Research Articles (Medical Microbiology)
Permanent URI for this collectionhttp://hdl.handle.net/2263/1754
Browse
Recent Submissions
Now showing 1 - 20 of 456
Item Editorial : Emerging antimicrobials : sources, mechanisms of action, spectrum of activity, combination antimicrobial therapy, and resistance mechanismsMajewski, Piotr; Brown, Amanda Claire; Schneiders, Thamarai; Osei Sekyere, John (Frontiers Media, 2025-12-16)No abstract available.Item “I believe in my ancestors, and I participate and believe” : negotiating identity, tradition, and HIV-related health among SGM communities in the Eastern CapeRutt, Kelly; De Vos, Lindsey; Metula, Aphiwe; Peters, Remco P.H.; Bongo, Cikizwa; Van der Merwe, Leonashia Leigh Ann; Daniels, Joseph A. (Elsevier, 2026-06)BACKGROUND : Sexual and gender minority (SGM) individuals in South Africa's Eastern Cape face dual challenges navigating progressive constitutional protections alongside persistent cultural conservatism. Traditional Xhosa practices, including initiation schools (Ulwaluko) and ceremonial rituals, enforce rigid gender roles that conflict with SGM identities. With HIV prevalence reaching 49.5 % among men who have sex with men yet only 25.7 % achieving viral suppression, understanding how SGM individuals negotiate cultural traditions while managing HIV remains critically understudied. METHODS : This qualitative study explored post-intervention experiences of 31 SGM individuals living with HIV in the Eastern Cape following participation in the SOAR (Speaking Out & Allying Relationships) intervention. Semi-structured interviews, guided by Social Cognitive Theory, were conducted in participants' preferred language by trained local interviewers. Thematic analysis through the Minority Stress Model examined four domains: traditional practices, family dynamics, community perceptions, and intervention impact. RESULTS : Participants demonstrated resilience through selective participation in cultural practices, balancing ancestral reverence with identity authenticity. Family acceptance was often conditional, tied to economic contributions or heteronormative expectations. Health communication barriers persisted due to stigma and traditional beliefs linking HIV to moral failing. SOAR enhanced participants' status-sharing confidence, treatment adherence, and skills for navigating cultural tensions, though community stigma remained pronounced in rural areas. CONCLUSION : SGM individuals exhibit remarkable adaptability in negotiating intersecting cultural, familial, and health challenges. While SOAR effectively builds individual resilience and HIV management skills, findings underscore the need for multi-level interventions combining skill-building with community mobilization and cultural sensitization to address structural barriers in traditional contexts. HIGHLIGHTS • SGM individuals employ selective participation strategies to navigate traditional practices • SGM experience complex challenges of family acceptance and support systems of sexual identity and HIV status. • There is a complicated intersection of cultural practices with minority stress and HIV management. • The SOAR intervention is effective in building resilience and health skills related to HIV disclosure and adherence. • There is a need for broader structural interventions to address persistent community-level barriers.Item Phenotypic and genotypic antimicrobial resistance profiles of clinical Clostridioides difficile isolates collected from private and public health settings in South AfricaShirinda, Hlambani; Smith, Anthony Marius; Said, Mohamed; Prinsloo, Ben; Moodley, Mishalan; Kock, Marleen M.; Ehlers, Marthie Magdaleen (Springer, 2025-10)PURPOSE : Antimicrobial resistance (AMR) is important in the pathogenesis and spread of Clostridioides difficile infection (CDI). However, very little is known about the association of AMR and C. difficile in South Africa. The present study aimed to investigate the phenotypic and genotypic antimicrobial profiles of clinical C. difficile isolates. METHODS : Phenotypic antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) were used to characterize the isolates. RESULTS : The AST showed that 43 isolates were susceptible to metronidazole and vancomycin. The WGS revealed a PnimB promoter mutation associated with reduced metronidazole susceptibility in all sequence type (ST) 1 strains (42%, 18/43). No vancomycin resistance determinants were found. Distinct lineages displayed specific resistance traits, such as fluoroquinolone resistance in ST1 strains due to a DNA gyrase (gyrA) mutation (Thr82Ile) and multidrug resistance (MDR) in ST37 strains, which contained resistance determinants for five antimicrobial classes. Overall, 95% (40/43) of strains had AMR determinants for at least three antimicrobial classes, indicating MDR. A qacG efflux pump gene, conferring resistance to disinfectants, was found in all strains. CONCLUSION : Antimicrobial resistance to metronidazole and vancomycin remains rare, however, high MDR prevalence particularly among ST1 and ST37 strains, suggests a risk of AMR gene transmission to other pathogens. The high rate of MDR C. difficile may reflect extensive antimicrobial use driven by comorbidities in immunocompromised individuals, contributing to AMR. These findings underscore the importance of ongoing AMR surveillance, effective antimicrobial stewardship and infection control to manage CDI and mitigate AMR spread.Item Editorial : Microbial source tracking (MST) tools to identify the origins of fecal pollution in environmental water resources and the impact of microbial contaminants on human healthBucci, Antonio; Ehlers, Marthie Magdaleen; Monaco, Pamela (Frontiers Media, 2026-02-04)Editorial on the Research Topic : Microbial Source Tracking (MST) tools to identify the origins of fecal pollution in environmental water resources and the impact of microbial contaminants on human health.Item Carbapenem-resistant Acinetobacter baumannii at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencingStrysko, Jonathan; Thela, Tefelo; Feder, Andries; Thubuka, Janet; Machiya, Tichaona; Mkubwa, Jack; Mochankana, Kagiso; Tiroyakgosi, Celda; Kgomanyane, Kgomotso; Ntereke, Tlhalefo Dudu; Zankere, Tshiamo; Lechiile, Kwana; Gatonye, Teresia; Tembo, Chimwemwe Viola; Vurayai, Moses; Mannathoko, Naledi; Mokomane, Margaret; Moustafa, Ahmed M.; Goldfarb, David M.; Richard-Greenblatt, Melissa; Mcgann, Carolyn; Coffin, Susan E.; Nakstad, Britt; Cancedda, Corrado; Lautenbach, Ebbing; Bogoshi, Dineo; Smith, Anthony Marius; Planet, Paul J. (American Society for Microbiology, 2026-01)Carbapenem-resistant Acinetobacter baumannii (CRAb) has emerged as a major and often fatal cause of bloodstream infections among hospitalized patients in low- and middle-income countries (LMICs). CRAb outbreaks are hypothesized to arise from reservoirs in the hospital environment, but outbreak investigations in LMICs are often limited in scope due to lack of access to whole genome sequencing (WGS). We performed WGS on 43 stored isolates (blood cultures [n = 23] and environmental swabs [n = 20]) presumptively identified as A. baumannii collected during 2021–2022 from a 530-bed referral hospital in Gaborone, Botswana, where CRAb infection incidence was rising. Taxonomic assignment, multilocus sequence typing, antimicrobial resistance gene identification, K and O locus typing, and phylogenetic analyses were performed using publicly accessible analysis pipelines. All 23 blood and 25% (5/20) of environmental isolates were confirmed as A. baumannii, 79% (n = 22) of which were sequence type 1 (ST1). All ST1 isolates harbored genes encoding carbapenemases (blaNDM-1, blaOXA-23). Phylogenetic analysis demonstrated that nearly identical ST1 isolates spanned wide ranges in time (>1 year), suggesting ongoing transmission from environmental sources. One highly similar clade (average difference of 2.3 single nucleotide polymorphisms) contained all eight neonatal blood isolates and three environmental isolates from the neonatal unit. Environmental isolates included a sample from a sink drain, which is likely a major reservoir in this setting and highlights the need for targeted environmental remediation. Using a phylogenetically informed approach, we also identified diagnostic genes that distinguish this outbreak clone. These markers hold the potential to provide a low-cost method for tracking future CRAb isolates related to this outbreak. IMPORTANCE : Carbapenem-resistant Acinetobacter baumannii is an increasingly significant cause of hospital-acquired bloodstream infections, particularly in low- and middle-income countries where limited resources often prevent the use of advanced outbreak investigation methods. This study leveraged whole genome sequencing to uncover transmission patterns of these antibiotic-resistant infections which were occurring more frequently in a referral hospital in Botswana. By linking clinical and environmental samples collected over an 18-month period, we identified a cluster of infections genetically linked to samples collected from the environment, including a sample taken from a sink drain in the neonatal unit. Furthermore, the study identified key genes specific to outbreak strains that could be used as diagnostic markers to track future outbreaks, even in the absence of genomic sequencing. These findings demonstrate how combining genomic sequencing with targeted gene identification can guide infection prevention and control efforts, helping to curb the spread of antibiotic resistance in resource-limited settings.Item Point-of-care testing to strengthen sexually transmitted infection case management in resource-constrained settingsPeters, Remco P.H.; Manguro, Griffins; Ong'wen, Patricia A.; Mdingi, Mandisa M.; Applegate, Tanya L.; Stuart, Robyn; Harding-Esch, Emma M.; Manabe, Yukari C.; Ndowa, Francis; Van der Pol, Barbara (BMJ Publishing Group, 2026)Syndromic management remains the standard approach for sexually transmitted infection (STI) care in many low-resource settings. Recent advances in point-of-care (POC) diagnostic testing offer the opportunity to improve STI case management by enabling targeted treatment, reducing unnecessary antibiotic use, and strengthening partner services. This educational article summarizes key insights from a symposium organised by the World Health Organization and Gates Foundation at the STI & HIV World Congress 2025. Evidence from modeling studies in Zimbabwe and South Africa demonstrates significant reductions in overtreatment and population-level STI burden with POC test integration. Acceptability among end-users and providers is high, contingent on rapid, confidential testing linked to same-day treatment. The article reviews the current landscape of STI POC tests, including WHO’s REASSURED criteria and target product profiles, and discusses regulatory progress and technical specifications for prequalification. Implementation strategies emphasize integration into existing health services, capacity building, stakeholder engagement and importance of robust quality assurance processes. While cost-effectiveness data remain limited, strategic investment and policy development are essential to scale up STI POC testing. With growing technological feasibility and public health urgency, POC testing represents a paradigm shift in STI management, offering a pathway to more effective, equitable, and sustainable care in resource-constrained settings.Item Association between partner treatment and repeat sexually transmitted infections positivity in pregnant women in East London, South AfricaMdingi, Mandisa M.; Gigi, Ranjana M.S.; Babalola, Chibuzor M.; Taylor, Christopher M.; Muzny, Christina A.; Medina-Marino, Andrew; Klausner, Jeffrey David; Peters, Remco P.H. (BMJ Publishing Group, 2026)OBJECTIVES : Sexually transmitted infections (STIs) are common in pregnant women. Effective partner treatment of women with an STI is essential to prevent reinfection. We evaluated the impact of partner notification and treatment based on the occurrence of repeat STIs in pregnant women in South Africa. METHODS : We used data from one of the intervention arms in a randomised clinical trial of STI diagnostic screening strategies in pregnancy. In this cohort, women were tested at their first antenatal care visit (<27 weeks gestational age) using onsite Xpert test assays (Cepheid, Sunnyvale, California, USA) for Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. Women with a positive STI result received pathogen-directed treatment, partner notification slips, and a test-of-cure visit was scheduled 21-35 days post-treatment. At the test of cure visit, sexual behaviour and partner treatment data were collected, and STI testing was repeated. Cure was defined as a negative result at the test-of-cure visit. RESULTS : Of 754 women tested, 193 (26%) tested positive for an STI and 183 (95%) received pathogen-directed treatment. A test-of-cure visit was attended by 108/183 (59%) women within the time window. Of those, 19/108 (18%) had a positive repeat STI result. Most women attending the test-of-cure visit (95%; 103/108) reported disclosure of their STI to their partner; however, only 44% (48/108) reported that their partner received treatment. Among those who reported partner treatment, the repeat STI positivity was 4% versus 27% in those with reported untreated partners (risk ratio 0.15 with 95% CI 0.03 to 0.7). CONCLUSIONS : Reported partner treatment reduced the likelihood of a repeat positive test result in pregnant women. Strengthening partner notification and treatment is essential to prevent reinfection.Item Integrating point-of-care screening for curable sexually transmitted infections with HIV, syphilis and hepatitis B screening in antenatal care services in Zimbabwe : a mixed-methods process evaluationMartin , Kevin; Mackworth-Young, Constance R.S.; Dauya, Ethel; Nyamwanza, Rangarirayi; Chikwari, Chido Dziva; Tshuma, Maureen; Tucker, Joseph D.; Simms, Victoria; Bandason, Tsitsi; Ndowa , Francis; Katsidzira, Leolin; Mugurungi, Owen; Machiha, Anna; Peters, Remco P.H.; Marks , Michael; Kranzer, Katharina; Ferrand, Rashida A. (BMJ Publishing Group, 2025-12-05)INTRODUCTION : Sexually transmitted infections (STIs) in pregnancy are associated with adverse birth outcomes. We investigated the uptake and yield of point-of-care screening for Chlamydia trachomatis, Chlamydia trachomatis, integrated with HIV, syphilis and hepatitis B virus (HBV) screening in antenatal care (ANC) in Zimbabwe, and conducted a mixed-methods process evaluation of the strategy. METHODS : A prospective interventional study was conducted in two public-sector ANC clinics in Harare. Clients attending for ANC were screened in parallel for C. trachomatis, N. gonorrhoeae, T. vaginalis, HBV, HIV and syphilis, using four different point-of-care tests. Uptake of STI testing and treatment was recorded. Interviews and focus group discussions with pregnant women, healthcare professionals and the intervention team were conducted and analysed thematically. Implementation, mechanisms of impact and context were explored using the Medical Research Council Process Evaluation Framework. RESULTS : Between 12 January 2023 and 23 October 2023, there were 13 500 ANC attendances over 207 implementation days. Of 1105 (8.2%) assessed for eligibility, 1103 (99.8%) were eligible, of whom uptake of the full screening package was 91.0% (1004/1103). Curable STI prevalence was 30.7% (308/1003), of whom 303 (98.4%) received same-day treatment. HBV prevalence was 1.4% (14/1003). The prevalence of HIV was 10.5% (105/1003), with 20 (19.0%) being new diagnoses. Although the intervention was highly acceptable, diagnostic capacity and workload were barriers to recruitment. In particular, the collection and testing of multiple sample types with different tests, with a range of reading times, was challenging. CONCLUSION : We demonstrated high levels of acceptability, screening uptake and same-day treatment. However, a low proportion of ANC attendees were enrolled overall, and current technological limitations preclude this particular testing strategy from being scaled up beyond low-volume settings. We recommend investment into the development of STI point-of-care tests with shorter analytic times and research into alternative strategies involving laboratory-based high-throughput testing.Item Modifiable risk factors for anemia in pregnancy : an umbrella review of systematic reviews and meta-analysesDagne, Woldeteklehaymanot Kassahun; Shiferaw, Mulu; Gedfie, Solomon; Jemal, Abdu; Gashaw, Muluken; Kumie, Getinet; Bazezew, Alembante; Sisay, Assefa; Abebe, Wagaw; Nigatie, Marye; Misganaw, Tadesse; Asmare, Zelalem; Getachew, Ermias; Gashaw, Yalewayker; Ashagre, Agenagnew; Tefera, Zewdu; Alemu, Bewuketu Belete; Tamrat, Ephrem; Kassanew, Brhanu; Dejazmach, Zelalem; Reta, Melese Abate (BioMed Central, 2025-12-01)BACKGROUND : Anemia during pregnancy affects more than one-third of women globally, with the heaviest burden in low- and middle-income countries. It contributes substantially to maternal morbidity, adverse birth outcomes, and increased neonatal mortality. Despite extensive research, there remains a lack of comprehensive and up-to-date synthesis on modifiable determinants to guide effective, targeted interventions. This umbrella review aimed to consolidate evidence from systematic reviews and meta-analyses on modifiable risk factors associated with anemia in pregnancy. METHODS : A systematic search was conducted across PubMed, Scopus, ScienceDirect, Epistemonikos, Hinari, Google Scholar, and the Cochrane Library. Search terms combined controlled vocabulary and free-text keywords including anemia, hemoglobin, iron deficiency, determinants, pregnant women, systematic review, and meta-analysis. Boolean operators (OR/AND) were applied, and the search was limited to English-language publications from 2014 to 2024. Eligible studies included systematic reviews and meta-analyses examining risk factors for anemia among pregnant women. Methodological quality was assessed using the Joanna Briggs Institute (JBI) critical appraisal tool, and synthesis followed JBI guidance to ensure rigor and transparency. Certainty of evidence assessed using GRADE. RESULTS : Of 13,348 records identified, 10 systematic reviews and meta-analyses were included. The synthesis highlighted several modifiable risk factors. Nutritional determinants included low dietary diversity (RR = 2.38-3.59), poor dietary practices (AOR = 1.63-2.97), and inadequate iron/folic acid supplementation (AOR = 1.38-1.82). Maternal health conditions, particularly intestinal parasite infections (AOR = 2.18-4.34) and malaria (AOR = 1.94-11.19), showed strong associations. Sociodemographic risks included low maternal education (AOR = 1.34-2.04), short birth intervals (< 24 months; AOR = 1.27-2.84), adolescent pregnancy (AOR = 2.60), large family size (AOR = 1.58-1.95), and rural residence (RR = 1.56). Limited healthcare access, especially lack of antenatal care (AOR = 1.36-2.02), further increased risk. Considerable heterogeneity (I²=0-94.5%) and low-to-moderate certainty ratings (GRADE) suggest variability across settings and highlight context dependence. CONCLUSIONS : Anemia during pregnancy arises from multiple modifiable factors, including poor nutrition, low dietary diversity, adolescent pregnancy, and infections like malaria and intestinal parasites. This umbrella review highlights the importance of developing context-specific interventions and implementing multisectoral policies that integrate nutrition and infection-control strategies to reduce the global burden of maternal anemia.Item Investigation of a suspected cholera outbreak within a closed community of trainees at a college in Hammanskraal, Gauteng Province, South Africa, June 2023Sekwadi, Phuti; Malomane, Rixongile; Kwenda, Danai; Kodi, Keabetswe; Marumo, Andani; Kgatswetswe, Lerato; Mokgetle, Refilwe; Matjokotja, Tebogo; Smith, Anthony Marius; Ngomane, Mimmy; Erasmus, Linda (BioMed Central, 2025-11-22)Cholera, as defined by the US Center for Disease Control and Prevention (CDC), is an acute diarrhoeal disease caused by infection of the intestine with the toxin-producing Vibrio cholerae serogroup O1 or O139 bacterium. We investigated a suspected outbreak of cholera at a training college with the aim of determining the magnitude of the outbreak and identifying possible risk factors. We conducted a retrospective cohort study including all persons attending training or living in the college premises between 8 May and 1 June 2023. A case was defined as anyone attending training courses on campus who experienced diarrhoea and/or vomiting between 8 May and 1 June 2023. Data were collected through an online questionnaire. R Studio was used to calculate attack rates and risk ratios to identify possible risk factors associated with illness. Two hundred and thirty-eight participants completed the online questionnaire on 1 June 2023, of which 37% (88/238) reported illness during the study period. The median age of cases was 35 years with a predominance of males (67/88; 76%). Risk factors associated with illness included brushing teeth with tap water (RR = 1.8; CI = 1.2–2.6), sex (RR = 1.6; CI = 1.1–2.5) and unavailability of hand washing soap in the bathrooms (RR = 1.6; CI = 1.2–2.3). Eating food bought outside the college (RR = 0.5; CI = 0.4–0.8) and availability of hand washing soap in the bathrooms were protective against illness (RR = 0.4; CI = 0.3–0.7). This diarrheal disease outbreak was likely caused by multiple pathogens including Vibrio cholerae, a pattern usually seen when there is suspected/possible fecal contamination of drinking water sources. Recommendations included ongoing provision of safe water to the trainees attending courses at the college and anyone living in the college until such time that the municipal drinking water was declared safe for drinking by the responsible stakeholders.Item Modifiable risk factors for anemia in pregnancy : an umbrella review of systematic reviews and meta-analysesDagne, Woldeteklehaymanot Kassahun; Shiferaw, Mulu; Gedfie, Solomon; Jemal, Abdu; Gashaw, Muluken; Kumie, Getinet; Bazezew, Alembante; Sisay, Assefa Legesse; Abebe, Wagaw; Nigatie, Marye; Misganaw, Tadesse; Asmare, Zelalem; Getachew, Ermias; Gashaw, Yalewayker; Ashagre, Agenagnew; Tefera, Zewdu; Alemu, Bewuketu Belete; Tamrat, Ephrem; Kassanew, Brhanu; Dejazmach, Zelalem; Reta, Melese Abate (BioMed Central, 2026-01)BACKGROUND : Anemia during pregnancy affects more than one-third of women globally, with the heaviest burden in low- and middle-income countries. It contributes substantially to maternal morbidity, adverse birth outcomes, and increased neonatal mortality. Despite extensive research, there remains a lack of comprehensive and up-to-date synthesis on modifiable determinants to guide effective, targeted interventions. This umbrella review aimed to consolidate evidence from systematic reviews and meta-analyses on modifiable risk factors associated with anemia in pregnancy. METHODS : A systematic search was conducted across PubMed, Scopus, ScienceDirect, Epistemonikos, Hinari, Google Scholar, and the Cochrane Library. Search terms combined controlled vocabulary and free-text keywords including anemia, hemoglobin, iron deficiency, determinants, pregnant women, systematic review, and meta-analysis. Boolean operators (OR/AND) were applied, and the search was limited to English-language publications from 2014 to 2024. Eligible studies included systematic reviews and meta-analyses examining risk factors for anemia among pregnant women. Methodological quality was assessed using the Joanna Briggs Institute (JBI) critical appraisal tool, and synthesis followed JBI guidance to ensure rigor and transparency. Certainty of evidence assessed using GRADE. RESULTS : Of 13,348 records identified, 10 systematic reviews and meta-analyses were included. The synthesis highlighted several modifiable risk factors. Nutritional determinants included low dietary diversity (RR = 2.38–3.59), poor dietary practices (AOR = 1.63–2.97), and inadequate iron/folic acid supplementation (AOR = 1.38–1.82). Maternal health conditions, particularly intestinal parasite infections (AOR = 2.18–4.34) and malaria (AOR = 1.94–11.19), showed strong associations. Sociodemographic risks included low maternal education (AOR = 1.34–2.04), short birth intervals (< 24 months; AOR = 1.27–2.84), adolescent pregnancy (AOR = 2.60), large family size (AOR = 1.58–1.95), and rural residence (RR = 1.56). Limited healthcare access, especially lack of antenatal care (AOR = 1.36–2.02), further increased risk. Considerable heterogeneity (I²=0–94.5%) and low-to-moderate certainty ratings (GRADE) suggest variability across settings and highlight context dependence. CONCLUSIONS : Anemia during pregnancy arises from multiple modifiable factors, including poor nutrition, low dietary diversity, adolescent pregnancy, and infections like malaria and intestinal parasites. This umbrella review highlights the importance of developing context-specific interventions and implementing multisectoral policies that integrate nutrition and infection-control strategies to reduce the global burden of maternal anemia.Item Reply to Datta, “Is static or cidal antibiotic falsifiable?”Spellberg, Brad; Wald-Dickler, Noah; Holtom, Paul; Meyer-Sautter, Pascal; Camp, Austin; Diaz Diaz, Alejandro; Buhamad, Ranya; Meza Vazquez, Ali Sebastian; Aguirre-Garcia, Gloria Mayela; Stanton, Matthew; Butler-Wu, Susan M.; Chiu, Isabelle; Ergenc, Zeynep; Bhoojhawon, Guru; Murri, Rita; Maraolo, Alberto Enrico; Cabanilla, Gabriela; Riccardi, Niccolò; Tshisevhe, Vhudzani; Behenna, Curtis; Williams, Karen S.; Kufel, Wesley D.; Wojciaczyk, Natalia; Pimentel, Bernardo Vidal; Muyidi,, Ahmed; Costa, Rodrigo P.L.; Motta, Fabrizio; Bortolussi-Courval, Émilie; Lee, Todd C.; McDonald, Emily G.; Ghanem, Bassam; Nelson, Zachary (American Society for Microbiology, 2025-11)We would like to thank Dr. Datta for his interest in our article. Dr. Datta wishes to defend the static vs. cidal antibiotic model against “absolutist framing.” He invokes “mono-parametric” assays like “MBC/MIC ratios or…reactive oxygen species generation” to suggest that in vitro static vs. cidal phenomenology may be phenotypically real.Item Whole-genome sequencing for surveillance of Salmonella at a public health institution in South AfricaSmith, Anthony Marius; Sekwadi, Phuti; Ngomane, Hlengiwe M.; Disenyeng, Bolele; Erasmus, Linda K.; Thomas, Juno; Bogoshi, Dineo; Smouse, Shannon L.; Tau, Nomsa P. (AOSIS, 2025-12-09)BACKGROUND : Whole-genome sequencing (WGS) is transforming communicable disease surveillance globally. The National Institute for Communicable Diseases, South Africa, participates in national laboratory-based surveillance for human isolates of Salmonella. OBJECTIVE : This study was to investigate human Salmonella isolates from South Africa, 2020–2023, using WGS analysis. METHODS : WGS was performed using Illumina NextSeq Technology. Data were analysed using multiple bioinformatics tools, including those available at the Center for Genomic Epidemiology, Pathogenwatch and EnteroBase. Data analysis allowed for identification and characterisation of isolates. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates. RESULTS : Of the 8006 isolates of Salmonella that were analysed using WGS, 130 distinctive serovars and subspecies were identified. Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) (4271/8006; 53.3%) and Salmonella Typhimurium (1430/8006; 17.9%) were the most prevalent serovars, accounting for 71.2% of all isolates. This was followed by Salmonella Typhi (482/8006; 6.0%). Sixteen per cent (1288/8006) of isolates showed the presence of antimicrobial resistance (AMR) determinants associated with ≥ 2 classes of antimicrobials. Salmonella Isangi (167/8006; 2.1%) showed the highest prevalence of AMR, with most isolates (159/167; 95.2%) showing AMR determinants associated with ≥ 7 classes of antimicrobials. Core-genome multilocus sequence typing was used to confirm several suspected clusters and outbreaks and identified additional cryptic or unreported clusters and outbreaks. Investigation of clusters and outbreaks mostly involved Salmonella Enteritidis and Salmonella Typhi. CONCLUSION : The implementation of WGS has enabled genomic surveillance of Salmonella, which allows for enhanced characterisation and AMR determination of isolates and identification of clusters and outbreaks, which informs targeted public health investigation and response. What this study adds: This study describes the population structure of Salmonella isolated from humans in South Africa and hugely contributes to the available Salmonella WGS data from Africa.Item A retrospective analysis of uropathogens isolated and antimicrobial susceptibility patterns at a regional hospital in North West province, South AfricaTeixeira, Miguel J.; Pretorius, Vian; Hunt, Robert C.J.G.; Morar, Sanam; Colloty, Jamie; Radebe, Caleb M.; Morar, Rajen (AOSIS, 2025-11-30)BACKGROUND : Urinary tract infections are among the most common infections affecting the general population. Their high incidence, as well as frequent antimicrobial use, contribute significantly to the development of antimicrobial resistance (AMR). OBJECTIVE : To determine the profile and prevalence of uropathogens isolated from urine specimens at a regional hospital and assess susceptibility patterns to commonly used antimicrobials recommended by the National Essential Medicines List (NEML). METHODS : This was a retrospective evaluation of laboratory reports for all urine specimens submitted between 01 January 2020 and 31 December 2023. RESULTS : The most frequently cultured organisms were Escherichia coli (n = 1481; 42%); Klebsiella pneumoniae (n = 568; 16%); Enterococcus faecalis (n = 249; 7%); Proteus mirabilis (n = 229; 7%), Enterobacter cloacae (n = 137; 4%), and Candida albicans (n = 119; 3%). Escherichia coli maintained high sensitivity to antimicrobials such as nitrofurantoin (92.2%) and gentamicin (90.6%), whilst K. pneumoniae had decreased sensitivities of 40% and 77%, respectively. Cumulative sensitivities of commonly used first-line antimicrobials showed low rates of susceptibility to ciprofloxacin (77%), nitrofurantoin (67%), and amoxicillin/clavulanate (68.7%). CONCLUSION : Escherichia coli was the most commonly identified isolate and remains sensitive to nitrofurantoin. It was, however, resistant to ciprofloxacin, amoxicillin/clavulanate, and trimethoprim sulfamethoxazole, as were all the other Gram-negative organisms. These sensitivity patterns do not align with the antimicrobials recommended in the current NEML guidelines, and highlight the need for targeted therapy and interventions. What this study adds: This retrospective analysis identifies predominant uropathogens’ updated antimicrobial susceptibility profiles, some of which misalign with NEML guidelines. Insights will guide targeted antimicrobial stewardship, empiric therapy, and local surveillance to curb AMR.Item Lactobacillus-rich cervicovaginal microbiome associated with lower BV, HPV, and cytology outcomes in womenOsei Sekyere, John; Trama, Jason; Adelson, Martin; Trikannad, Charulata; DiBlasi, Desiree; Schuster, Rachel; Yang, Jing Jing; Mordechai, Eli (Elsevier, 2025-10-17)The cervicovaginal microbiome modulates susceptibility to bacterial vaginosis (BV), high-risk human papillomavirus (hrHPV) infection, and epithelial cell abnormalities that precede cervical cancer. We retrospectively analyzed 15 607 qPCR-profiled cervicovaginal specimens from U.S. women (ages 14–95; 32 states) and integrated microbiome abundances, hrHPV genotyping, Pap-cytology, and demographics. BV was present in 53% and hrHPV in 11% of samples. Lactobacillus crispatus, L. gasseri, and L. jensenii were enriched in BV-negative and cytologically normal (NILM) samples, whereas L. iners and BV-associated anaerobes co-occurred with hrHPV and abnormal cytology. Machine-learning models confirmed age, hrHPV status, and L. crispatus abundance as the strongest multivariate predictors of BV and cytological outcomes (BV AUROC ≈0.97). Interaction analyses revealed synergistic associations between specific hrHPV genotypes and Gardnerella/Fannyhessea that further increased cytological risk. These findings underscore the clinical value of microbiome profiling and support probiotic strategies that promote protective Lactobacillus communities to reduce BV and hrHPV-related cervical pathology.Item Prevalence of colistin resistance in multidrug-resistant Klebsiella pneumoniae recovered from clinical samples in AfricaGashaw, Yalewayker; Asmare, Zelalem; Sisay, Asefa; Getatachew, Ermias; Gedfie, Solomon; Ashagre, Agenagnew; Bitew, Getachew; Tigabie, Mitkie; Reta, Melese Abate (Oxford University Press, 2025-08)BACKGROUND : Colistin resistance in multidrug-resistant (MDR) Klebsiella pneumoniae is a growing concern in Africa, complicating treatment and public health management. Colistin is a last-resort antibiotic for Gram-negative infections, but its resistance in clinical settings presents significant challenges. This study aims to determine the pooled prevalence of colistin resistance in MDR K. pneumoniae isolates from clinical specimens in Africa. METHODS : Articles were sourced from PubMed, Scopus, ScienceDirect and Google Scholar. Studies included were those reporting colistin resistance in MDR K. pneumoniae from clinical specimens in Africa, using EUCAST and CLSI-standard drug susceptibility testing. Data were extracted into Excel and analysed using STATA 17 with a random-effects model to determine the pooled prevalence. Heterogeneity was assessed using the I2 statistic, and publication bias was checked with Egger’s test. Subgroup analyses were performed to explore heterogeneity. RESULTS : The study analysed data from 30 articles on colistin resistance in MDR K. pneumoniae. The pooled prevalence was 21.59% (95% CI: 12.12–31.06), with high heterogeneity (I2 = 99.71%). Sub-regional variation was significant (P < 0.001), with prevalence rates differing across regions: 42.34% in East Africa, 37.1% in West Africa, 17.1% in Southern Africa and 13.0% in North Africa. Country-specific rates were highest in Nigeria (39.12%), followed by Kenya (22.52%), South Africa (17.12%) and Egypt (14.0%) (P < 0.001). CONCLUSIONS : Colistin resistance in MDR K. pneumoniae is high in Africa, with notable regional differences. The study calls for strict colistin regulations, robust antimicrobial stewardship and rapid diagnostic tools for resistance detection.Item Nocardia species epidemiology and susceptibility profiles from 2019 to 2022 in South AfricaThomas, T.; Lowe, M.; Le Roux, K.; Strydom, Kathy-Anne (South african Medical Association, 2025-08)BACKGROUND : Nocardia species cause infections in humans, from localised to disseminated disease. They constitute a public health threat owing to the lack of sufficient information about them. In South Africa (SA), the last publication on this organism was in 2010. Predominant species types and antibiotic susceptibilities may have changed over this period. OBJECTIVE : To address the knowledge gap surrounding Nocardia species and their antibiotic susceptibilities in SA. METHODS : This was a retrospective and cross-sectional study. Data were collected from the Central Data Warehouse (CDW) of the National Health Laboratory Service (NHLS) on suspected Nocardia species from 1 January 2019 to 31 December 2022. Organism speciation was performed using 16S rRNA sequencing and antibiotic susceptibility testing (AST) by the broth microdilution (BMD) method. Data analysis included patient age, sample types from which the organism was cultured, distribution in the various SA provinces, species types and species AST profiles, including a record of trimethoprim-sulfamethoxazole (TMP/SMX) non-susceptibility. RESULTS : One hundred and sixty-five positive culture results were analysed. The majority of positive cultures (28%, n=46) were from the 30 - 39-year age group. The organism was predominantly cultured from pus samples (31%, n=51). The top two provinces from which the largest numbers of isolates were submitted were Gauteng (69%, n=114) and Western Cape (18%, n=30) provinces. Two percent (n=4) of isolates were not sequenced, and 18% (n=30) of isolates lacked AST results. Twenty-nine percent (n=47) of the Nocardia species that were sequenced could not be speciated using 16S rRNA sequencing. The top two species country-wide were N. abscessus complex (25%, n=42) and N. cyriacigeorgica (18%, n=29). Approximately 90% (n=121) of all isolates tested were TMP/SMX susceptible. CONCLUSION : The predominant isolation of Nocardia species from pus samples suggests that the majority were deep-seated infections. The most common Nocardia species types and the AST profiles have changed over time. The study highlights the need for alternative methods for the speciation of this organism.Item Spectrum of sexual partner types among adults screened for sexually transmitted infections in the Eastern Cape, South AfricaDe Vos, Lindsey; Mdingi, Mandisa M.; Gigi, Ranjana M.S.; Gebengu, Avuyonke; Peters, Remco P.H. (Public Library of Science, 2025-05-07)In South Africa, Chlamydia trachomatis prevalence is 14.7% in women and 6.6% in men, while Neisseria gonorrhoeae rates are 6.0% and 3.4%. Partner management, including identifying and screening for STIs, is essential for STI control efforts but challenging due to relationship dynamics, fear of disclosure and stigma. This study aims to understand how adults in the Eastern Cape report partner types when seeking STI care, enhancing partner notification strategies and reducing transmission. From February-August 2023, a cross-sectional evaluation of a Neisseria gonorrhoeae lateral flow assay was conducted among asymptomatic adults aged 18-49 years at four primary healthcare facilities in Buffalo City, Eastern Cape. Participants completed surveys classifying partners into LUSTRUM team's 8 partner types and 5 type-classifications. Data were analyzed using StataSE 17, examining associations between partner types and variables like gender, location, number of sexual partners, and STI test results. A total of 500 men and 400 women (median ages 31 and 32) were recruited. The most reported partner types were main/serious/long-term partners (41%) and girlfriend/boyfriend (29%) or LUSTRUM's 4: established (67%) and occasional partners (28%). Participants reporting main/long-term partners, steady, or boyfriend/girlfriend showed variability in partner numbers. Male adults more commonly reported casual partner types like friends with benefits (21% vs. 9%) and fuck buddy/booty call (9% vs. 3%), with significant associations for super casual/hook-up/meet/one-night stand (p = 0.02). Regional differences in partner types and a significant association between new partners and NG Xpert positivity (p = 0.01) were observed. This study confirms the diverse spectrum of sexual partner types. Findings reveal that men and women may have different relationships, and regional variations suggest context-specific approaches are needed. Identifying partner types can enhance communication and treatment strategies and address significant gaps in partner notification and STI care.Item Mobile genetic elements of global Escherichia coli ST131 clades with carbapenemasesPeirano, Gisele; Matsumara, Yasufumi; Pitout, Johann D.D. (Springer, 2025-09)Please read abstract in the article.Item Genomic epidemiology of Pseudomonas aeruginosa sequence type 111Matsumara, Yasufumi; Peirano, Gisele; Kock, Marleen M.; Pitout, Johann D.D. (Springer, 2025-02)Please read abstract in the article.