Research Articles (Medical Microbiology)

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Rapid commercial CTX-M diagnostics : performance, limitations and clinical impact
Aldeia, Claudia; Peirano, Gisele; Pitout, Johann D.D.; Endimiani, Andrea (Springer, 2026-02)
CTX-M enzymes account for more than 90% of all extended-spectrum β-lactamases (ESBLs) identified in Enterobacterales. Therefore, rapid identification of these enzymes could improve clinical outcomes in patients infected or colonized by such pathogens. In this review, we described the characteristics and limitations of commercially available rapid tests for detecting CTX-M proteins (lateral flow immunoassays) or blaCTX−M genes (microarrays, quantitative PCR, or loop-mediated isothermal amplification). Additionally, we summarized and discussed their potential clinical impact. Some commercial CTX-M assays - particularly those analyzing aliquots from positive blood cultures (i.e., Verigene, BioFire FilmArray, ePlex) - demonstrated clear advantages over standard-of-care methods, shortening the interval to effective therapy and improving overall patient outcomes. However, the widespread adoption of these rapid assays in routine laboratories remains limited due to several factors, including high costs and the lack of robust evidence supporting their positive impact. To address these implementation challenges, laboratories should focus on a defined patient subgroup in whom the application of these assays is likely to yield the greatest clinical impact. In particular, we propose that all laboratories at least perform rapid CTX-M assays on all Gram-negative-positive blood cultures (including those with sterile fluids) obtained from critically ill patients, such as ICU-patients with septic shock. This strategy is best when accompanied by active communication between the laboratory and key stakeholders in patient management. Providing rapid results for this subpopulation of patients may facilitate timely initiation of appropriate therapy and ultimately improve patient outcomes.
Population structure and phylogenetic analysis of Vibrio cholerae non-O1/O139 by whole genome sequencing
Wells, Taylor; González-Durán, Elizabeth; Smith, Anthony Marius; Banerjee, Swapan K.; Tamber, Sandeep; Knox, Natalie; Nadon, Celine (Public Library of Science, 2026-03-05)
Toxigenic Vibrio cholerae serogroups O1 and O139 are well known for causing excessive diarrhea leading to devastating cholera epidemics and pandemics. Over 200 other serogroups, usually lacking the cholera toxin, are denoted non-O1/O139 V. cholerae (NOVC), and cause vibriosis leading to sporadic gastroenteritis and other extraintestinal infections. NOVC infections are not a notifiable disease in Canada and thus underreported. From 2010 to 2023, 160 cases and a small 2018 outbreak were reported in Canada caused by NOVC, provoking considerable public health concern. In this study, 242 Canadian V. cholerae isolates were sequenced, characterized and compared with over 1500 other V. cholerae isolates from around the world to determine their genetic relationships. All Canadian NOVC and two O139 isolates lacked the cholera toxin-producing genes typically harbored by pathogenic O1 and O139. All 14 Canadian O1 isolates were identified from travel-related cases as members of the toxigenic 7th pandemic lineage, whereas one O139 isolate was acquired domestically. Phylogenetic analysis based on core genome single nucleotide polymorphisms classified the Canadian isolates into five clades. Eight new lineages of NOVC, denoted CAD1–8, were identified from the Canadian isolates. A new lineage was defined as clusters formed by three or more isolates in the phylogeny. These lineages were comprised of isolates from clinical origin alone, environmental origin, or a mixture of both. Some lineages spanned multiple years and regions. CAD-2 was comprised of clinical and environmental isolates associated with the 2018 outbreak. Several virulence genes were detected among NOVC, including hemolysins, toxins and secretion system encoding genes. A proportion of virulence genes differed between isolation source (clinical or environmental) and clinical manifestations (gastrointestinal or extraintestinal). Our study identified environmental sources of NOVC with the potential to cause human infection. Tracking the emergence of NOVC with pathogenic potential is essential for understanding the risk to Canadians.
CTX-M-producing Escherichia coli : history, molecular epidemiology and laboratory detection
Peirano, Gisele; Endimiani, Andrea; Pitout, Johann D.D. (Dove Medical Press, 2025-12-10)
From being a curiosity in the 1990s, CTX-M-producing Escherichia coli invaded most parts of the globe during the 2000s and 2010s, with multidrug-resistant (MDR) clone ST131 and CTX-M-15 leading the charge. The most widely distributed CTX-M types, with the highest global frequencies (up to 70% in certain lower- and middle-income countries), are CTX-M-15, CTX-M-14 and CTX-M-27. E. coli isolates with bla CTX-M-27 are currently emerging globally. The worldwide ascendancy of E. coli with bla CTX-M genes occurred via the spread of IncF plasmids between isolates and the existence of certain successful clones (eg, ST131) that acted as repositories for these genes. This is an impressive "gene survival strategy" that aided with the endurance of bla CTX-M in different environments, including the community and hospitals. The detection of extended-spectrum β-lactamase (ESBL)-producing E. coli (including CTX-M isolates) in clinical laboratories is reasonably straightforward. However, different methodologies (eg, immunogenic and genomic) have recently become available to specifically identify CTX-Ms in bacterial isolates as well as human specimens. The role of such tests is currently unclear. E. coli with CTX-M β-lactamases have indirectly been driving the carbapenemase pandemic and are forces to be reckoned with.
Colistin-resistance among Acinetobacter baumannii and Pseudomonas aeruginosa from clinical specimens in Africa : a systematic review and meta-analysis
Gashaw, Yalewayker; Sisay, Assefa; Getachew, Ermias; Asmare, Zelalem; Geteneh, Alene; Tamrat, Ephrem; Abebe, Wagaw; Bitew, Getachew; Birhanu, Abebe; Tigabie, Mitkie; Wondmagegn, Mitikie; Reta, Melese Abate (Oxford University Press, 2026-04)
BACKGROUND : Acinetobacter baumannii and Pseudomonas aeruginosa are multidrug-resistant Gram-negative pathogens increasingly resistant to colistin, a last-resort antibiotic. This study estimated the pooled prevalence of colistin resistance among clinical isolates of these bacteria in Africa. METHODS : Relevant studies were retrieved from PubMed, Scopus, ScienceDirect and Google Scholar. Eligible studies reported colistin resistance in A. baumannii and P. aeruginosa from clinical specimens in Africa using EUCAST or CLSI standards. Data were analysed in STATA 17 using a random-effects model. Heterogeneity was assessed with the I2 statistic, and publication bias with Egger’s test. Subgroup and sensitivity analyses explored heterogeneity sources. RESULTS : Twenty-five studies on A. baumannii and seventeen on P. aeruginosa were included. The pooled prevalence of colistin resistance was 13.75% (95% CI: 5.99%–21.51%), for A. baumannii and 14.42% (95% CI: 3.35%–25.48%) for P. aeruginosa, both showing high heterogeneity I2 > 99%. Resistance varied significantly across countries P ≤ 0.001. In A. baumannii, prevalence was 18.26% in Egypt and 10.89% in South Africa, with regional rates of 10.9%, 13.53% and 20.05% in Southern, North and East Africa, respectively. For P. aeruginosa, regional rates were 20.73% in East, 10.85% in North and 7.19% in Southern Africa. Resistance rose over time; from 5.64% to 16.45% in A. baumannii and from 2.26% to 30.54% in P. aeruginosa between 2010–2017 and 2018–2023. CONCLUSIONS : Colistin resistance in A. baumannii and P. aeruginosa is rising across Africa, emphasizing the urgent need for robust antimicrobial stewardship, infection control and molecular surveillance.
Genomic characterization of Klebsiella pneumoniae causing invasive disease in South African infants : observational studies between 2018 and 2023
Olwagen, Courtney P.; Izu, Alane; Khan, Shama; Jones, Stephanie; Briner, Carmen; Kwatra, Gaurav; Van der Merwe, Lara; Dean, Nicholas J.; Baillie, Vicky L.; Mahtab, Sana; Storath, Kimberleigh; Dunn, Imaan; Andrew, Lubomira; Rajyaguru, Urvi; Nakwa, Firdose L.; Velaphi, Sithembiso C.; Wadula, Jeannette; Strehlau, Renate; Van Niekerk, Anika M.; Naidoo, Niree; Ramsamy, Yogandree; Said, Mohamed; Donald, Robert G.K.; Simon, Raphael; Dangor, Ziyaad; Madhi, Shabir A. (Oxford University Press, 2026-01-20)
Please read abstract in the article.
SeqAfrica : empowering Africa’s fight against antimicrobial resistance through genomics
Nilsson , Pernille; Gibson, Christa Twyford; Thornval, Natasia R.; Lacy-Roberts, Niamh; Odgaard, Christina; Owusu-Nyantakyi , Christian; Amuasi, Grebstad Rabbi; Boateng, William; Mohktar, Quaneeta; Bortey, Alfred; Odih, Erkison Ewomazino; Sunmonu , Gabriel Temitope; Kumburu, Happiness H.; Sonda, Tolbert; Bhiman, Jinal N.; Amoako, Daniel G.; Du Plessis, Mignon; Adu , Bright; Van Zwetselaar, Marco; Von Gottberg, Anne; Mmbaga , Blandina T.; Okeke, Iruka N.; Smith, Anthony Marius; Egyir , Beverly; Hendriksen, Rene S. (Frontiers Media, 2025-12-17)
The ongoing threat of antimicrobial resistance (AMR) demands capacity strengthening in Africa for improved pathogen surveillance. The high-resolution picture of AMR provided by pathogen whole genome sequencing (WGS) can help close data gaps and inform disease prevention strategies, interventions and public health actions. Here, we report on phase 1 of the Fleming Fund-supported SeqAfrica project (2019–2023), one of the first genomic AMR surveillance networks in Africa. SeqAfrica established five regional sequencing hubs across West, East, and Southern Africa, expanded infrastructure, and delivered hybrid training programs to strengthen workforce capacity. During phase 1, the network generated 29,269 pathogen genomes (18,264 bacterial, 300 fungal, and 10,705 SARS-CoV-2) from 21 African countries, contributing to 40 scientific publications and substantial genomic data for national and global surveillance efforts, supporting outbreak investigations and antimicrobial stewardship initiatives. The median turnaround time from sample receipt to data release was 12 weeks (range: 3–104 weeks), demonstrating the feasibility of genomic AMR surveillance despite logistical challenges. By nurturing a community of practice, expanding the workforce, and translating data into actionable insights, SeqAfrica has advanced the integration of pathogen genomics into national and regional surveillance frameworks. However, sustaining this capacity remains a challenge amid global funding constraints, procurement bottlenecks, and workforce retention issues. Lessons learned from implementation include successes in regional collaboration and persistent challenges in procurement, workforce retention, and metadata completeness, which informed the design of phase 2. As Africa continues to invest in genomic health infrastructure, SeqAfrica provides a proven model for embedding pathogen genomics into public health strategies and strengthening AMR surveillance across the continent.
Prevalence and associated factors of syphilis among female sex workers in East Africa : a systematic review and meta-analysis
Gedfie , Solomon; Kassahun, Woldeteklehymanot; Jemal, Abdu; Gashaw, Muluken; Bazezew, Alembante; Nigatie, Marye; Kumie, Getinet; Misganaw, Tadesse; Tefera , Zewdu; Alemu , Bewuketu Belete; Mezgebu, Bahriew; Kassanew, Brhanu; Abebe, Wagaw; Ashagre, Agenagnew; Sisay, Assefa; Gashaw, Yalewayker; Reta, Melese Abate (Frontiers Media, 2025-06-25)
BACKGROUND : Syphilis is the most common sexually transmitted infection caused by Treponema pallidum, a pathogen that is exclusive to humans. Syphilis is a highly treatable infection, but if left untreated, it can result in serious health complications, including adverse reproductive outcomes, diminished quality of life, and an increased risk of Human Immunodeficiency Virus (HIV) transmission. Female sex workers (FSWs) are considered a high-risk group for the transmission of syphilis. Therefore, this review aimed to estimate the pooled prevalence of syphilis and identify the associated factors among female sex workers in the East African region. METHODS : This systematic review and meta-analysis was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Databases such as PubMed/MEDLINE, Scopus, ScienceDirect, and Google Scholar search engines were explored to access eligible articles. STATA 11 statistical software was used to carry out the meta-analysis. A random-effects model was employed to estimate the pooled prevalence of syphilis and its predictors among female sex workers in the East African region. Higgen’s I2 test statistics was done to assess the heterogeneity of the included articles. Publication bias was evaluated visually using funnel plots and statistically through Egger’s weighted regression test. RESULTS : A total of 16,456 articles were retrieved, among which 24 studies involving 25,979 female sex workers were included in the final meta-analysis. The pooled estimates of syphilis among female sex workers were 14.7% (95%CI: 11.06–18.35) and I2 of 99.1%, p = 0.000. Sub-group analyses were conducted based on country and publication year to address heterogeneity. The results revealed that the highest prevalence was 18.48% (95% CI: 11.064–25.899) in Ethiopia and 2.79% (95% CI: 1.49–4.09) in Kenya. Regarding publication year, the prevalence was 16.3% (95% CI: 12.01–20.61) in studies conducted before 2014 and 12.5% (95% CI: 5.85–19.16) in studies conducted after 2014. Among the factors old age was a significant predictor of syphilis among female sex workers. CONCLUSION : This review revealed a relatively higher prevalence of syphilis compared to the global estimate. To effectively curb syphilis among female sex workers in East Africa, intervention strategies should address the high prevalence and key associated factors through comprehensive approaches.
Editorial : Emerging antimicrobials : sources, mechanisms of action, spectrum of activity, combination antimicrobial therapy, and resistance mechanisms
Majewski, Piotr; Brown, Amanda Claire; Schneiders, Thamarai; Osei Sekyere, John (Frontiers Media, 2025-12-16)
No abstract available.
“I believe in my ancestors, and I participate and believe” : negotiating identity, tradition, and HIV-related health among SGM communities in the Eastern Cape
Rutt, 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.
Phenotypic and genotypic antimicrobial resistance profiles of clinical Clostridioides difficile isolates collected from private and public health settings in South Africa
Shirinda, 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.
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 health
Bucci, 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.
Carbapenem-resistant Acinetobacter baumannii at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing
Strysko, 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.
Point-of-care testing to strengthen sexually transmitted infection case management in resource-constrained settings
Peters, 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.
Association between partner treatment and repeat sexually transmitted infections positivity in pregnant women in East London, South Africa
Mdingi, 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.
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 evaluation
Martin , 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.
Modifiable risk factors for anemia in pregnancy : an umbrella review of systematic reviews and meta-analyses
Dagne, 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.
Investigation of a suspected cholera outbreak within a closed community of trainees at a college in Hammanskraal, Gauteng Province, South Africa, June 2023
Sekwadi, 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.
Modifiable risk factors for anemia in pregnancy : an umbrella review of systematic reviews and meta-analyses
Dagne, 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.
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.
Whole-genome sequencing for surveillance of Salmonella at a public health institution in South Africa
Smith, 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.

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