a National Public Health Institute of South Africa (NAPHISA). This will expand the surveillance platform from communicable to non-communicable diseases, as well as occupational health and injury prevention. The Centre for Cancer now provides the most updated information on the incidence of cancers in South Africa, benchmarked against global reporting standards. This data has been used to develop the South African National Cancer Control Plan, which includes breast and cervical cancer policies. In conclusion, the NICD continues to entrench itself as a pivotal component in the effort to promote the health and well-being of South Africans. This is done through robust surveillance of current and imminent communicable disease threats to the country. As has been the case in the past, this would not have been achievable without the remarkable dedication of the staff of the NICD and the unwavering support of the DoH. With the imminent establishment of NAPHISA, which is currently undergoing Cabinet and Parliamentary approval, providing robust communicable disease and non-communicable disease surveillance in South Africa will lay the foundation for the practice of precision medicine and in the process inform health policy for the benefit of all South Africans. 152 National Health Laboratory Service

154 NATIONAL INSTITUTE FOR OCCUPATIONAL HEALTH (NIOH) The National Institute for Occupational Health (NIOH) celebrated its 60th anniversary during the reporting period. We had the opportunity to reflect on the history of the NIOH, but more importantly, we can look confidently ahead to a future of decent work, reduced absenteeism and more sustainable, more equal and more productive workplaces. In the current challenging global economic and financial climate the world of work faces major challenges and the NIOH itself is not spared these challenges. This changing world of work with more technological innovations provides golden opportunities for sustainable preventive practices in occupational and environmental health and safety (OEHS) as well as the greater preservation of workers health. The Institute has profiled ways in which the heavy burden of OEHS diseases presenting to health services, including those of the national and provincial Departments of Health, can be reduced effectively through better compliance and a mind-set change towards prevention. As a follow-up to the inclusive occupational health and safety (OHS) concept paper of 2015, the NIOH and the broader OEHS community contributed to the all-important business case discussions for the establishment of the National Public Health Institute of South Africa (NAPHISA). The concept paper reviewed international best practice about the nature of occupational health and safety systems (OHSS). Due consideration was given to the role of the NIOH, since, in the poorly resourced area of OEHS, the multi-disciplinary Institute constitutes a core component. An important role is the support for government departments for the development of effective OEHS systems. Dr Sophia Kisting The NIOH continued to facilitate contributions from the broader OEHS fraternity for the inclusion of OEHS in the ongoing National Health Insurance (NHI) consultative process, which is expected to last for several financial years to come. In our review of OEHS systems, we identified an important gap specifically regarding gender concerns in the world of work. To find appropriate solutions, the NIOH continued to work on the findings of the participatory gender audit supported by national and international gender experts and the very active NIOH Gender Committee. With support from government departments, trade unions, employer organisations and international agencies, we celebrated the first anniversary of the launch of the NIOH s Programme on 8 March Achievements towards greater gender equity during the past year were celebrated with the National Health Laboratory Services (NHLS) and the broader world of work and we are deeply appreciative of their support and encouragement. The observed progress on gender concerns and the collaborative interventions undertaken auger well for greater unity of purpose to help overcome gender inequalities at work. Components of OEHS services to prevent occupational diseases and injuries are often underdeveloped or at times totally lacking in South African workplaces. Consequently, the need for OEHS services, especially the specialised services of the NIOH, is considerable in most industrial sectors, as well as in the informal economy. The NIOH and its partners in government and in the private sector undertook a very wide range of activities to address OEHS needs in different sectors of our economy. These activities covered OEHS policy advice, teaching and training, technical support to at least 16 government departments, trade unions and employers; research and different aspects of OEHS surveillance; teaching and training; information services as well as the provision of specialised laboratory services. The NIOH further strengthened the understanding of workplace ethics for OEHS professionals and is in the process of developing an application that will facilitate access to information on ethics and work. We have significantly increased our engagement with informal economy workers and as a World Health Organization (WHO) Collaborating Centre (CC), the NIOH currently leads the WHO initiative on better OHS for vulnerable workers. The engagement with governments, trade unions, employer organisations and the informal economy was strengthened mainly through collective teaching and training programmes and targeted service delivery. A significant development in the reporting period was the initiative by the Department of Health in collaboration with the WHO to develop an HIV and TB policy for health workers. This is a most significant undertaking by the National Department of Health (NDoH) and we will continue to support this process to finalisation and implementation. Annual Report 2016/17 153

155 The NIOH supports the Sustainable Development Goals (SDGs) adopted by the United Nations in September The SDGs include decent work, health, gender equity, youth employment, sustainable economies and sustainable environments. All of these are of great importance for healthier, productive, sustainable workplaces and the protection of the health of workers. The SDGs are intended to promote human rights, engender greater equity and peaceful and inclusive societies, create decent and sustainable jobs, and address the enormous environmental challenges of our time, including climate change. According to the WHO, environmental pollution (secondary to industrial and other workplace activities) contributes enormously to the burden of non-communicable diseases in many countries, including our own. This should further encourage all workplace stakeholders to greater compliance with OEHS legislation through effective and efficient preventive interventions at workplaces. Research The NIOH aims to continue to generate new knowledge through the rigour of good scientific research on key OEHS issues, especially those facing South Africa and the rest of the African continent. Collectively, the research projects of each division described in this Annual Report are testimony to the many OEHS issues requiring new knowledge, but also to the growing scope of the institute s research efforts and the strategic and greater engagement of younger researchers. It is notable that the research focus of the NIOH has broadened to include aspects of environmental health, gender concerns and reproductive health, problems related to climate change, as well as important policy concerns. The scientific publications listed in the NIOH Annual Report demonstrate a focus on many of the priority OEHS issues facing our country. Among the topics covered were asbestos in brake dust, in schools and in homes; preventing tuberculosis in individuals with silicosis; tuberculosis prevention in healthcare workers; noise-induced hearing loss and hearing conservation; occupations and lung cancer; water quality in hospitals; health effects in populations living around gold mine tailings; pesticides; and nanoparticles and health. Specialised and Other Services The NIOH continues to provide discipline-specific information services to many industrial sectors and government departments. Its laboratory services include asbestos identification and counting; diagnostic lung pathology; analytical chemistry (e.g. for biological monitoring specimens); the identification of components of dusts (respirable crystalline silica in particular); microbial air sampling; allergy diagnostics; nanoparticles and in vitro risk assessments. Discipline-specific services include occupational medicine, occupational hygiene, occupational toxicology, immunology and microbiology, and occupational epidemiology. Information services are a core service of many national institutes of health around the world, due partly to scarcity of sources of information elsewhere, as is the case in South Africa. The extent and diversity of information services offered by the NIOH, many of them with limited availability elsewhere in the country, are obvious from this report. The unique national occupational health library continues to provide support and information well beyond the borders of South Africa. The Biobank housed within the NIOH has grown significantly in the year under review, and is successfully housing thousands of specimens from different government departments. The HIV and TB Programme of the NIOH continue to make important contributions to both scientific research and service delivery, especially in the mining and health sectors, in close collaboration with the WHO and the International Labour Organization (ILO). The support for health workers has been most welcome as is the roll-out of training in different countries in Southern Africa on the WHO/ILO Health WISE Programme. The Marketing and Communications Section has done particularly well in profiling the history of the Institute and in strengthening engagement with OEHS programmes nationally and internationally. The Finance and General Services Section has made us all proud by maintaining the historical nature of the old building and making it a special home to the NIOH. The strategic and careful upgrading of the building has continued, and it has become a pleasure to work in this nearly hundred-year-old building. The Safety Health and Environment (SHE) and Information Technology (IT) Programmes made significant strides on the pioneering Occupational Health and Safety Information System (OHASIS). This user-friendly information system supports compliance with OEHS legislation, enables online training and provides information for research analysis. The OHASIS has gone from strength to strength and is increasingly being rolled out to centres beyond the NHLS and NIOH as well as in neighbouring countries. This bodes extremely well for the much needed strengthening of OEHS information systems for research and evidence-informed workplace interventions. We are inspired by the roll-out in Namibia, the Gauteng Health Department and the current initiatives in Mpumalanga and the Western Cape Departments of Health. Looking to 2017 and beyond, the NIOH will continue to help reduce the decent work deficit in our country, support ongoing efforts to reduce workplace inequality and strengthen the protection of human rights. Given our heavy burden of disease, it is incumbent upon the Institute to help nurture a culture of greater prevention of OEHS diseases and injuries. Health challenges, such as hypertension, diabetes, TB and stress, which are very often exacerbated by poor conditions of work, will also be addressed. Important areas that will require more attention relate to OEHS gender concerns, and OEHS for migrant workers, subcontracted workers, young workers and workers with disabilities. We have constituted a Green Committee and look to greater emphasis on greener workplaces and green jobs. NIOH staff members and the City of Johannesburg made concerted efforts on a voluntary basis throughout the year to provide subcontracted workers in the fields of security, cleaning and gardening services with training in skills ranging from fire fighting and first aid competency, to basic computer training. However, more strategic efforts are needed to reach more workers in precarious work. 154 National Health Laboratory Service

156 The greatly talented NIOH Choir has gone from strength to strength over the last year and has provided the most beautiful renditions of national, regional and international songs at our major public events. We are proud of the contribution of each and every member of the choir and trust that they will continue to grow and include more and more OEHS songs from across the globe in their repertoire. Retirements Mr Kevin Renton (Occupational Hygiene Department) Mr Kevin Renton retired in September Kevin began his career at the CSIR in 1977 after completing a BSc Honours in Biochemistry at Natal University (now the University of KwaZulu-Natal) and later a part-time Master s degree at the University of the Witwatersrand (Wits). He moved to the South African Institute for Medical Research (SAIMR) in 1980 working as a medical technician doing fertility research in the endocrine laboratory. In 1986, he joined the NIOH (then known as the NCOH) in the Analytical Section. He moved to the Occupational Hygiene Section and won a scholarship to study occupational hygiene at the University of Michigan. In 2000, he returned with new skills to contribute to the protection of workers health. Kevin was selected to be the Southern African Institute of Occupational Hygiene s Hygienist of the Year in He presented at 19 health-related conferences, and was first author of seven and a co-author of 12 publications in peer-reviewed national and international journals. Kevin continues to assist the NIOH Occupational Hygiene Section, especially in its work for the Department of Correctional Services (DCS), and he teaches in the Wits School of Public Health in an honorary position. Mrs Rosina Soko (Pathology Department) Mrs Rosina Soko joined the NIOH in 1980 and was a conscientious, diligent and hard-working employee in the Pathology Department. Despite having no formal qualification, Rosina performed all the functions of a laboratory technician, delivering more than what was required of her at a high standard and with an admirable work ethic. Obituary: Dr Danuta Kielkowski Dr Danuta Kielkowski (PhD), who retired in December 2014 after 30 years of dedicated service at the NIOH, died on 3 July Danuta provided invaluable expertise, first to the Epidemiology Section at the NIOH and thereafter as Deputy Director of the National Cancer Registry. Danuta s work on death certification and occupational disease surveillance, as well as her asbestos and reproductive health research, are just some of the highlights of her long and productive career. She made an invaluable contribution to the growth and strengthening of occupational epidemiology in South Africa, in the Africa region and beyond. She published widely on occupational health in peer-reviewed journals and her scientific rigour contributed immensely to new knowledge in public health in South Africa and beyond. She also wrote technical reports which had a direct impact on public health policy. She supervised, nurtured and enthused numerous young epidemiologists, and was widely respected for the collegial and inclusive manner in which she shared her skills. Above all, Danuta exemplified the beautiful spirit of national and international collaboration to address major health concerns through collective research. Rest in peace, Danuta: you will always be fondly remembered and you are dearly missed. Acknowledgements and Appreciation We wish to acknowledge the significant contribution of so many to the ongoing success of the OEHS interventions of the NIOH. We wish to acknowledge the significant and strategic support from the NHLS and from our government departments, in particular the departments of Health, Labour, Mineral Resources, Science and Technology, Environmental Affairs, Defence, Agriculture and Correctional Services. Special appreciation goes to the National Institute for Communicable Diseases (NICD) for the strategic leadership role in the NAPHISA process. We wish to acknowledge all the employer organisations and the growing number of trade unions, which continue to challenge us for an on-going positive impact on workplaces and better worker health. Our appreciation goes to the many professional OEHS organisations including the South African Society of Occupational Medicine (SASOM), South African Society of Occupational Health Nursing Practitioners (SASOHN) and Southern African Institute for Occupational Hygiene (SAIOH), as well as international organisations, including the WHO, ILO, UN Women and UNAIDS, for their collegial support and great collaboration. We are particularly appreciative of the collaborative support from our sister OEHS institutes in Africa and across the globe. We owe a particular gratitude to current and former staff of the NIOH, both academic and non-academic, for making and maintaining the Institute as an internationally recognised, accessible centre of excellence in OEHS research, teaching and training, and service delivery. Conclusion We invite the actors of the world of work and the broader South African public to join us on our journey of building on our collective strength to utilise the potential of all workplaces for better OEHS, for decent jobs and happier workplaces, and for the protection of human rights, greater productivity, and ultimately for sustainable economies. Annual Report 2016/17 155

157 PART C Governance

158 Introduction Corporate governance is concerned with the structures, systems, processes and practices in place for decision-making, accountability, control and behaviour within an organisation, beginning at the top level of the organisation. Corporate governance sets the tone for behaviour down to the lowest levels. The NHLS confirms that its structures, systems, processes and practices are reviewed on a regular basis to ensure compliance with legal obligations; use of funds in an economical, efficient and effective manner; and sustained performance of the services offered. Processes and practices are characterised by reporting on economic, environmental and social responsibilities. Such reporting is underpinned by the principles of openness, integrity and accountability, representing an inclusive approach that recognises the importance of all stakeholders with respect to the viability and sustainability of the NHLS. Portfolio Committees Adv. Mpho M Mphelo The NHLS is accountable to parliament through Parliamentary Portfolio Committee on Health. The NHLS appeared before the Parliamentary Portfolio Committee on Health on 12 April 2016, presenting the Annual Performance Plan 2017/18 and on 12 October 2016 presenting the Audited Annual Financial Statements and Annual Report for the financial year ended 31 March The Parliamentary Portfolio Committee on Health continues to conduct oversight visits to the NHLS facilities to determine efficiencies and service delivery to the South African citizens. Executive Authority The Minister of Health is the Executive Authority of the NHLS, as defined by the Public Finance Management Act, No 1 of He is responsible for the appointment of Board members in line with Section 7 of the NHLS Act, No. 37 of Annual Report 2016/17 157

159 The Accounting Authority/Board INTRODUCTION The NHLS Board of Directors is the Accounting Authority of the NHLS in terms of the NHLS Act and the Public Finance Management Act (PFMA). The Board is committed to business integrity, transparency and professionalism in all its activities. As part of this commitment, it supports the highest standards of corporate governance and the ongoing development of best practice. The Board meets on a quarterly basis and is responsible for providing strategic direction and leadership, ensuring good corporate governance and ethics, determining policy, agreeing on performance criteria and delegating the detailed planning and implementation of policy to its Executive Committee (EXCO). The Board considers submissions and recommendations made by management and makes independent decisions based on their fiduciary responsibilities and the strategic direction of the service. ROLE OF THE BOARD Management s compliance with policy and achievements against objectives is evaluated and monitored. A structured approach is followed for delegation, reporting and accountability, which includes reliance on various Board committees. The chairperson guides and monitors the input and contribution of Board members. The Board has unlimited access to professional advice on matters concerning the affairs of the NHLS, at the NHLS expense. The Board evaluates its own effectiveness on an annual basis and formulates plans to mitigate any shortcomings identified in the evaluation process. BOARD CHARTER The mandate of the NHLS Board is set out in the NHLS Act and has been encapsulated in the NHLS Board Charter. The mandate of the Board as set out in the Board Charter is aligned with the requirements stipulated by the Protocol on Governance in Public Entities. In addition, an approved Code of Corporate Practice and Conduct, including terms of reference, provides guidance to the Board members in discharging their duties and responsibilities. COMPOSITION OF THE BOARD In line with the stipulations of the NHLS Act, No. 37 of 2000, the Board comprises 22 members including the Chief Executive Officer, Chairperson and Vice-Chairperson. Twenty-one members (the vast majority) are non-executive members and one member is an executive. The members of the Board were appointed by the Minister of Health in accordance with Section 7 of the NHLS Act. In terms of Section 9 of the NHLS Act, the Minister has appointed a Chairperson and a Vice-Chairperson. The Chairperson is a non-executive and independent director (as recommended by good corporate governance practices) and is a standing member of all committees of the Board. 158 National Health Laboratory Service

160 Board Members The members of the Board during the year and to the date of this report are as follows: Chairmanship/ Position 1 May January 2017 Board until 1 January 2017 Name Representing Directorship Date Appointed Date Retired Prof. Barry Schoub Minister of Health Non-executive Board Member and Chairperson of the Board Prof. Eric Buch Council on Higher Education Council on Higher Education Minister of Health Non-executive Board Member Non-executive Board Member Non-executive Board Member and Chairperson of the Board Prof. Gregory Hussey Minister of Health Non-executive Board Member and Vice- Chairperson of the Board Re-appointed 20 April April 2015 (reappointed) Appointed Chairperson of the Board with effect from 1 January 2017 Dr Sibongile Zungu Minister of Health Vice-Chairperson 20 April 2017 Dr Thokozani Mhlongo Mpumalanga Non-executive Board 02 January 2015 Province Member (re-appointed) National Academic Pathology Committee (NAPC) Board and GSEC 1 September January 2017 Remuneration and Human Resources Committee with effect from 6 July July 2016 Remuneration and Human Resources Committee Mr Ben Durham Department of Science and Technology Non-executive Board Member 01 November 2014 Dr Tim Tucker Mr Michael Manning Mr Andre Venter Dr Patrick Moonasar Mr Lunga Ntshinga Public Nominee: Research Western Cape Province National Department of Health National Department of Health Public Nominee: Finance Non-executive Board Member Non-executive Board Member Non-executive Board Member Non-executive Board Member Non-executive Board Member Mr Thamsanqa Stander Free State Province Non-executive Board Member Mr Stanley Harvey Northern Cape Province Non-executive Board Member Dr Balekile E Mzangwa Free State Province Non-executive Board Member Dr Zwelibanzi Abie Mavuso SALGA Non-executive Board Member Prof. Mary Ross Minister of Health Non-executive Board Member Prof. Willem Sturm Minister of Health Non-executive Board Member 01 January 2016 (re-appointed) 30 April 2015 (reappointed) 02 January 2015 (re-appointed) 01 February January 2016 (re-appointed) Research Committee (sub-committee of NAPC) Appointed Chairperson of the NAPC with effect from 24 January 2017 Information Technology Governance Committee Finance Committee Audit and Risk Committee 01 February November 2016 Governance, Social and Ethics Committee 01 February November December August 2015 Research Committee 27 August January 2017 Annual Report 2016/17 159

161 Chairmanship/ Position 1 September 2015 Remuneration of Human Resources Committee with effect from 24 January November 2015 Name Representing Directorship Date Appointed Date Retired Ms Nelisiwe Mkhize Minister of Health Non-executive Board Member Dr Gerhard Goosen Minister of Health Non-executive Board Member Mr Michael Shingange Organised Labour Non-executive Board Member Ms Sphiwe Mayinga Prof. Obi Chikwelu Lawrence Ms Ntombikayise Mapukata Public Nominee: Legal Council of Higher Education Eastern Cape Province Non-executive Board Member Non-executive Board Member Non-executive Board Member 1 February April April February 2015 Prof. Haroon Saloojee Minister of Health Non-executive Board 27 August 2015 Member Ms Joyce Mogale CEO NHLS Executive Member 01 September 2015 Chief Executive Officer EXCO Prof. Shabir Madhi Acting CEO NHLS Executive Member 24 February 2017 Acting CEO EXCO Board Member Qualifications and External Directorships The NHLS Board members have the relevant skills, knowledge and experience to bring judgement to bear on the business of the NHLS. In situations where Board members may lack experience, detailed induction and formal mentoring and support programmes are implemented. Board members are requested to declare direct and individual business interest that they might have in any matter which is relevant to the NHLS. The Company Secretary keeps a register of members declaration of interest and directorship. The Chairperson, together with the Board, has carefully considered the directorships that members hold in other companies. The relative size and complexity of the companies in question have been taken into account. The Board members are satisfied that they have the ability and capacity to discharge their duties. The qualifications and external directorships of NHLS Board members are disclosed in the table below: Name Prof. Barry Schoub Qualifications and External Directorships Qualifications OMS, MBBCh, MMed (Micro), MD, DSc, FRCPath, FFPath, MAASAf Prof. Eric Buch Directorships Vice-Chairman: Poliomyelitis Research Foundation Qualifications MBBCH, MSc (Med), FFCH(cm)(SA), DTM&H,DOH Prof. Gregory Hussey Directorships None Qualifications MBChB, MMED, DTM & MSc CTM FFCH Dr Sibongile Zungu Directorships UCT Lung Institute, CosH Private Academic Hospital, Isisombululo Community, Improvement Programme, Hussey Family Trust, University of Cape Town Qualifications MBChB, BAdmin, Strategic Transformation Programme, Postgraduate Certificate in Occupational Health, Improving Quality in the Health Sector, Entrepreneurial Management of Health Services, Public Sector Reform, Postgraduate Studies in Applied Population Studies Training and Research, Making Decentralisation Work, Human Resources for Health. Directorships Inkosi of the Madlebe Traditional Authority 160 National Health Laboratory Service

162 Name Dr Thokozani Mhlongo Qualifications and External Directorships Qualifications BCur, BSc, MBChB Mr Andre Venter Dr Patrick Moonsar Dr Tim Tucker Mr Michael Manning Mr Lunga Ntshinga Ms Ntobikayise Mapukata Prof. Mary Ross Prof. Willem Sturm Mr Thamsanqa Stander Mr Stanley Harvey Mr Ben Durham Mr Michael Shingange Directorships Njomani Projects cc Qualifications NDip: Government Finance (RVQ13), Cert: Financial Management in Public Sector, Postgrad Dip: Public Health Management Directorships None Qualifications PHD (Public Health) Directorships None Qualifications MBChB, PHD, Dip FCPath(SA)Viro, Wits Dip (Business Strategy) Directorships SEAD Consulting, NHLS Research Trust, SA HIV Clinicians Society, Tucker Family Trust Qualifications BCom, BCom Hons, PG Dip (Accounting) SAICA, CA(SA) Directorships Trustee Isele Trust, Independent Audit Committee Member of Mine Health and Safety Council Qualifications B Com, PG Dip (Business Management), Certificate in Debt Counselling, Internal Audit Quality Assessment Course Directorships Hlumisa Consulting, Agnul Investments Qualifications MDP, Dip (Labour Law) BTech, Dip (Human Resource Management) ND MED Tech Directorships Kaobry Trading Enterprise (Pty) Ltd, Agnul Investments Qualifications BSc (Hons), MBChB, Dip (Datametrics), Dip Health Admin, DTM & H, DPH, DOH, FCPHM, FOM (UK),FPH (UK), FFTM (RCP&S GLASGOW), FACTM (Australia) Directorships None Qualifications MD, PhD Directorships None Qualifications ND Med Tech, ELDP Directorships Kasi 2 Kasi Trading & General Trading; Kasi Consciousness Revolution Qualifications ND Med Tech Directorships None Qualifications MSc, BSc (Hons), BSc, currently pursuing PHD in Technology and Innovation Management Directorships None Qualifications Cert Negotiating Skills, Dip Trade Union Movement, Cert Governance Directorships 1st Deputy President NEHAWU Annual Report 2016/17 161

163 Name Ms Nelisiwe Mkhize Prof. Haroon Saloojee Dr Gehardus Goosen Ms Joyce Mogale Dr Zwelibanzi Abie Mavuso Dr Balekile E Mzangwa Ms Sphiwe Mayinga Prof. Obi Chikwelu Lawrence Qualifications and External Directorships Qualifications MBA, PG Dip (Business Management), BSc ND Med Tech Directorships None Qualifications MBBCH, FCPaed (SA), MSc Directorships Soul City Institute, Starfish Greathearts Qualifications MBChB, Dip Obst (SA) Directorships ALENTI 25 (Not for Profit) Qualifications MBA, PG Dip (Public Health Management), BSc (Hons), ND Med Tech, HND Med Tech Directorships Klein Karoo Akademie, Ububele Capital, Ruby Stone Boutique Hotel, Marubini Holding, Metso Mining & Construction (SA), Ninator Thyssen Krupp Industrial Solutions (SA), Cynimart Investments, JL Properties, Limpopo Gambling Board, Tirisano Trust, Ububele Trust, Umvuso Trust, Kamatsu Trust, TETMC Trust, Westvaal Trust Qualifications Dental Therapy, MBBCH, MBA Directorships None Qualifications MBChB Directorships None Qualifications BProc, LLB, LLM, MAP, SLDP, Advanced Banking Law, Corporate Governance, Compliance Management Directorships Tiyisela Construction, UNISA SBL (Member of Risk and Audit Committee and Chairperson of Remuneration and Human Resources Committee) Qualifications BSc (Hons), MSc, PHD Directorships None Changes in Board Membership Upon the expiration of a Board member s term of office, the member may be eligible for re-appointment for a further term of office, providing that no member may be appointed for more than two consecutive terms to serve on the same committee. The table below indicates the changes to Board membership that took place during the year under review: Name Constituency/Representing Date of Appointment/ *Re-appointment Prof. Barry Schoub Minister of Health 1 May 2015 Reappointed 20 April 2017 Date of Resignation/*Retirement 1 January 2017 Prof. Gregory Hussey Minister of Health 1 September January 2017 Dr Thokozani Mhlongo Mpumalanga Province 2 January July 2016 Mr Thamsanqa Stander Free State Province 1 February November 2016 The NHLS Board is governed by the NHLS Act, No. 37 of 2000 and the NHLS Rules made in terms of the Act supra. The Board complies with the PFMA. In addition, the NHLS Board subscribes to the terms of King III. In the period under review, the Board complied with its Terms of Reference (ToR) as detailed in the NHLS Rules. In addition, the Board has provided strategic direction to the organisation as required by King III. Minutes of meetings were made and entered in the minute book as a true and accurate representation of what transpired at the meetings. 162 National Health Laboratory Service

164 Majority of the members of the Board attended the meetings for the year. Board resolutions were captured in the board resolution file. Board Meeting Attendance During 2016/17, the Board convened 15 times (including special meetings). The NHLS Board is required to hold at least four meetings per year. Only members of the Board voted at these meetings and all decisions were arrived at by consensus. In each of the meetings, a quorum for the meeting was met. In each meeting, members were given the opportunity to declare any personal conflict of interest in order to be recused from the deliberation of the matter in which a member was involved. The table below and accompanying legend illustrates meeting attendance of Board members for the financial year: Meeting Dates 17 May June July July August August September 2016 Name Prof. Barry Schoub A % % % % 10 Prof. Gregory Hussey A A A % % % % 7 Dr Thokozani Mhlongo % % % % % % % % % % % % 3 Mr Andre Venter A 14 Dr Patrick Moonasar A A A A A 10 Mr Lunga Ntshinga A A 13 Dr Tim Tucker A A 13 Prof. Eric Buch * A A A A A 10 Mr Michael Manning A 14 Ms Ntombikayise 14 A Mapukata Mr Thamsanqa Stander % % % % % % 9 Mr Stanley Harvey 15 Mr Ben Durham A A A A 11 Mr Michael Shingange A A A A A A A 8 Ms Nelisiwe Mkhize A A * 13 Prof. Mary Ross A A * 13 Prof. Willem Sturm A A 13 Prof. Haroon Saloojee A A A A A A A A A A 5 Ms Joyce Mogale A 14 Dr Gerhard Goosen C A A A 10 Dr Balekile Mzangwa C C C C C C C C A A 4 Dr Zwelibanzi Mavuso C C C C C C C C A A 4 06 October November November November January February February February 2017 Total Meeting Attendance Legend: = Present * = Appointed as Chairperson of the Board 01 January 2017 A = Apology B = Absent C= Not a member % = Retired/ Resigned % = Retired/Resigned % = Retired/Resigned COMMITTEES OF THE BOARD The Board as the Accounting Authority takes full ownership of the overall decision-making across the NHLS to ensure it retains proper direction and control. Without abdicating its own responsibilities, the Board has delegated certain powers to the CEO and to management but has reserved certain powers exclusively for the Board, as set out in the Board Charter. To help it meet its responsibilities, the Board has delegated certain functions to the following committees: Annual Report 2016/17 163

165 Audit and Risk Committee Remuneration and Human Resources Committee Information Technology Governance Committee Governance, Social and Ethics Committee (ad hoc Committee) Finance Committee National Academic and Pathology Committee Research Committee Executive Committee. The various committees of the Board each have formal terms of reference, embodied in a charter that further defines the mandates, roles and responsibilities of each committee. The charters are reviewed and updated on an annual basis where required. Audit and Risk Committee In keeping with Treasury Regulation 27 of the PFMA, the Board has appointed an Audit and Risk Committee to assist in the discharge of its duties by reviewing and reporting on the governance responsibilities of the Board and the NHLS. The terms of reference of the Audit and Risk Committee, its duties and functions, its composition and its modus operandi have been approved by the Board. Refer to page 173 for scheduled meetings and attendance. Remuneration and Human Resources Committee In terms of the NHLS Act, the Remuneration and Human Resources Committee (RHRC) serves to assist the Board with the performance of its functions and exercising of its powers. The committee reports on employment equity, employee turnover, skills development and labour relations. As part of the continued professional development programme, the Board periodically invites corporate governance experts, as recommended by the Institute of Directors from time to time, to present topical matters and latest developments in corporate governance practices. The RHRC met on seven occasions during the financial year. Meeting Dates Name Dr Thokozani Mhlongo % % % % 3 Mr Andre Venter A 6 Prof. Eric Buch A A A % 3 Ms Nelisiwe Mkhize * * 7 Mr Michael Shingange A A A A A A A 0 Mr Thamsanqa Stander % 6 Ms Ntombikayise Mapukata 7 Ms Joyce Mogale A 6 Mr Michael Manning**** C C C C C 2 Dr Gerhard Goosen ** C C C ** 4 Mr Lunga Ntshinga**** C C C C C 2 Prof. Gregory Hussey *** C C C *** % 3 21 April May June September October November March 2017 Total Meeting Attendance Legend: = Present * = Appointed as Chairperson 24 January 2017 A = Apology ** = Appointed 25 August 2016 B = Absent *** = Appointed 1 July 2016 C = Not a member % = Retired/Resigned **** = Attended by invitation 164 National Health Laboratory Service

166 IT Governance Committee The IT Governance Committee (ITGC) was established in terms of Section 12 of the NHLS Rules. The committee ensures that IT is a regular item on the Board agenda and that it is addressed in a structured manner. In addition, the committee ensures that the Board has the information it needs to make informed decisions that are essential to achieve the ultimate objectives of IT governance. These objectives are: The alignment of IT and the business The delivery of value by IT to the business The sourcing and use of IT resources The management of IT-related risks The tracking, monitoring and measurement of IT performance. The committee offers expert insight into and timely advice and direction on topics such as: The relevance of the latest developments in IT from a business perspective The alignment of IT with the business direction The formulation and achievement of strategic IT objectives The availability of suitable IT resources, skills and infrastructure to meet the strategic objectives Optimisation of IT costs The role and the value delivery of external IT sourcing Risk, return and competitive aspects of IT investments Progress on major IT projects The contribution of IT to the business (i.e. delivering the promised business value) Exposure to IT risks, including compliance risks Containment of risks of critical systems. The ITGC met six times in 2016/17. The Chairperson of the ITGC is appointed by the Board from eligible Board members. The committee comprises a minimum of three non-executive Board members. The Chairperson of the NHLS Board, Chief Financial Officer and the IT Executive have a standing invitation to attend all ITGC meetings. Meeting Dates Name Mr Michael Manning 6 Ms Joyce Mogale A A A A 2 Mr Stanley Harvey 6 Dr Tim Tucker A A A C C 1 Prof. Willem Sturm A A A 3 Dr Patrick Moonsar A A A A 2 Ms Ntombikayise Mapukata C C C C * 2 13 May July September November March March 2017 Total Meeting Attendance Legend: = Present * = Appointed 24 January 2017 A = Apology B = Absent % = Retired/Resigned C = Not a member Annual Report 2016/17 165

167 Governance and Social Ethics Committee This committee was established to assist the Board with the oversight of corporate governance and social and ethical matters, and to ensure that the organisation is and remains a committed, socially responsible corporate citizen. The commitment to sustainable development involves ensuring that the organisation conducts business in a manner that meets existing needs without knowingly compromising the ability of future generations to meet their needs. The committee s primary role is to supplement, support, advise and provide guidance on the effectiveness or otherwise of management s efforts in respect of governance, social and ethics and sustainable development-related matters which, inter alia, include: Safety Health and wellness, including occupational hygiene Environmental management Climate change Ethics management Corporate social investment Mine community development Stakeholder engagement The protection of company assets. The Committee undertakes the following: Reviews and approves the policy, strategy and structure to manage governance, social and ethics issues in the organisation Oversees the monitoring, assessment and measurement of the NHLS s activities relating to social and economic development, including its standing in terms of the goals and purposes of:»» The ten principles set out in the United Nations Global Compact Principles»» The OECD recommendations regarding corruption»» The Employment Equity Act, No. 55 of 1998»» The Broad-Based Black Economic Empowerment Act, No.53 of 2003 Oversees the monitoring, assessment and measurement of the NHLS s activities relating to good corporate citizenship, including its promotion of equality, prevention of unfair discrimination, addressing of corruption, contribution to development of the communities in which its activities are predominantly conducted or within which its services are predominantly marketed, and record of sponsorship, donations and charitable giving Oversees the monitoring, assessment and measurement of the NHLS s activities relating to the environment, health and public safety, including the impact of its activities and services Oversees the monitoring, assessment and measurement of the organisation s stakeholder relationships, including its advertising, public relations and compliance with consumer protection laws, to ensure that it adheres to its values Oversees the monitoring of the NHLS s labour and employment, including its standing in terms of the International Labour Organization Protocol on Decent Work and Working Conditions, its employment relationships, and its contribution toward the educational development of its employees Reviews the adequacy and effectiveness of the organisation s engagement and interaction with its stakeholders Considers substantive national and international regulatory developments, as well as practice in the fields of social and ethics management Reviews and approves the policy and strategy pertaining to the organisation s programme of corporate social investment Determines clearly articulated ethical standards (Code of Ethics) and ensures that the NHLS takes measures to achieve adherence to these in all aspects of its business, thus achieving a sustainable, ethical corporate culture Monitors that management develops and implements programmes, guidelines and practices congruent with its social and ethics policies Reviews the material risks and liabilities relating to the provisions of the Code of Ethics, and ensures that such risks are managed as part of the Risk Management Programme Obtains external assurance of the NHLS s ethics performance on an annual basis, and facilitates the inclusion of an assurance statement related thereto in the Annual Report Ensures that management has allocated adequate resources to comply with social and ethics policies, codes of best practice and regulatory requirements. 166 National Health Laboratory Service

168 The Committee met 11 times in the review period. Meeting Dates 14 April May June 2016 Name Mr Thamsanqa Stander % % % % % 6 Prof. Barry Schoub % % % % % 6 Dr Thokozani Mhlongo A % % % % % % % 3 Mr Andre Venter 11 Dr Tim Tucker A A A A 7 Prof. Eric Buch 11 Mr Lunga Ntshinga A A 9 Mr Michael Manning 11 Prof. Gregory Hussey * C C C C *A % % % % % 2 Prof. Mary Ross C C C C C C A 4 Ms Nelisiwe Mkhize C C C C C C 5 Legend: = Present * = Appointed July 2016 A = Apology % = Retired/Resigned B = Absent C = Not a member 24 June August October January February February March March 2017 Total Meeting Attendance Finance Committee The Finance Committee (FINCO) assists the Board in fulfilling its oversight responsibilities on an ongoing basis for matters relating to the financial practices and condition of the NHLS, by: Reviewing its financial policies and procedures Keeping informed of the NHLS financial conditions, requirements for funds, and access to liquidity Considering and advising the Board concerning the sources and uses of funds. In terms of good corporate governance practice, FINCO met on seven separate occasions during the financial year. Meeting Dates 07 April 2016 Name Mr Andre Venter 7 Mr Michael Manning 7 Mr Michael Shingange A A A A A A A 2 Mr Thamisanqa Stander % % 4 Dr Thokozani Mhlongo % % % % % % 3 Ms Ntombikayise Mapukata C C C C C C C 3 Mr Lunga Ntshinga 7 Ms Joyce Mogale A 6 Dr Gerhard Goosen* C C C 5 Prof. Gregory Hussey** C C C C C C C 2 Legend: = Present * = Appointed 24 January 2017 A = Apology % = Retired/Resigned B = Absent C = Not a member ** = Attended by invitation 10 May June September October November November February March 2017 Total Meeting Attendance Annual Report 2016/17 167

169 National Academic and Pathology Committee The National Academic and Pathology Committee (NAPC) met on five occasions during the financial year. Meeting Dates Name Prof. Eric Buch 5 Ms Joyce Mogale A 4 Dr Tim Tucker * 5 Ms Ntombikayise Mapukata C C 3 Mr Ben Durham 5 Mr Thami Stander % % 3 Ms Nelisiwe Mkhize A A * 3 Prof. Mary Ross A 4 Prof. Willem Sturm 5 Prof. Gregory Hussey A A A % % 0 15 July August November February February 2017 Total Meeting Attendance Legend: = Present A = Apology % = Retired/Resigned B = Absent C = Not a member The functions of the committee are to facilitate education by formulating policy with regard to: The conducting of basic research in association or partnership with any tertiary educational institution Co-operation with persons and institutions undertaking basic research in the Republic, and in other countries, by the exchange of scientific knowledge and the provision of access to the resources and specimens available to the NHLS Participation in joint research operations with government departments, universities, universities of technology, colleges, museums, scientific institutions and other persons Co-operation with educational authorities and scientific or technical societies or industrial institutions representing employers and employees, respectively, for the promotion of the instruction and training of pathologists, technologists, technicians, scientists, researchers, technical experts and other supporting personnel in universities, universities of technology, and colleges Any other matter as may be referred to the committee from time to time by the Board. As some of its duties, the committee monitors and manages the agreements entered into between the NHLS and each tertiary education institution, including: The development of policies and guidelines to determine the numbers of registrars for each discipline and the distribution of the registrar posts between the laboratories associated with each university health science faculty The development of policies and guidelines to determine the numbers of technologist training posts for each discipline and the distribution of the posts between the laboratories identified for this purpose Proposing guidelines relating to part-time, honorary and guest appointments of employees of the NHLS by tertiary education institutions Monitoring the guidelines for consultant appointments of personnel of tertiary education institutions in the NHLS as determined by the agreement between the NHLS and the universities Ensuring that the process of continuing professional development programmes provided by tertiary education institutions in the NHLS is used by NHLS employees to comply with Career Programme Development requirements Reviewing and managing arrangements for research being undertaken by tertiary education institutions in the laboratories of the NHLS Advising EXCO on matters relating to indemnity for employees of the NHLS or a tertiary education institution working between the facilities of both partners 168 National Health Laboratory Service

170 Advising EXCO on matters relating to discipline of personnel of the NHLS or a tertiary education institution working between the facilities of both partners Advising EXCO on financial matters, such as subsidies, bursaries and payment for academic-related services Monitoring, and evaluating and managing service level agreements and performance measures Advising, monitoring and evaluating the resolution of disputes if they should arise Ensuring the integrity of the process of managing partnerships Ensuring that professional ethics are adhered to Ensuring that the NHLS complies with the requirements of the Health Professionals Council in respect of registration requirements, ethics and conduct. Research and Innovation Committee The committee has been established as a vehicle for ensuring that the NHLS Research mandate receives attention at Board level. Members of the Research and Innovation Committee may be called on from time to time to interact with external stakeholders and funding agencies. The role of the Research and Innovation Committee is to advise the NHLS Board and the NAPC on research policies, strategies, initiatives and innovation that promote the research interests of the organisation and that nurture and enable high quality research. The objectives of the Research and Innovation Committee are aligned with those stipulated in the South African Health Research Policy of 2001, the National Department of Health 10-Point Plan and the National Health Research Committee (NHRC). This committee meets at least three times a year and in the period under review met three times. Meeting Dates Name Dr Tim Tucker 3 Prof. Eric Buch A % 1 Ms Joyce Mogale A A 1 Mr Ben Durham 3 Prof. Mary Ross** A * 2 Prof. Willem Sturm A 2 Dr Patrick Moonsar C C A 0 Prof. Haroon Saloojee C C * 1 10 August November February 2017 Total Meeting Attendance Legend: = Present * = Appointed 24 January 2017 A = Apology B = Absent % = Retired/Resigned C = Not a member ** = Appointed Chairperson 24 January 2017 The Executive Management Committee In terms of the NHLS Act, the Accounting Authority has appointed an Executive Management Committee (EXCO), which consists of: The Chief Executive Officer, who acts as Chairperson Regional Executive Managers Executive Managers from Support Services. The EXCO is responsible for the management of the NHLS in accordance with the policy of the NHLS and assists with performance of the Accounting Authority s functions and the exercise of its powers. In terms of good corporate governance practices, the EXCO met on a monthly basis during the financial year. Annual Report 2016/17 169

171 REMUNERATION OF BOARD MEMBERS The NHLS has a Board Manual which outlines the privileges and remuneration of Board members. The National Treasury guidelines and circular on remuneration of Non-official members, commissions, committees of inquiry and audit committees are reviewed annually. Employees of National, provincial and local government or institutions, agencies and entities of government serving on boards, commissions or committees of inquiry or audit committees are not entitled to additional remuneration. The following members received emoluments during the financial year under review: Members fees Other fees* Total R 000 R 000 R 000 B Schoub M Shingange T Stander Tim Tucker E Buch (Chairperson) T Mhlongo N Mapukata G Hussey L Ntshinga M Ross S Harvey N Mkhize G Goosen A Sturm , ,967 Risk Management The NHLS Board, through its Audit and Risk Committee is responsible for overall oversight of enterprise-wide risk management practices and processes. The responsibility for risk management implementation resides with management at all levels. A dedicated Risk Officer coordinates the implementation of the NHLS risk management philosophy and strategy as approved by the Board. The approach followed by the NHLS is to ensure that all significant risks are identified and managed. Enterprise-wide risk management is therefore embedded in the daily activities of operations and focuses on identifying, assessing, managing and monitoring all risks. Because the risks identified are often inter-linked, and cannot be managed in silos, they have been defined in three broad risk categories, namely strategic risks, operational/divisional risks and emerging risks. During the review period, risk assessment workshops were conducted and the risk register was updated to incorporate new risks and identify mechanisms to ameliorate them. The Board continues to discharge its responsibility through its Audit and Risk Committee and ensures that Risk Management is a standing item for discussion at each scheduled Board meeting. Internal Audit The NHLS has a co-sourced internal audit function that reviews NHLS operations. The Audit and Risk Committee approves the internal audit charter, the three-year rolling strategic audit plan, the one-year operational audit plan and the budget for the internal audit. To ensure that it maintains its independence the function reports administratively to the NHLS CEO and functionally to the Chairperson of the Audit and Risk Committee. Comprehensive reports on all internal audit findings are presented to management regularly and to the Audit and Risk Committee quarterly. 170 National Health Laboratory Service

172 Compliance with Laws and Regulations The nature of NHLS s business requires the assessment and integration of legal, regulatory and public policy requirements into the strategic and operational processes of the organisation, to meet its contractual, moral and corporate citizenship obligations. The observation of laws that govern the organisation and its activities forms the foundation for good corporate governance and demonstrates stewardship and responsibility to all stakeholders. During the year under review a regulatory compliance universe was compiled, which assists the organisation in tracking compliance with laws and regulations applicable to the NHLS business environment. No material non-compliances were identified, however, at the date of this report, the ownership of land and buildings had not been transferred into the name of the NHLS as required by the NHLS Act. The Accounting Authority has taken all appropriate measures to ensure the transfer process is effected by the Department of Public Works. In respect of the vacancies at Board level, only the Minister of Health can appoint members. Two vacant positions are in the process of being filled, namely SALGA and the Council of Higher Education. There are vacancies on the Board for which the Executive Authority is in the process of considering appointments. Fraud and Corruption A Fraud Prevention and Response Plan is in place to enhance integrity and reduce the risk of fraud, as well as assist staff in making decisions in the reporting of fraud, corruption and other criminal offences affecting NHLS. It is designed to protect public money and property; and protect the integrity, security and reputation of NHLS; while maintaining a high level of services to the community, consistent with the NHLS code of conduct. The NHLS uses the Fraud Hotline (Tip-Offs Anonymous) which is externally managed by an independent service provider. The NHLS protects the rights of whistle blowers to prevent victimisation by fellow employees or managers in contravention of the Protected Disclosures Act, No. 26 of During the period under review, a fraud risk assessment workshop was conducted and a fraud risk register compiled to assist the entity in raising awareness of fraud and ethics in the workplace and enable employees to identify incidents of possible misconduct and report allegations effectively. A consolidated record of allegations of fraud is maintained, together with the actions taken and their resolution. These are reported to the Board through the Audit and Risk Committee. Minimising Conflict of Interest The NHLS Board has adopted a code of business conduct and ethics for its members. The code is intended to focus the Board and each member on areas of ethical risk, provide guidance to directors to help them recognise and deal with ethical issues, provide mechanisms to report unethical conduct, and help foster a culture of honesty and accountability. The code requires all Board members to avoid conflict of interest, and encourages members to disclose promptly any situation that involves, or may reasonably be expected to involve, a conflict of interest. Some of the more common conflicts from which Board members must refrain include: a) Relationship of organisation with third parties. Directors may not engage in any conduct or activities that are inconsistent with the organisation s best interest or that disrupt or impair the organisation s relationship with any person or entity with which the organisation has or proposes to enter into a business or contractual relationship. b) Compensation from other sources. Directors may not accept compensation (in any form) for services performed for the organisation from any source other than the organisation. c) Gifts. Directors and members of their families may not accept gifts from persons or entities who deal with the organisation in those cases where any such gift is being made in order to influence the director s action as a member of the Board, or where acceptance of the gifts could create the appearance of a conflict of interest. Any acceptance of a single gift to the value of more than R500 or various gifts the accumulative value of which exceeds R1000 in any financial year must be declared with the Company Secretary and recorded in the gifts declaration register. Annual Report 2016/17 171

173 All members are requested to declare their interest in any matter included in the agenda before every meeting commences. Should any member declare any interest, he/she will be recused from the meeting when the matter is discussed. Code of Conduct The NHLS has a Code of Conduct which refers to the philosophical study of values and the rules that all employees, executives and nonexecutives members of the Board live by. The NHLS is committed to a policy of fair dealing and integrity in the conduct of its business. This commitment is actively endorsed by the NHLS Board and executives, and is based on a fundamental belief that business should be conducted honestly, fairly and legally. All employees are expected to share its commitment to high moral, ethical and legal standards. Health Safety and Environmental Issues While the Governance, Ethics and Social Committee provides guidance on health, safety and the environment, the NHLS has systems and processes in place that deal specifically with these issues. Health and safety issues are reported extensively in the National Institute for Occupational Health (NIOH) Annual Review 2016/17, published concurrently with this Annual Report. Social Responsibility NHLS BLOOD DRIVE Stakeholder relations and corporate social investment are one of the fundamental objectives of the NHLS. As part of the NHLS objectives of establishing partnership and of striving to be a good corporate citizen, it has partnered with the South African National Blood Services (SANBS) in hosting a blood drive every eight weeks. This is one of the Social Investment activities that the NHLS is involved in impacting on the lives of South Africans. For the year under review, the NHLS hosted six blood drives, and manage to collect 313 units of blood from 267 people. The volumes collected will definitely experience an experiential growth in the next few years as more people become educated about the importance of donating blood in saving lives. CELEBRATING MANDELA DAY Nelson Mandela International Day has been inspiring people across the country - and the world - to take action and effect some change, even if only for 67 minutes on 18 July each year. In honour of our late president, individuals and companies alike make the most of this day to demonstrate their commitment to social change, with some going over and above what they usually do for the community. During the year under review, various divisions within the NHLS also took part in this august initiative to make a difference in people s lives. These activities ranged from serving tea and scones by the Haematology Department at Chris Hani Baragwanath Academic Hospital (CHBAH), to assisting nurses at a Paediatric Ward with cleaning and tiding by staff from the Chemistry Department of the same hospital laboratory. TAKE A GIRL-CHILD TO WORK Take a Girl-Child to Work is an important initiative aimed at exposing female learners to the work environment, as well as stimulating their interest in various careers offered by various companies at an early age. During the year under review, the NHLS in collaboration with Cell C hosted a very successful Take the Girl-Child to Work day at its Sandringham campus with 20 school girls in grades from Waverley Girls High School. The learners had an opportunity to interact with various NHLS management and professionals to get an overview of the laboratory medicine environment, as well as to learn about the various career opportunities that exist within the organisation. 172 National Health Laboratory Service

174 Report of the Audit and Risk Committee We are pleased to present our report for the financial year ended 31 March AUDIT AND RISK COMMITTEE MEMBERS AND ATTENDANCE The Audit and Risk Committee (hereafter referred to as the Committee) consists of the members listed hereunder and is required to meet four times per annum as per its approved terms of reference. During 2016/17, four meetings were scheduled and held. The Committee confirms that it has discharged its responsibilities in terms of the National Health Laboratory Service (hereafter referred to as NHLS) Audit and Risk Committee Charter. The composition of the Committee is aligned with Section 77(a) of the PFMA and Treasury Regulation Meeting Dates Name Mr Lunga Ntshinga 4 Dr Balekile Mzangwa C C C A 0 Mr Andre Venter 4 Mr Goolam Manack A A 2 Mr Stanley Harvey 4 Prof. Gregory Hussey A A A % 0 Prof. Haroon Saloojee A A A 1 Mr Michael Shingane A C C C 0 Mr Michael Manning C C C 1 Ms Nelisiwe Mkhize A C C C 0 Mr Thamsanqa Stander C C C 1 Ms Joyce Mogale 4 26 May August November February 2017 Total Meeting Attendance Legend: = Present * = Appointed A = Apology B = Absent % = Retired/Resigned C = Not a member There was one retirement or resignation from the Committee during the year under review. AUDIT AND RISK COMMITTEE RESPONSIBILITY The Committee reports that appropriate formal terms of reference have been adopted in its charter, in line with the requirements of section 55(1)(a) of the PFMA and Treasury Regulation The Committee further reports that it has conducted its affairs in compliance with this charter. THE EFFECTIVENESS OF INTERNAL CONTROL The Committee has reviewed various reports prepared by the internal and external auditors, on adequacy and effectiveness of internal control systems as well as on the Group Annual Financial Statements. The Committee is satisfied that internal control systems and governance practices have been put in place. The Committee is satisfied with the content and quality of monthly and quarterly reports prepared and issued by the Accounting Authority of the economic entity during the year under review. The responsibility for risk management resides with management at all levels. Risk management is embedded throughout the organisation, from members of the Board to all employees. The approach followed by NHLS is to ensure that significant risks are identified and managed. Annual Report 2016/17 173

175 The NHLS has a dedicated Risk Officer to co-ordinate the implementation of its risk management philosophy and strategy as approved by the Board. The Board continues to discharge this responsibility through its Audit and Risk Committee and ensures that risk management is a standing item for discussion at each scheduled Board meeting. EVALUATION OF GROUP ANNUAL FINANCIAL STATEMENTS The Committee has: Reviewed the audited Group Annual Financial Statements with SizweNtsalubaGobodo (SNG) and the Board Reviewed SNG s management report and management s response thereto Reviewed changes in accounting policies and practices Reviewed the entity s compliance with legal and regulatory provisions Reviewed significant adjustments resulting from the audit. The Committee concurs with and accepts the external auditors report on the Group Annual Financial Statements, and is of the opinion that the audited Group Annual Financial Statements should be accepted. COMPETENCY OF THE FINANCE DEPARTMENT In compliance with governance principle 3.6 of the King 3 Code of governance principles, the Audit and Risk Committee is satisfied that there is sufficient expertise, resources and experience within the NHLS finance function. INTERNAL AUDIT The Committee is satisfied that there is an internal audit function in the organisation and that it has addressed the risks pertinent to the economic entity and its audits. The Committee has reviewed internal audit reports and ensured that reported items are addressed effectively. The Committee is considering enhancing internal audit capacity and leadership. CONCLUSION The Committee agrees that the adoption of the going concern premise is appropriate in preparing the Group Annual Financial Statements for the 2016/17 period. The Committee has therefore recommended the adoption of the Group Annual Financial Statements by the NHLS Accounting Authority at their meeting held on 27 July Lunga Ntshinga Chairperson: Audit and Risk Committee 174 National Health Laboratory Service

176 PART D Human Resources Annual Report 2016/17 175

177 Introduction The 2016/17 financial year was to be the year marked with optimism and hope for improvement in the working climate at the National Health Laboratory Service (NHLS), with all employees being more engaged, involved and participating in programmes that affect their lives and the way they work. The year began with the signing of a collective agreement with Organised Labour, expressing the organisation s commitment to honouring and delivering on all outstanding matters. Key amongst these was Phase One (Part 2) of the Remuneration and Reward (R&R) Project, which led to the development of new pay scales and salary adjustments for all employees towards the 50% mark of their then earning against the minimum of the new pay scale; as well as the standardisation of all similar jobs across the organisation through a job evaluation process. Phase One (Part 2) was successfully implemented in April HR Executive Dr Mojaki Mosia The remaining part of the R&R Project is Phase Two, which is the implementation of the Performance-Proficiency Matrix for the four key health professional roles i.e. Pathologist, Medical Scientist, Medical Technologist and Medical Technician. The intent of Phase Two is to differentiate reward as the level of performance increases, in so doing encouraging employees to acquire and demonstrate high levels of competencies. This equates to rewarding the competency demonstrated within the role. This will enable the organisation to promote employees subject to demonstrable performance at the aspirant level of work. This approach will also mitigate the promotion of employees or the allowing of employees to progress with the hope of success when they are not ready for the position. Rather, promotion will become an appreciation of delivery at the next level of work. In addition to the above, through stakeholder engagement, the Human Resource Department updated, consulted and approved critical policies, namely recruitment and selection; performance management; performance pay progression; remuneration and reward; and employment equity and diversity. These are deemed a priority if the NHLS is to be placed on a positive trajectory towards being an efficient, high performing organisation. Furthermore, the Board approved the implementation of the newly developed workforce model, which will provide NHLS leadership with a tool for better workforce planning scenarios and identification of areas of inefficiency. The commitment towards learning, training and development of staff and communities continued, with 100 scholarships being provided to students studying towards diplomas and degrees in Biomedical Science, and 194 bursaries awarded to NHLS staff members in various NHLS careers. The total permanent employee complement stabilised at 6 692, with a total annual remuneration bill of approximately R2.6 billion, inclusive of fixed-term contracts of greater than 18 months and registrars. The staff, organisational and team commitment is proudly solid with a turnover rate of about 5.2% relative to last year s 5.6% (of which 3.6% were voluntary resignations and the remainder mandatory). This 5.2% equates to 348 employees over a total workforce of 6 692, which is inclusive of fixed-term contracts of 18 months and registrars. These numbers depict a healthy turnover rate, which allows the organisation to renew itself. The single concern about this turnover rate, however, is its composition, since 44.5% of it comprises Pathologists (22), Scientist (14), Technologists (88), Technicians (11), Laboratory Supervisors (7) and Managers (13) all of whom are core to the organisation s operations. The year under review recorded progress towards the NHLS 2020 Strategy, more so focusing on goal number seven, which is to strengthen the organisation s position through adequate, competent and motivated human capital. Overall progress made was as follows: The approval of the updated performance management policy, which integrates performance moderation and 360 Leadership Assessment as core components to enable consistency and living whilst demonstrating the NHLS values. All leadership across the regions received training in this regard to ensure shared understanding. 176 National Health Laboratory Service

178 The development of the Performance-Proficiency Matrix for each of the four key health roles. The process went through multiple stakeholder consultations i.e. task teams consisting of discipline experts and role players, Executive Committee, Remuneration and Human Resources Committee and the Board. The project is at the costing stage and is awaiting final financial approval by the Finance Committee. As previously reported the Integrated Talent Management Policy was developed and approved. The next step in this regard is the operationalisation of the policy and the determination of the NHLS Talent Strength; as well as the development of strategies to close identified gaps. In this regard, the NHLS equity profile will be prioritised in key roles where under-representation has been identified. All these plans will be integrated into the Employment Equity Plan for the next five years, which is effective from April To ensure the successful facilitation of the NHLS Strategy and implementation thereof by leadership, the reconfiguration and realignment of the NHLS structure and the re-profiling of its roles is critical. The Board approved the updated organisational structure and gave effect to a more integrated matrix structure, in which human resources, finance and quality improvement functions within the region report directly to the Area Manager. This will ensure that all matters are resolved at their point of origin, as well as provide a one stop service within the region, with functional expertise provided through dotted line reporting. The NHLS relationship with various stakeholders continues to improve, with the Bargaining and Labour Relations Forum having no matters of dispute referred to the Commission for Conciliation Mediation and Arbitration (CCMA) in the reporting period. The creation of two full-time Shop Steward positions has been beneficial in facilitating deeper and more meaningful engagements on matters of mutual interest before they become disputes. Moving forward, Organised Labour will continue to be an integral part of the NHLS processes, with full participation status in the interviewing, performance moderation, performance-proficiency assessment and insourcing task team processes. In conclusion, the year ahead will be characterised by how well we operationalise all approved policies, as well as activate focus groups to unpack the employee climate-engagement survey findings. In addition, the process of obtaining and giving feedback on the 360 Leadership Assessment pilot for the senior leadership-management cohort will be crucial. The biggest challenge for the year ahead will be the proposed insourcing of the security, cleaning and gardening services in respect of affordability and sustainability, relative to the overall budget of the NHLS. Human Resources Oversight Statistics Table HR1: Personnel cost Total Expenditure for the Entity (R) Personnel Expenditure (R) Personnel Expenditure as a % of Total Expenditure (%) Number of Employees Average Personnel Cost per Employee (R) Total Remuneration Cost % Table HR1 reveals that 37% of total expenditure is attributable to personnel cost. In the period under review, the year ended with an inclusive staff complement of (i.e. all personnel types inclusive of students, sessional workers and post retirement). Table HR2 reflects the cost by occupational category. Table HR2: Personnel cost by salary band Salary Band Personnel Expenditure (R) % of Personnel Expenditure to Total Personnel Cost (%) Number of Employees Average Personnel Cost Per Employee (R) Top Management Senior Management Professional qualified Skilled Semi-skilled Unskilled Training (Students/Learners) Total Table HR 2 also reveals that the greatest cost lies in three categories, namely professional, skilled and semi-skilled, which consist of positions at grade B, C and D. Annual Report 2016/17 177

179 Performance rewards by salary band No bonuses were paid in the 2016/17 financial period. Table HR3: Training costs Training Type Non-PIVOTAL* programmes (short courses, workshops, seminars, congresses and continuous professional development interventions) PIVOTAL programmes for nonemployees (higher education qualifications) PIVOTAL programmes for non-employees participating in learnerships, on-the-job training and workplace experience Personnel Expenditure R 000 Training Expenditure R 000 Training Expenditure as a % of Personnel Cost (%) Number of Employees Trained Average Training Cost per Employee (R) % * PIVOTAL = Professional, Vocational, Technical and Academic learning programmes that result in occupational qualifications or part qualifications on the National Qualifications Framework. The NHLS continues to fulfil its role in promoting and prioritising skills development through the analysis of its employees skills needs by implementing the Workplace Skills Plan. Multiple learning programmes were offered through short learning programmes, in-service conferences and congresses, as well as continuing professional development programmes to enable the organisation to comply with legislation, improve quality of services, ensure business continuity and assist in the mitigation of risks. In the past year, the NHLS achieved 91% of the planned training target, as compared to the legislated target of 60%, which reflected an amount of learners who had attended technical and non-technical short learning programmes, workshops, seminars, on-the-job training and seminars in 2016/17. In addition to regular training for learnership and professional registrations, 100 scholarships were awarded to needy students across the country studying towards the National Diploma in Biomedical Technology and the Bachelor of Health Science, and bursaries were given to NHLS staff wishing to pursue career development by way of formal qualifications. Table HR4: Employment and vacancies Occupational Level 2015/16 No. of Employees 2015/16 Approved Posts 2016/17 No. of Employees 2016/17 Vacancies % of Vacancies Top Management Senior Management Professional qualified Skilled Semi-skilled Unskilled Registrars Total % Table HR4 reveals a vacancy rate of 14% relative to approved positions, however the number of active vacancies was far less. Though more vacancies exists, only few critical positions were advertised due to the financial challenges experienced by the NHLS. Accordingly, in this reporting period, mainly core positions were advertised. In total, 351 positions were successfully filled, inclusive of registrars. From Table HR5, the overall turnover, less the End of contract category, reveals that the turnover level has stabilised at less than the 10% ratio, with voluntary resignations being 241 employees. Specific concern is the fact that the organisation loses people that are experienced. Their replacements are less experienced particularly the pathologists and technologists since these appointees were from the cohort that had recently completed training. 178 National Health Laboratory Service

180 Table HR5: Employment changes Employment at Occupational Level Beginning of Period Appointments Terminations Employment at End of the Period Top Management Senior Management Professional qualified Skilled Semi-skilled Unskilled Registrars Total The terminations in Table HR5 reflect only loss of permanent employees (this excludes fixed term contractors less than 18 months, sessional, post retirees and students). Students, other than registrars whose contracts are over 18 months, are excluded from the 323 appointments and 348 employees terminations reported. Table HR6: Reasons for leaving Reason Number % of Total Staff Leaving Death Resignation Dismissal Discharged Retirement Ill health Expiry of contracts Contract not valid Total % Table HR6 reveals voluntary resignations at 3.6%, which constitutes over 40% of the total staff turnover when the category Expiry of Contracts is excluded. The second highest staff turnover category was Retirements at 0.87%. Table HR7: Labour relations Misconduct and disciplinary action Nature of Disciplinary Action Number Written warning 28 Final written warning 33 Dismissal 15 Not guilty 4 Resignation 3 Demotion 1 Total 84 The NHLS dealt with 84 material disciplinary cases in the 2016/17 year resulting in 15 dismissals and 61 final and written warnings being issued. Overall, formal cases were at 1.2%, excluding various verbal warnings. Annual Report 2016/17 179

181 Table HR8 (a): Equity target and employment equity (EE) status Male Male African Coloured Indian White Level Current Target Current Target Current Target Current Target Top Management Senior Management Professionally qualified Skilled level Semi-skilled Unskilled Total Table HR8 (b): Equity target and employment equity status Female Female African Coloured Indian White Level Current Target Current Target Current Target Current Target Top Management Senior Management Professionally qualified Skilled level Semi-skilled Unskilled Total Tables HR9 (a) and (b) indicate the EE profile of NHLS as at 31 March The targets reflected in the table were generated through the analysis of the workforce profile in alignment with the economically active population demographics, as provided by the Department of Labour annually. The workforce profile indicates an under-representation of African males and females, and Coloured males and females at the senior management, professionally qualified and skilled occupational levels. The gaps in the under-represented groups have informed the target-setting process, based on approved, budgeted vacancies and vacancies that will be created by employees retiring in the next year. Table HR8 (c) Equity target and employment equity status Staff with Disabilities Male Female Level Current Target Current Target Top Management Senior Management Professionally qualified Skilled level Semi-skilled Unskilled Total The targets for People with Disabilities are not highly ambitious because an environmental audit is required to establish the areas that are currently disability friendly so that progress can be made in those areas while the NHLS prepares to increase the level of disability-friendly spaces across its campuses. 180 National Health Laboratory Service

182 PART E Financial Information Annual Report 2016/17 181

183 National Health Laboratory Service Audited Group Annual Financial Statements for the year ended 31 March 2017 Chief Financial Officer s report OVERVIEW: STATEMENT OF FINANCIAL PERFORMANCE A summary of the financial performance for the 2016/17 fiscal year is as follows: Acting CFO Mr Ben Wikner The NHLS generated a deficit amounting to R1.9 billion compared to a surplus of R273 million surplus in the previous financial year. Revenue grew from R6.4m to R7.1 billion. Revenue from provincial budgets amounted to 90% of the total revenue generated. Production costs, including direct labour and material, grew from R4.8 billion to R5.8 billion. This equated to a 21% increase (2015/16: 14% increase) mainly due to increases in labour, test volumes, price increases as well as fluctuations in the exchange rate. Labour constituted 43% of the total revenue compared to 37% in the previous financial year. Average test revenue per capita increased by 5.2% (2015/16: 7% increase). Operational costs increased by 91%. This increase in support costs is largely due to an increase in the provision for doubtful debt. OVERVIEW: STATEMENT OF FINANCIAL PERFORMANCE A summary of the financial position for the 2016/17 financial year is as follows: Assets decreased from R3.9 billion to R2.9 billion, which translates to a 44% decrease, mainly due to a 46% decrease in accounts receivable. The closing bank balance stood at R391 million compared to R739 million in the previous financial year. The current liability increases were mainly driven by the increases in leave provision and the trade payables balance. The leave provision had an overall increase of 32% to R186 million, and trade payables increased by 12% to R973 million. The organisation struggled to stabilise the delivery of operations during the reporting period. The implementation of the NHLS Strategic Plan is being hampered by poor cash flows. Should the provincial DoHs continue to pay the NHLS, the organisation will improve the diagnostic laboratory model, continue to deliver on its mandate and further improve its financial performance. CASH FLOW During the reporting period, the NHLS received R7.2 billion from customers. Of the R7.2 billion, R3.2 billion was used for personnel costs and R3.9 billion for goods and services. Compared to the prior financial year, payments from customers amounted to R6.6 billion, while R2.5 billion was used for personnel costs and R3.9 billion for goods and services. BUDGET VARIANCE ANALYSIS The total revenue is 5.5% over budget, with a Rand value of R392 million due to a 4.8% increase in demand for diagnostic laboratory services in 2016/17. The positive variance is mainly attributable to the increase in priority tests as per alignment of the NDoH s protocols. Personnel costs are over budget by 6.5% due to the introduction of the 13 th cheque for the A C band staff in 2016/17. Material expenditure remains constant at 44% (2016: 44%) as a percentage of revenue. 182 National Health Laboratory Service