Jane Y. Carter

The External Quality Assessment (EQA) for Africa (EQuAFRICA) project aimed at building regional capacity to provide a One Health bacteriology proficiency testing (PT) programme for reference and sentinel laboratories supporting antimicrobial resistance (AMR) surveillance and submission of data to the World Health Organization Global Antimicrobial Resistance and Use Surveillance System (WHO GLASS). We analysed the performance of participating laboratories in pathogen specific identification (ID) and qualitative antimicrobial susceptibility testing. The programme covered all GLASS and other bacterial pathogens of importance. One survey was distributed in 2021 and 2023 and two surveys in 2022, 2024 and 2025, with five isolates per survey. Participants were selected among reference and designated sentinel AMR laboratories from the 14 Fleming Fund recipient countries in Africa. The Clinical Microbiology Proficiency Testing (CMPT) marking scheme was used to score performance. The number of invited, enrolled and responding laboratories differed by survey; an average of 85% of enrolled laboratories submitted results. Participants scored 83% for organism ID across all cycles. Microbiology laboratories from the human health sector represented the majority in all cycles (75%). The average scores for antibiotic susceptibility testing (AST) was 73%, no participants that scored zero. Critical AST errors with clinical implications for directed treatment included vancomycin and cefoxitin for staphylococci. Our manuscript highlights that the use of EQA programmes to detecting gaps in laboratory processes and maintaining the quality and accuracy of AST is vital for effective AMR surveillance and control. This report illustrates that poorly performed AST at the beginning of the programme improved over the time. Building sustainable capacity for bacteriology testing, including AST, is critically important at all laboratory levels across Africa, from routine clinical and surveillance sites to national AMR reference laboratories.

Persistent gaps in access to quality diagnostic tests undermine progress toward improved health outcomes and resilience to disease outbreaks in Africa. Furthermore, resources for strengthening laboratory systems have faced growing constraints owing to recent reductions in official direct financial assistance, highlighting an urgent need to identify investments that are high impact and minimally donor reliant. In this Perspective, we present a set of priority systems strengthening interventions based on expected impact and feasibility. These include the need for efficient and integrated testing networks, the establishment and implementation of national essential diagnostic lists, modernized procurement and supply chain practices, improved digital health standards and targeted strengthening of testing infrastructure for epidemic-prone diseases. These initiatives should be customized to local contexts and supported by reliable financing, enhanced national leadership and management capacity and updated policies. We propose that collective action focused on these priorities will improve health outcomes and be cost-saving—and will be superior to existing, more fragmented efforts to close gaps in testing. This also provides a pathway to self-reliance in health security and universal healthcare in the Africa region.

Introduction: People living with HIV (PLHIV) are at increased risk of COVID-19-related mortality. However, the burden of and immune response to SARS-CoV-2 infection among PLHIV, particularly in sub-Saharan Africa, remains poorly understood. Methods: We conducted a four-round serial cross-sectional surveillance survey using HIV viral load testing remnant samples from PLHIV on antiretroviral treatment (ART) in Kenya to assess trends in SARS-CoV-2 antibody seroprevalence from February 2021 to October 2022. SARS-CoV-2 IgG antibodies were detected using a validated two-assay ELISA serial algorithm. Samples with ELISA-positive or borderline result samples were further tested using a multiplex bead assay (MBA) to distinguish potential infection and/or vaccination status. Results: National SARS-CoV-2 antibody seroprevalence among PLHIV on ART increased from 16.1% in round 1 to 91.7% in round 4: round 1: 16.1% (95% CI 6.9% to 33.1%), round 2: 29.6% (95% CI 13.7% to 52.7%), round 3: 84.2% (95% CI 67.7% to 93.1%) and round 4: 91.7% (95% CI 86.5% to 95.0%). These estimates corresponded to approximately 186 891 (95% CI 38 639 to 3 35 143), 363 590 (95% CI 114 267 to 612 913), 1 072 496 (95% CI 914 449 to 1 230 452) and 1 173 399 (95% CI 1 120 224 to 1 226 574) PLHIV on ART with SARS-CoV-2 antibodies across the four rounds. MBA testing of ELISA-positive and borderline samples showed that 97% had evidence of probable infection and/or vaccination while 3% tested negative by MBA. Conclusions: Monitoring SARS-CoV-2 infection in PLHIV is essential. Seroprevalence among PLHIV on ART in Kenya increased substantially during 2021–2022, reflecting both infection and vaccination. Protecting the health of PLHIV through sustained prevention, treatment and vaccination strategies remains critical in mitigating the threat of COVID-19.

Objectives: To assess the prevalence of SARS-CoV-2 antibodies in the residents of Kibera informal settlement in Nairobi, Kenya, before vaccination became widespread, and explore demographic and health-related risk factors for infection. Design: A cross-sectional study. Setting: Kibera informal settlement, Nairobi, Kenya. Participants: Residents of Kibera informal settlement between October 2019 and August 2021, age 1 year and above who reported no current symptoms of COVID-19. Main outcome measures: Associations were determined between SARS-CoV-2 positive tests measured with one rapid test and two ELISAs and demographic and health-related factors, using Pearson’s χ ² test. Crude OR and adjusted OR were calculated to quantify the strength of associations between variables and seropositive status. Results: A total of 438 participants were recruited. Most (79.2%) were age 18–50 years; females (64.2%) exceeded males. More than one-third (39.1%) were unemployed; only 7.4% were in formal, full-time employment. Less than one-quarter (22.1%) self-reported any underlying health conditions. Nearly two-thirds (64.2%) reported symptoms compatible with COVID-19 in the previous 16 months; only one (0.23%) had been hospitalised with a reported negative COVID-19 test. 370 (84.5%) participants tested positive in any of the three tests. There was no significant difference in SARS-CoV-2 seropositivity across age, sex, presence of underlying health conditions, on medication or those ever tested for SARS-CoV-2. Multiple logistic regression analysis showed that COVID-19 symptoms in the previous 16 months were the only significant independent predictor of seropositivity (p=0.0085). Conclusion: High SARS-CoV-2 exposure with limited morbidity was found in the residents of Kibera informal settlement. The study confirms other reports of high SARS-CoV-2 exposure with limited morbidity in slum communities. Reasons cited include the high infectious disease burden on the African continent, demographic age structure and underreporting due to limited testing and lack of access to healthcare services; genetic factors may also play a role. These factors require further investigation.

Introduction The performance of a rapid test was evaluated against two ELISAs as a potentially useful tool to determine exposure to SARS-CoV-2 in low resource settings. A serosurvey was conducted in Kibera informal settlement, Nairobi, Kenya, where low numbers of COVID-19 were recorded during the pandemic. Materials and methods A cross-sectional study was performed in 10 of 14 villages in Kibera informal settlement, Kenya’s largest slum community, in August 2021, before general vaccine roll-out. Participants were age one year and above with no symptoms of COVID-19. Capillary blood samples were tested using the Standard Q COVID-19 IgM/IgG Combo rapid test, Platelia SARS-CoV-2 Total Ab (IgM/IgG/IgA) Assay, and Wantai Total Ab (IgM/IgG/IgA) ELISA for SARS-CoV-2 which served as the reference test. Results Samples were obtained from 438 participants; in 72 samples blood was insufficient for the Platelia ELISA. Specificity of the rapid test and Platelia ELISA were similar (>93%) but sensitivity was low (rapid test 61.3%; Platelia ELISA 83.4%). The Wantai ELISA showed greater positivity (82.6%) than the rapid test (51.8%) and Platelia ELISA (69.7%). Conclusions The Wantai ELISA showed superior performance in this serosurvey. Point-of-care tests for convenient screening for SARS-CoV-2 exposure for surveillance studies need to be developed.

Visceral leishmaniasis (VL) is a severe parasitic disease transmitted by phlebotomine sandflies. VL is endemic in West Pokot County, Kenya, where effective strategies to interrupt transmission are impeded by the limited understanding of VL risk factors. Therefore, this case-control study aimed to explore environmental, behavioral and household determinants of VL in West Pokot. From November 2022 to January 2023, a structured questionnaire was administered to 36 symptomatic primary VL cases attending the Kacheliba Sub-County Hospital and to 50 controls from local villages. The VL status of all participants was confirmed using an rK39 rapid diagnostic test. In an age-corrected univariate logistic regression analysis, significant associations were found between VL and housing characteristics, such as window presence and floor type. Furthermore, outdoor activities, including traveling outside the residence for more than 2 weeks, activities near termite mounds, and forest activities during the rainy season increased the risk of VL. VL cases more frequently reported the presence of cattle, dogs and sheep in their house yards at night. VL was also associated with cutting down trees in the house yard and house proximity to several Acacia tree species. To conclude, this work reports a number of previously undescribed risk factors for VL in the understudied West Pokot focus. Our findings warrant further research into sandfly ecology and potential zoonotic parasite reservoirs in West Pokot.

Background: Rapid Diagnostic Tests (RDTs) have become the cornerstone for the management of malaria in many endemic settings, but their use is constrained for several reasons: (i) persistent malaria antigen (histidine-rich protein 2; HRP2) leading to false positive test results; (ii) hrp2 deletions leading to false negative PfHRP2 results; and (iii) limited sensitivity with a detection threshold of around 100 parasites/μl blood (pLDH- and HRP2-based) leading to false negative tests. Microscopy is still the gold standard for malaria diagnosis, and allows for species determination and quantitation, but requires trained microscopists, maintained microscopes and has detection limit issues. Consequently, there is a pressing need to develop and evaluate more sensitive and accurate diagnostic tests. To address this need we have developed a direct on blood mini PCR-NALFIA test that combines the benefits of molecular biology with low infrastructural requirements and extensive training. Methods: This is a Phase 3 diagnostic evaluation in 5 African countries. Study sites (Sudan, Ethiopia, Burkina, Kenya and Namibia) were selected to ensure wide geographical coverage of Africa and to address various malaria epidemiological contexts ranging from high transmission to near elimination settings with different clinical scenarios and diagnostic challenges. Study participants will be enrolled at the study health facilities after obtaining written informed consent. Diagnostic accuracy will be assessed following the WHO/TDR guidelines for the evaluation of diagnostics and reported according to STARD principles. Due to the lack of a 100% specific and sensitive standard diagnostic test for malaria, the sensitivity and specificity of the new test will be compared to the available diagnostic practices in place at the selected sites and to quantitative PCR as the reference test. Discussion: This phase 3 study is designed to validate the clinical performance and feasibility of implementing a new diagnostic tool for the detection of malaria in real clinical settings. If successful, the proposed technology will improve the diagnosis of malaria. Enrolment started in November 2022 (Kenya) with assessment of long term outcome to be completed by 2023 at all recruitment sites. Trial registration: Pan African Clinical Trial Registry (www.pactr.org) PACTR202202766889963 on 01/02/2022 and ISCRTN (www.isrctn.com/) ISRCTN13334317 on 22/02/2022.

A two-phase survey of epilepsy was conducted in selected villages in Mundri West and East Counties (26 June–8 July, 2021), an onchocerciasis-endemic area in Western Equatoria State in South Sudan. In the first phase, households were visited by a trained research team to identify persons suspected to have epilepsy. In the second phase, persons suspected to have epilepsy were interviewed and examined by a clinician to confirm the diagnosis. A total of 364 households agreed to participate in the survey, amounting to 2588 individuals. The epilepsy screening questionnaire identified 91 (3.5%) persons with suspected epilepsy, of whom the diagnosis of epilepsy was confirmed by a clinician in 86 (94.5%). The overall prevalence of confirmed epilepsy was 3.3% (95% CI: 2.7–4.1%), and of nodding syndrome was 0.9% (95% CI: 0.6–1.4%). In 61 (16.8%) households there was at least one person with epilepsy. Only 1212 (46.9%) of 2583 people took ivermectin during the last distribution round in 2021. The annual epilepsy incidence was 77.3/100,000 (95% CI: 9.4–278.9/100,000) and the annual epilepsy mortality was 251.2/100,000 (95% CI: 133.8–428.7/100,000). In conclusion, a high prevalence and incidence of epilepsy was observed in villages in Mundri. Urgent action is needed to prevent children from developing onchocerciasis-associated epilepsy by strengthening the local onchocerciasis-elimination programme.