Tuberculosis testing patterns in South Africa to identify groups that would benefit from increased investigation.

The National Health Laboratory Service (NHLS) collects all public health laboratory test results in South Africa, providing a cohort from which to identify groups, by age, sex, HIV, and viral suppression status, that would benefit from increased tuberculosis (TB) testing. Using NHLS data (2012-2016), we assessed levels and trends over time in TB diagnostic tests performed (count and per capita) and TB test positivity. Estimates were stratified by HIV status, viral suppression, age, sex, and province. We used logistic regression to estimate the odds of testing positive for TB by viral suppression status. Nineteen million TB diagnostic tests were conducted during period 2012-2016. Testing per capita was lower among PLHIV with viral suppression than those with unsuppressed HIV (0.08 vs 0.32) but lowest among people without HIV (0.03). Test positivity was highest among young adults (aged 15-35 years), males of all age groups, and people with unsuppressed HIV. Test positivity was higher for males without laboratory evidence of HIV than those with HIV viral suppression, despite similar individual odds of TB. Our results are an important national baseline characterizing who received TB testing in South Africa. People without evidence of HIV, young adults, and males would benefit from increased TB screening given their lower testing rates and higher test positivity. These high-test positivity groups can be used to guide future expansions of TB screening.

Low prevalence of transmitted genetic drug resistance in a cohort of HIV infected naïve patients entering antiretroviral treatment programs at two sites in northern South Africa.

Infection with drug resistant viruses influences the outcome of antiretroviral therapy (ART). This study was carried out to determine the transmitted genetic drug resistance profile in a cohort of patients prior to initiation of treatment at two treatment sites in northern South Africa. These study sites were among the first to benefit from antiretroviral drugs in this region. Data on HIV drug resistance are also limited in northern South Africa; and resistance testing prior to initiation of treatment is not undertaken. In 2008, 80 protease and 80 reverse transcriptase nucleotide sequences obtained from 80 patients were analyzed for genetic drug resistance using the calibrated population resistance tool for transmitted drug resistance. Viral genetic subtypes were determined by phylogenetic analysis. Two drug resistance mutations (M41L and K103N) were detected in two different patients (2.5%; 95% CI: 0.0077-0.0863). Twenty-three sequences (29%) harbored at least one secondary mutation in the reverse transcriptase gene; while all sequences had at least one minor mutation in the protease gene. Phylogenetic analysis of the protease and reverse transcriptase genes showed that 79 out of 80 viruses were HIV-1 subtype C, and one was an A1/C recombinant. The observations suggest that after 4 and 8 years access to ART in Mankweng and the Bela Bela communities respectively, drug resistance mutations in the naïve population was low. Regular studies are needed to update information on drug resistant viruses in treatment naïve patients to inform better treatment policies.

"I would watch her with awe as she swallowed the first handful": A qualitative study of pediatric multidrug-resistant tuberculosis experiences in Durban, South Africa.

BACKGROUND: There are limited data on the experiences of children being treated for drug-resistant tuberculosis (DR-TB), and most work in the area has been done with older children and adolescents. Comprehensive explorations of the caregiver experiences in this area are also lacking. OBJECTIVE: To describe the experiences of being treated for drug-resistant tuberculosis of children and their caregivers. METHODS: This was a qualitative study done using focus group discussions (FGDs) among three different groups of participants: 1) health care providers involved in the care of children being treated for DR-TB (including physicians, nurses, and pharmacists)-herein referred to as providers; 2) household caregivers of children being treated for DR-TB-herein referred to as caregivers; and 3) children who were being treated for DR-TB-herein referred to as children. The population was a convenience sample and included children hospitalized between January 1, 2018, and June 30, 2020, ages 0-14 years old, as well as their caregivers and providers. Focus group transcripts and notes were analysed using a thematic network analysis based in grounded theory The analysis was iterative and the coding system developed focused on "stressful experiences" as well as ways to address them along the diagnostic and treatment journey. This paper follows the COREQ guidelines. RESULTS: 16 children between the ages 7 and 14 years participated in 5 FGDs, 30 caregivers participated in 7 FGDs, and 12 providers participated in 3 FDGs. Data from the children and the caregivers were the focus of this analysis, although some themes were informed by the discussions with the providers as well. In general, it was reported that for a child diagnosed with DR-TB, there is a lived experience of stress that impacts their physical, mental, and social well-being. These pediatric patients and their families therefore develop strategies for coping with these disruptions to their lives. In general, there were major disruptive experiences that resulted from the process around receiving a diagnosis of DR-TB and second distinct set of stressful experiences that occurred during the treatment of DR-TB once the diagnosis had been made. These stresses occur in the physical, mental, and social realms, and families develop multiple strategies to cope with them, demonstrating resilience in the face of this disease. CONCLUSION: Addressing the stresses experienced by children and their caregivers through child-friendly DR-TB testing, treatment, and counseling is not only essential for ending TB but also for enacting a human-rights based approach to child health in general. Children with DR-TB are a vulnerable population, and they have often been the last to benefit from advances in general pediatric care and in DR-TB care more specifically.

Xpert MTB/RIF versus sputum microscopy as the initial diagnostic test for tuberculosis: a cluster-randomised trial embedded in South African roll-out of Xpert MTB/RIF.

BACKGROUND: In South Africa, sputum smear microscopy has been replaced with Xpert MTB/RIF as the initial diagnostic test for tuberculosis. In a pragmatic parallel cluster-randomised trial, we evaluated the effect on patient and programme outcomes. METHODS: We randomly allocated 20 laboratories (clusters) in medium-burden districts of South Africa to either an Xpert (immediate Xpert) or microscopy (Xpert deferred) group (1:1), stratified by province. At two primary care clinics per laboratory, a systematic sample of adults giving sputum for tuberculosis investigation was assessed for eligibility. The primary outcome was mortality at 6 months from enrolment. Masking of participants' group allocation was not possible because of the pragmatic trial design. The trial is registered with the ISRCTN registry (ISRCTN68905568) and the South African Clinical Trial Register (DOH-27-1011-3849). FINDINGS: Between June and November, 2012, 4972 people were screened, and 4656 (93·6%) enrolled (median age 36 years; 2891 [62%] female; 2212 [62%] reported being HIV-positive). There was no difference between the Xpert and microscopy groups with respect to mortality at 6 months (91/2324 [3·9%] vs 116/2332 [5·0%], respectively; adjusted risk ratio [aRR] 1·10, 95% CI 0·75-1·62]). INTERPRETATION: Xpert did not reduce mortality at 6 months compared with sputum microscopy. Improving outcomes in drug-sensitive tuberculosis programmes might require not only better diagnostic tests but also better linkage to care. FUNDING: Bill & Melinda Gates Foundation.