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ACT for TB/HIV Access to Facilities

Our facilities have unique combination of experience and strengths listed below to produce research of high impact. All facilities have the necessary infrastructure and staff capacity to conduct quality research.

The Aurum Institute Klerksdorp, Tembisa and Rustenburg Clinical Research Centres (CRC) (Dr Wallis, Dr Charalambous, Dr Maenetje, Dr Edward, Prof Churchyard)

The 3 Aurum Institute Clinical Research Centres in Klerksdorp, Tembisa and Rustenburg have managed 9 vaccine trials (TB or HIV) and 6 treatment or prevention trials (TB and/or HIV), with capacities to enroll 500, 1000 and 500 subjects annually, respectively. Each site has access to unique patient populations and are fully established to conduct epidemiological and clinical trial Phase I to Phase IV studies. Aurum CRCs have access to Primary Healthcare Facilities – unique patient referral centres for protocol defined populations. Established active community boards / special group leaders serve as effective platforms for: i) Community Awareness Campaigns; ii) Disseminating key research findings; iii) TB/HIV education; and iv), recruiting interested members of various patient populations.

These sites have established Data Management and Quality Assurance and Control Departments equipped for data capturing / faxing and 100% SDV. Pharmacies provide contraceptive medication sourced through DoH for promoting participant protocol compliance. On-site laboratories perform validated rapid HIV, rapid urine pregnancy and urine microscopy. The Klerksdorp and Rustenburg laboratory also perform immunological techniques such as PBMC isolations and cell culture. The Tembisa laboratory is able to perform PBMC isolations, but additional workspace is required. Biobanking facilities are available across all Aurum laboratories; however an additional liquid nitrogen tank would need to be procured for the Tembisa CRC. All laboratory and pharmacy equipment fridges, freezers and room temperature regulating air conditioners are calibrated and linked to an automated continuous temperature monitoring system that notifies staff of temperature deviations.

Klerksdorp CRC: The site is in the Matlosana sub-district a part of the Dr Kenneth Kaunda Health District and in the North West Province. Economic activity is predominantly gold mining and agriculture. This provides opportunity for conducting clinical trials in a unique population hardest hit by the TB and HIV epidemics. The Matlosana sub-district has 16 primary clinics (4 CHC’s). The CRC has a well-established relationship with the local department of health with 9 years of clinical trial experience, the site is well established and has successfully completed numerous phase I and II clinical trials. The layout of the Klerksdorp CRC is reconfigurable to streamline operational aspects for various trial designs, with dedicated TB treatment and infection control facilities.

Rustenburg CRC: The Site is situated in the Bojanala Platinum District of the North West (NW) Province. Economic activity is predominantly platinum and other mineral mining. A growing mining industry over the past two decades has resulted in many migrant populations relocating to Rustenburg, making Rustenburg one of the fastest growing cities in South Africa. The Rustenburg sub-district has 24 Department of Health clinics. With 7 years of research experience, the site has experience in both observational cohorts, household contact tracing and clinical trials. The site has experience with special populations which include adolescents and men having sex with men (MSM) and a high HIV incidence female cohort (13.7/100pyrs). The Rustenburg CRC is ideally located within the central business district of Rustenburg central to participants residing in the surrounding neighbourhoods using established public transport infrastructure systems – promoting protocol compliance and retention.

Tembisa CRC: The Site is situated on the grounds of the Tembisa Academic and Tertiary Hospital in Ekurhuleni North, in the Gauteng Province. The site has been operational since 2008 and is experienced in TB treatment trials, TB vaccine trials, HIV prevention trials, HIV treatment trials and HIV vaccine trials. The site has established a positive relationship with the study community and its main source of recruitment – 26 Primary Healthcare Clinics. The Tembisa CRC maximises utilisation of space and effective infection control cover-age by installing recycled shipping containers into 4 blocks, each with 4 adjacent and perpendicularly arranged containers around a covered central participant waiting area with steady airflow, UV germicidal lights (waiting areas and clinic rooms) and reverse-blade ceiling fans (waiting areas) to extract and kill infectious agents. An Aurum Investigator Initiated and led study of SSI’s H1/IC31® TB vaccine was successfully tested (safety and immunogenicity) in an HIV population for the first time globally at the Tembisa CRC and collaborating Ifakara Health Institute in Tanzania.

The Setshaba Research Centre (SRC) (Dr. Ahmed & Dr. Malahleha)

This site was founded in 2004 as a medical research centre with the objective of creating value and contributing to the greater good of society. The centre was developed with a core focus of conducting HIV prevention studies, specifically aimed at reducing the risk of HIV infection for women in particular, who are often a vulnerable population for a number of reasons. Since its foundation in 2004, the centre has grown extensively and has developed the capacity to conduct large scale biomedical and social scientific research studies. Although its primary focus still remains on HIV prevention in women, we have expanded our portfolio to include TB research (including TB diagnostic, new drug trials and vaccine studies), other vaccine, clinical and socio-behavioural studies. The centre is optimally situated in a residential area in Block H, Soshanguve Township (next to the “Transfer” area), as an independent site. The unit is easily accessible by minivan taxis – the common mode of transport of most South Africans and the local residents. Since 2008, the SRC has been registered as a section 21 Non-Governmental Organization/Non-Profit Organization (NGO/NPO) and functions as an independent entity. The Setshaba Research Centre has the infrastructure and staff capacity to conduct clinical trials on a medium to large scale basis and allows various trials to be conducted in various buildings simultaneously

WITS University Department of Nuclear Medicine (Prof Vangu)

This facility is used for combined PET/CT scanning that can be integrated with TB/HIV research, through the Charlotte Maxeke Johannesburg Academic Hospital, Chris Hani Baragwanath Academic Hospital, and the Donald Gordon Medical Centre. The units perform approximately 10,000 conventional nuclear medicine scans and over 1000 PET/CT scans annually. PET capabilities include 18F-FDG and 68Ga.

The Welkom Kopanong DoH MDR-TB Treatment Unit / The Aurum Institute Welkom MDR TB CRC (Dr Zakhura)

This new, under resourced, rural development site is situated in the Lejeweleputswa district of the Free State Province in an established town in and around large gold and uranium mines, where the prevalence and incidence of MDR-TB is high. An average of 2400 MDR-TB diagnoses are made each year at the facility. The implementation of standardized systems across all sites plus support from experienced sites will ensure rapid site establishment and training of staff. The site will soon be initiating their first MDR TB trial.

This site regarding clinical research is naïve and is being established in collaboration with the Free State Department of Health, to conduct a broad range of MDR TB research. The Welkom MDR TB CRC therefore meets the requirements of being a new, under resourced, previously disadvantaged site that will provide access to a unique population with a high burden of MDR TB. The Welkom MDR TB Clinical Research Centre will strive to implement research that meets national and global priorities. A substantial proportion of the consortium’s budget will be focused on building capacity at this site. 135 patients with MDR-TB are hospitalised and treated for 4 months and followed-up and treated for an additional 2 months throughout the year. Due to the high burden of MDR-TB in the mines in and around Welkom, an additional 200 outpatients are diagnosed and start treatment every month with 2 400 MDR-TB patient diagnoses annually. A dedicated area for clinical trials exists, including workspace, consulting rooms waiting areas, pharmacy, outside sputum collection booths and 2-8°C refrigeration. The Welkom CRC was built to maximize airflow with plenty windows and state of the art UV germicidal lights. Patients are hospitalised in sections based upon the duration of treatment received to reduce cross-infection amongst MDR-TB patients. A separate area is dedicated solely for XDR-TB patients – an average of 3 XDR-TB cases are hospitalised each year.

The Inkosi Albert Luthuli Central Hospital sites Prof Ndungu

The Collaboration will expand its sites to include Prof Thumbi Ndungu’s and Dr Emily Wong’s HIV Pathogenesis Programme based at the Inkosi Albert Luthuli Central Hospital in Kwa-Zulu Natal. This is a newly established site that has integrated clinical/laboratory capability to conduct research bronchoscopies to study ways in which HIV alters lung immunity to TB. The Inkosi Albert Luthuli Central Hospital site in Kwa-Zulu Natal is a new site started from scratch at the end of 2012 and the research bronchoscopy program is truly nascent and in need of further development.

ACTS and Legogote clinics (Prof Penn)

These clinics in Mpumalanga have an excellent home based care programme, which would be a potential site for some of Prof Claire Penn’s behavioural and training interventions.

WITS Health Communication Research Unit (HCRU) (Prof Penn)

This facility has created an international profile of its research output over the past decade in terms of research techniques, publications and training of postgraduate students. The standardization of qualitative methods to describe language behaviours has done much to address concerns of precision and validity. Aside from the accumulating archive of easily accessible data-bases of interactional data, novel approaches to analyse complex data have been developed into effective guidelines for management of translation and transcription, and analysis techniques. The HCRU has access (in rural and previously disadvantaged under resourced urban settlements) for research purposes to clinic staff, home based care workers, community members, TB patients, clinic staff, home-based care workers primarily in the Mpumalanga (ACTS Clinic) and Gauteng provinces (Sizwe Tropical Disease Hospital, Helen Joseph Hospital, South Rand Hospital) – populations crucial to investigating TB patients’ illness experiences, cultural perspectives and their link with communication processes in TB care versus cure contexts. Through the PATA network (Paediatric Aids Treatment for Africa) Professor Penn has facilitated workshops across Africa on communication aspects.

The work conducted by the Wits HCRU is innovative as it pays careful attention to the dynamics of health care interactions and to language and cultural barriers to care. The role of the mediator or cultural broker in the system is critical and evidence suggest the positive effects of site specific team training in these matters and their impact on adherence. This evidence from HIV has been published and acknowledged. The methods used include qualitative methods, narratives and drama methods, which are novel and effective for gathering information and team training as well as developing capacity for both patients and health care workers. Language barriers seem particularly important with MDRTB.

 K-RITH (Prof Ndung’u)

The HIV Pathogenesis Programme (HPP)-UKZN has been involved in studies of HIV-1 immunopathogenesis for the last 15 years. The laboratory has undertaken ground-breaking work on the role of human leukocyte antigens, cytotoxic T cell responses, innate immunity and humoral immune mechanisms associated with control of HIV-1 infection with over 70 publications in the last 3 years. The laboratory (400m2) is located in the Doris Duke Medical Research Institute (DDMRI) and consists of: an exploratory research section, a receiving area, a repository and a diagnostic section.

WITS University node of the CBTBR (Prof Kana)

The facility includes 2 Biosafety Level II and III (under negative pressure) laboratories respectively, walk-in cold rooms and a radioactive lab (registered with DoH and Radiation services). The laboratories house all necessary equipment to conduct biomedical TB research and are registered with the South African National Department of Agriculture Forestry and Fisheries, providing ideal environments to conduct cross-disciplinary research spanning the study of fundamental concepts to translational research aimed at describing mechanisms underpinning various manifestations of TB disease. High-level mycobacteriology expertise is combined with clinical research in a manner unique to South Africa. Several specialist laboratory assays have been developed that allow for monitoring of dormant bacterial populations in patients with TB disease. The combination of BSL2 and 3 laboratories (together with the ability to use radio-isotopes) is unique in the region, offering an exciting platform for future collaborative research. The Centre is in the process of developing novel methods to more accurately quantitate bacterial burden in TB infected individuals through the assessment of a suite of methods that are targeted at detecting and quantifying differentially culturable tubercle bacteria. There is a growing body of evidence that points to a significant population of non-culturable bacteria in patients with active TB disease. These organisms would evade detection by conventional culture, which would result in overall underestimate of the total organ bacillary load. Using most probable number assays combined with power statistics and artificial neural networks, researchers at the CBTBR have developed robust methodology for quantification of non-culturable bacteria. This adds a dynamic aspect of innovation to our overall approach and will allow for measurement of drug sterilizing activity.

Centre for Tuberculosis (CTB) (Dr Ismail)

The facility incorporates the National TB Reference Laboratory for South Africa – responsible for public health surveillance for TB. This role is performed by utilizing laboratory based approaches with a state of the art BSL 3 facility. A full spectrum of phenotypic testing including drug susceptibility testing for first second and novel drug resistance testing is provided with established MIC testing for TB and most recently large scale whole genome sequencing (WGS) for TB. Thus the infrastructure is capable of performing high level laboratory work. Staff are specialized in WGS including bioinformatics, molecular epidemiology of TB utilizing Spoligo, MIRU-VNTR 24 loci and RFLP (manual and automated) and laboratory specialist including pathologist and SANAS QA assessor. An Epidemiology section with specialized data systems and development capability is available. The Centre has innovated in establishing Whole Genome Sequencing as a diagnostic tool for detecting the molecular basis of drug resistance in TB including the study of compensatory mutations. This is becoming increasingly relevant as current tools are applying targeted approaches which may miss key pathways that impact on patient outcomes and potentially new avenues for drug discovery. The second large focal area is on the molecular epidemiology of TB examining the role of strain types and associated factors related to poor patient outcomes. This is important to inform targeted approaches in health care delivery.

Clinical Laboratory Services (CLS) (Mr Suliman Minty)

This facility consists of a specialized pre-analytical division, an analytical laboratory for safety (Haematology, Chemical Pathology and Serology testing), a PBMC laboratory, a comprehensive diagnostic BSL III TB laboratory, a Biorepository and access to certified referral academic laboratories for testing not conducted in-house. CLS has been awarded the H3 A Biorepository Grant to provide biorepository support for the H3 A projects conducted in Africa. The staff compliment is made up of 6 experienced technical staff members trained in microbiology / mycobacteriology and the laboratory manager. The CLS laboratory is British Qualogy GCLP, FHI DAIDS and SANAS certified and participates in CAP SMILE monitored EQA and processes between 600 and 800 clinical trial sputum specimens per month and currently performs approximately 200 TB Gold assays, 600 Auramine or ZN smears, 100 HAIN PCR tests, 600 MGIT cultures and 200 drug susceptibility tests (primary and secondary). They are able to perform: Microscopy: ZN and Aura-mine smears; MGIT culture and sensitivity for first and second line drugs; DST: (1st line: INH, RIF, EMB, STR, PZA; 2nd line: Amikacin, Capreomycin, Kanamycin, Ofloxacin, Moxifloxacin); Solid media culture on LJ and Ogawa media and Hain PCR testing for: i.) MTB identification and detection of resistance to INH and Rif; ii.) Mycobacterial species identification; iii.) Direct detection of 5 clinically relevant mycobacterial species from patient specimens (GenoType Mycobacterial Direct); iv.), second line resistance testing for fluoroquinolones, aminoglycosides and EMB; v.) GenXpert MTB real-time PCR; and vi.), TB Quantiferon testing. A data base system to store, track and review MGIT results is established together with a TB isolate biorepository.