Phenotypic and genotypic characterisation of mycobacterium tuberculosi strains in relation to the transmission of tuberculosis in South African mines

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy.The prevalence of tuberculosis in South African miners is substantially higher than that of in the general population. Through exposure to dust which leads to different degrees of silicosis, and by working in enclosed spaces where coughed out bacilli can survive in droplet nuclei and be inhaled by other workers, miners are especially prone to to become infected with M. tuberculosis and develop the disease. It is not only the working conditions which promote transmission of M. tuberculosis, but the living conditions as well. Most miners live and sleep in rooms shared by up to eight other men, which increases the opportunity for transmission, leading to both primary and reinfection tuberculosis.IT201

The importation and establishment of community transmission of SARSCoV- 2 during the first eight weeks of the South African COVID-19 epidemic

BACKGROUND : We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures. METHODS : Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt). FINDINGS : From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28 49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/ 2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial Rt was 2.08 (95% confidence interval (CI): 1.71 2.51). INTERPRETATION : The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces.The South African governmenthttps://www.journals.elsevier.com/eclinicalmedicineam2022School of Health Systems and Public Health (SHSPH

POPIA Code of Conduct for Research

No abstrac

Corrigendum: POPIA Code of Conduct for Research

No abstrac

High Diversity of Mycobacterium tuberculosis Genotypes in South Africa and Preponderance of Mixed Infections among ST53 Isolates ▿

The reemergence of tuberculosis (TB) has become a major health problem worldwide, especially in Asia and Africa. Failure to combat this disease due to nonadherence or inappropriate drug regimens has selected for the emergence of multiple-drug-resistant (MDR) TB. The development of new molecular genotyping techniques has revealed the presence of mixed Mycobacterium tuberculosis infections, which may accelerate the emergence of drug-resistant strains. There are some studies describing the local distribution of circulating strains in South Africa, but to date, reports describing the frequency and distribution of M. tuberculosis genotypes, and specifically MDR genotypes, across the different provinces are limited. Thus, 252 isolates (of which 109 were MDR) from eight of the nine provinces of South Africa were analyzed by spoligotyping. Spoligotyping showed 10 different lineages, and ST53 (11.1%) and ST1 (10.3%) were the most frequent genotypes. Of the 75 different spoligopatterns observed, 20 (7.9%) were previously unreported. Analysis of the mycobacterial interspersed repetitive units of variable-number tandem repeats of the ST53 and ST1 isolates revealed that ∼54% of the ST53 isolates were of mixed M. tuberculosis subpopulations. Drug resistance (defined as resistance to at least isoniazid and/or rifampin) could only be linked to a history of previous anti-TB treatment (adjusted odds ratio, 4.0; 95% confidence interval, 2.27 to 7.10; P = <0.0001). This study describes a high diversity of circulating genotypes in South Africa in addition to a high frequency of mixed M. tuberculosis subpopulations among the ST53 isolates. MDR TB in South Africa could not be attributed to the spread of any single lineage

Status of South Africa’s national health research system : a 2018 update

South Africa’s pursuit of universal health coverage requires contextualised scientific knowledge to guide the development of health system-strengthening strategies. Urgent concerted action is needed to strengthen the national health research system (NHRS), with a view to generating high-quality knowledge and promoting its utilisation in population health.Four of the authors (MM, MB, TN and JMK) were funded by the EDCTP2 programme, supported by the European Union.http://www.journals.co.za/content/journal/healthram2019School of Health Systems and Public Health (SHSPH

Pyrazinamide Resistance among South African Multidrug-Resistant Mycobacterium tuberculosis Isolates▿

Pyrazinamide is important in tuberculosis treatment, as it is bactericidal to semidormant mycobacteria not killed by other antituberculosis drugs. Pyrazinamide is also one of the cornerstone drugs retained in the treatment of multidrug-resistant tuberculosis (MDR-TB). However, due to technical difficulties, routine drug susceptibility testing of Mycobacterium tuberculosis for pyrazinamide is, in many laboratories, not performed. The objective of our study was to generate information on pyrazinamide susceptibility among South African MDR and susceptible M. tuberculosis isolates from pulmonary tuberculosis patients. Seventy-one MDR and 59 fully susceptible M. tuberculosis isolates collected during the national surveillance study (2001 to 2002, by the Medical Research Council, South Africa) were examined for pyrazinamide susceptibility by the radiometric Bactec 460 TB system, pyrazinamidase activity (by Wayne's assay), and sequencing of the pncA gene. The frequency of pyrazinamide resistance (by the Bactec system) among the MDR M. tuberculosis isolates was 37 of 71 (52.1%) and 6 of 59 (10.2%) among fully sensitive isolates. A total of 25 unique mutations in the pncA gene were detected. The majority of these were point mutations that resulted in amino acid substitutions. Twenty-eight isolates had identical mutations in the pncA gene, but could be differentiated from each other by a combination of the spoligotype patterns and 12 mycobacterial interspersed repetitive-unit loci. A high proportion of South African MDR M. tuberculosis isolates were resistant to pyrazinamide, suggesting an evaluation of its role in patients treated previously for tuberculosis as well as its role in the treatment of MDR-TB

Corrigendum: POPIA Code of Conduct for Research

Jerome Amir Singh's affiliation was erroneously given as: Centre for Medical Ethics and Law, Stellenbosch University, Stellenbosch, South Africa. Thecorrect affiliation is: School of Law, Howard College, University of KwaZulu-Natal, Durban, South Africa. The error appears in the Discussion Document by Adams et al. [https://doi.org/10.17159/sajs.2021/10933] on Page 1 under Affiliations (no. 22) and on Page 11 in the table under Authors' information, as well as in the accompanying Commentary by Adams et al. [https://doi.org/10.17159/sajs.2021/10935] in Table 1 on Page 3

POPIA Code of Conduct for Research (with corrigendum)

The POPIA Code of Conduct for Research, as it is currently being considered, pertains to research conducted in South Africa, which, as part of the research process, uses personal information as defined under POPIA. This Discussion Document outlines the main areas relating to the processing of personal information for research purposes which the proposed Code will address, including what consent models would be permissible under POPIA; the issues in relation to genetic research and the processing of personal information contained in inherited characteristics; the use of information matching programmes by researchers; and the use of personal information obtained from social media platforms for research. With ongoing and wide consultation with the scientific community in South Africa and all relevant stakeholders, it is hoped that the Code will provide guidance in supporting the lawful and responsible use of personal information while conducting scientific research in South Africa. The purpose and scope of the Code of Conduct for Research are set out in the accompanying Commentary available at https://doi.org/10.17159/sajs.2021/1093