National Health Laboratory Service

Escherichia coli (E. coli) is a leading cause of bloodstream infections (BSIs) globally, with multidrug-resistant (MDR) strains complicating treatment outcomes. In South Africa, genomic data on such isolates remain scarce. To elucidate the genomic landscape of E. coli isolates from bloodstream infections (BSIs) collected over a one-year period in the uMgungundlovu District, South Africa, with a focus on the resistance and virulence genes, mobile genetic elements (MGEs), genetic synteny, sequence types (STs), and phylogenomic context. Twenty-five non-duplicate E. coli isolates were recovered from blood cultures and subjected to antimicrobial susceptibility testing. All twelve MDR isolates underwent whole-genome sequencing and bioinformatic analysis. The MDR isolates comprised six distinct STs, notably high-risk international lineages ST131 (33.3%) and ST69 (25.0%), spanning five phylogroups, predominantly B2 and D. Eight O: H serotypes were identified, with O25:H4 and O45:H16 being most frequent. CH-typing revealed dominant CH types CH40-30 (ST131) and CH35-27 (ST69) and fimH alleles such as fimH30 and fimH27. The isolates encoded β-lactamases, including blaCTX-M-15, blaTEM-1B and blaOXA-1, frequently co-located with MGEs. Notably, blaCTX-M-15 was chromosomally integrated within a Tn3–ISEcp1 transposon unit, while blaTEM-1B and blaOXA-1 were associated with diverse plasmid-associated syntenic architectures flanked by IS1, IS91, or integron-associated regions. Other antibiotic resistance genes were detected, conferring resistance to aminoglycosides (aph(3’)-Ia, aac(3)-IIa, aac(3)-IIe, aadA1, aadA2), sulfonamides (sul1, sul2) and trimethoprim (dfrA variants). A diverse array of virulence genes was identified, associated with adhesion, iron acquisition, serum resistance, and toxin production. Phylogenomic clustering revealed close relationships between local ST131/ST69 isolates and counterparts across Africa. The study identifies diverse MDR E. coli clones circulating in bloodstream infections, notably high-risk lineages ST131, ST69 and ST10, with complex resistance and virulence gene arsenals facilitated by MGEs. These insights reinforce the imperative for genomic surveillance to guide infection control and antibiotic stewardship in high-burden settings.

Abstract Background The COVID-19 pandemic required South African public sector HIV viral load (VL) laboratories to scale up Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing while maintaining essential HIV services. This placed additional pressure on diagnostic services. This dual mandate introduced significant occupational and environmental challenges (OEC) for staff that remain underexplored. Objective This study aimed to investigate the OEC and effects that staff experienced during the implementation of COVID-19 testing at public sector VL laboratories in South Africa. Methods A quantitative, cross-sectional study utilised a census approach among technical and support staff. Data were collected via a structured REDCap questionnaire using 5-point Likert scales. Pre- and post-implementation challenges were assessed across four domains: workload, environmental conditions (space, ventilation, waste), communication, and PPE availability. Statistical analyses included the Wilcoxon Signed-Rank and Spearman’s correlation tests. Results Perceived occupational challenges increased significantly across all domains post-implementation. Staff workload saw the highest rise (mean score 3.02 to 3.53). Adverse health effects were pervasive; 80.2% of staff reported burnout/fatigue, and 76.5% reported increased anxiety/stress. A strong positive correlation was observed between post-COVID-19 challenges and adverse mental and physical health outcomes (rho = 0.449, p < 0.001). Furthermore, 35.8% of staff considered resigning due to increased job demands. Conclusion Integrating COVID-19 testing exacerbated systemic weaknesses, causing measurable psychological injury and threatening workforce retention. Findings suggest that the diagnostic workforce requires formal crisis surge staffing models and institutionalised mental health support to safeguard personnel and maintain essential services during future health emergencies.

Although radiotherapy is an essential part of comprehensive cancer care, access is heavily limited in most sub-Saharan African (SSA) countries. Patients' barriers to care can be grouped as availability, accessibility, accommodation, affordability, and acceptability. We aimed to assess cancer patient- and caregiver-reported barriers in nine SSAn countries (Republic of the Congo, Ethiopia, Gabon, Kenya, Mali, Nigeria, Tanzania, Uganda, and Zimbabwe). We conducted a telephone-based survey among 553 randomly selected patients with breast, cervical, colorectal, and prostate cancer, Kaposi sarcoma and non-Hodgkin lymphoma diagnosed between 2018 and 2019 registered in population-based registries of the African Cancer Registry Network. We inquired about receipt of radiotherapy and barriers irrespective of recalling a recommendation. Among all categories, 21.6% (Use of alternative medicine) to 39.6% (Cost of treatment) of patients reported severe barriers. Most common was problematic Cost of treatment (69.0% overall). A high share of patients from Congo, Kenya, Nigeria, and Tanzania reported barriers. Higher education and wealth were associated with reduced problems in all categories except increased problems with Fear and Use of alternative medicine. Receipt of radiotherapy was associated with fewer problems with Availability of transport (odds ratio [OR]: 0.34; 95% confidence interval [CI], 0.13-0.88) and Trust in healthcare workers (OR: 0.44; 95% CI, 0.24-0.8), and increased Fear (OR: 2.33; 95% CI, 1.33-4.05). Seeing that one-third of the patients reported severe problems in all dimensions, shortage of radiotherapy units is not the only problematic aspect of access to radiotherapy. Improvements in affordability, patient-healthcare worker communication, and psychosocial support are needed.

Background/Objectives: The overuse and misuse of antibiotics contribute to antimicrobial resistance (AMR) globally. The appropriateness of antibiotic prescribing at the primary healthcare (PHC) level must be urgently addressed to reduce high levels of inappropriate antibiotic prescribing and associated AMR. This study aimed to develop quality indicators, based on the World Health Organization (WHO)'s Access, Watch, Reserve (AWaRe) guidance, to assess the appropriateness and quality regarding antibiotic prescribing in public PHC settings in South Africa. Methods: Potential indicators were identified from indicators developed by City St George's, University of London (SGUL); a review of AWaRe-based indicators; and the results from point prevalence surveys at PHC clinics in South Africa. The indicators were developed using the RAND/UCLA Appropriateness Method. In Round 1, 12 experts individually rated 78 indicators for clarity and appropriateness. In Round 2, 10 experts rated 89 indicators for appropriateness and feasibility during an interactive online meeting. Results: The final set had 61/89 indicators (68.5%) that were rated both appropriate and feasible with agreement. Dental infections (9/9; 100%) alongside skin and soft tissue infections (11/13; 84.6%) had the highest percentage of indicators that were rated appropriate and feasible with agreement. Lower urinary tract infections (6/11; 54.5%) and general (4/8; 50%) categories had the lowest percentage of indicators rated appropriate and feasible with agreement. Conclusions: The process proved valuable in developing potential indicators for use in future antimicrobial stewardship programmes to improve antibiotic prescribing in public sector PHC facilities in South Africa and beyond.

Introduction 14Fecal contamination of water bodies poses significant risks to both human health and ecological 15 systems, as it introduces organic matter, nutrients such as nitrogen and phosphorus, and potentially 16 pathogenic microorganisms. Such contamination can compromise water quality, leading to 17 environmental degradation, waterborne microbial infections and economic losses, particularly in 18 sensitive settings such as drinking water supplies, recreational waters, and shellfish harvesting areas. 19The frequent detection of enteropathogens across diverse aquatic ecosystems underscores the 20 importance of rapidly and reliably identifying the sources of fecal pollution to support effective water 21 quality management, remediation efforts, and public health risk assessments.

ABSTRACTBackgroundDigital participatory surveillance (DPS) may provide information on reported influenza‐like illnesses (ILI). Combining DPS with laboratory testing allows pathogen identification. We assessed the feasibility of DPS and home‐based self‐swabbing (HBSS) in South Africa.MethodsWe enrolled a cohort of individuals aged ≥ 18 years who completed weekly respiratory symptoms questionnaires from March to October 2022. We calculated the weekly percentage of reported ILI and COVID‐19 and compared it with weekly private sector respiratory consultations (WPSRC). Symptomatic participants were offered HBSS for influenza and SARS‐CoV‐2 detection by polymerase chain reaction (PCR). We assessed six feasibility indicators.ResultsRecruitment capability: Twenty‐six percent (249/954) of participants accessed the platform and enrolled, and 92% (81/88) of participants eligible for HBSS were enrolled. Acceptability: Fifteen percent (32/249) completed the acceptability questionnaire with 100% (32/32) willing to participate in future studies, and 16% (39/249) withdrew from the study. Representativeness: Fifty percent (125/249) were aged 18–39 years, predominantly female 71%, and 79% had a tertiary qualification. Reliability: Thirty‐eight percent (80/210) were active participants, median weekly active participation of 23% (interquartile range [IQR]: 19%–29%). Accuracy: Two percent (31/1440) and 25% (359/1440) of reports met ILI and COVID‐19, respectively. Influenza and SARS‐CoV‐2 were detected in 7% (6/81) and 32% (26/81) of tested samples, respectively. There was low correlation with WPSRC (0.08, 95% CI, 0.27–0.43) for ILI and (0.36, 95% CI, 0.11–0.62) for COVID19. Usefulness: Symptoms were reported in 32% (459/1440) of reports, and 11% (49/459) sought medical care.ConclusionThe study was feasible; however, low enrolment numbers limit power. Linkage to HBSS was successful and demonstrates the potential for pathogen confirmation.

BackgroundThere is a paucity of information on the burden of Klebsiella pneumoniae invasive disease (KPn-ID) in Africa. We conducted a multicentre, observational study on the clinical and microbiological epidemiology of KPn-ID in hospitalized adults in South Africa, focusing on clinical outcomes and KPn susceptibility profiles.MethodsSurveillance for culture-confirmed KPn from blood and CSF was undertaken from 15 May 2023 to 14 May 2024. Phenotypic antimicrobial susceptibility was analysed, and the presence of carbapenemases was assessed with a lateral flow assay test.ResultsWe enrolled 524 of 617 individuals with KPn-ID. The median age was 48 (IQR: 35–61) years, and 84.4% (442/524) were presumed healthcare-associated infections. Comorbidities included HIV (26.9%; 141/524) and diabetes mellitus (16.4%; 86/524). There was a high prevalence of carbapenem resistance (55.0%; 288/524), with the OXA-48 carbapenemase detected in 71.5% (181/253), and OXA-48 and NDM co-detected in 20.9% (53/253) of tested isolates. Colistin resistance was detected in 7.6% (19/251) of tested isolates. The in-hospital case fatality risk (CFR) was 56.5% (296/524). Urethral catheterization [adjusted odds ratio (aOR) 3.30; 95% CI: 1.51–7.23] and an admission quick sepsis-related organ failure assessment score of 1 to 3 (aOR 2.14; 95% CI: 1.25–3.68) were independently associated with in-hospital death. Achieving source control was associated with lower odds of death (aOR 0.18; 95% CI: 0.10–0.30).ConclusionsWe observed a high prevalence of MDR and high CFR in adults with KPn-ID. These data show the urgent need for strategies to mitigate KPn-ID in settings such as ours.

Nonpharmaceutical interventions, implemented during the COVID-19 pandemic, affected the transmission of other respiratory pathogens. Systematically collected respiratory illness surveillance data and consistent case definitions were used to describe changes in influenza and respiratory syncytial virus (RSV)-associated outpatient visits and hospitalisations in South Africa during the first 3 years of the COVID-19 pandemic relative to a pre-COVID-19 pandemic period (2017-2019). In 2020, influenza circulation almost ceased. In 2021 an out-of-season circulation was observed with a return to prepandemic timing, albeit with a higher peak in 2022. During the pandemic period, influenza-associated influenza-like illness (ILI) was more common in those aged ≥ 5 years compared to < 6 months. Patients with influenza-associated severe respiratory illness (SRI) were less likely to be ≥ 45 years versus < 6 months and less likely to be admitted to ICU (aOR 0.2, 95% CI 0.04-0.8). RSV circulation declined at the start of the pandemic, with an out-of-season spring resurgence in 2020 followed by a return to prepandemic timing in 2021 and a higher peak in 2022. During the pandemic, compared to the prepandemic period, patients with RSV-associated SRI were more likely to be aged 1-4 years (aOR 1.5, 95% CI 1.2-1.8) versus < 6 months and less likely to be admitted to ICU (aOR 0.5, 95% CI 0.3-0.8). We report low levels of influenza circulation and out-of-season RSV circulation in 2020 with changes in the age distribution of cases and risk of ICU admission. Return to prepandemic timing was earlier for RSV, with higher seasonal peaks for influenza-associated ILI and RSV-associated SRI in 2022.