Research Articles (Medical Microbiology)

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Wild birds as reservoirs of antimicrobial-resistant enterococci : genomic surveillance in Gauteng, South Africa, during the migratory season
Govender, Theevasha; Ueckermann, Veronica; Hamiwe, Thabo; Van der Zel, Gerbrand A.; Makumbi, John Paul; Shirinda, Hlambani; Ehlers, Marthie Magdaleen (Elsevier, 2026-09)
Wild birds, including migratory species, are understudied reservoirs of enterococci in South Africa. This study investigated the resistome, mobilome, virulome and genetic diversity of enterococci from wild birds frequenting water bodies during the migratory season in Gauteng, South Africa. Faecal samples were collected from five sites between November 2023 and March 2024. Enterococci were isolated on selective media and identified with polymerase chain reaction and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, with 48 isolates undergoing whole-genome sequencing analysis: Enterococcus faecalis (E. faecalis) [56.3% (27/48)], Enterococcus faecium (E. faecium) [18.8% (9/48)] and other enterococci [25.0% (12/48)]. Aminoglycoside resistance genes aph(3′)-III [11.1% (3/27)] and ant(6’)-Ia [7.4% (2/27)] were detected in E. faecalis and linked to Inc18 and RepA_N plasmids. Linezolid resistance was confirmed in an E. faecalis (MIC = 24 μg/mL) and E. faecium (MIC = 8 μg/mL) isolate carrying optrA and rplD_N130K, respectively, with optrA linked to plasmid-derived sequences. A daptomycin resistance-associated liaS_E192G mutation was identified in one E. faecium isolate (MIC = 4 μg/mL). Five potential multidrug-resistant E. faecalis and E. faecium isolates belonged to infrequently described strains. Clinically relevant virulence genes in E. faecalis included: gelE (100%), asa1 [25.9% (7/27)], hylA [59.3% (16/27)], hylB [74.1% (20/27)] and sex-pheromone genes (100%). Phylogenetic analysis revealed wild bird-adapted strains, alongside One Health-relevant E. faecalis ST16 and ST21 and E. faecium ST54 and ST800 lineages, with limited clustering with global isolates. Wild birds harbour enterococcal lineages carrying antimicrobial resistance genes, underscoring surveillance within a One Health framework in low- and middle-income countries. HIGHLIGHTS • Aminoglycoside, linezolid and daptomycin resistance determinants detected. • Linezolid resistance expressed in E. faecalis (optrA) and E. faecium (rplD_N130K). • Mobile genetic elements linked to antimicrobial resistance genes. • Potentially virulent E. faecalis isolates harbouring asa1, gelE and hylAB genes. • Diverse and uncommon STs reflecting wild bird-adapted strains and genome plasticity.
Viral variant but not host factors associate with SARS-CoV-2 viral kinetics
Hahn, William O.; Fisher, Leigh H.; Ward, Amy; Grant, Shannon; Yen, Catherine; Randhawa, April Kaur; Li, Xiaohong; Ramirez, Shelly; Espy, Nicole; Hural, John; Hanke, Jennifer; Roychoudhury, Pavitra; Kelley, Colleen F.; Rouphael, Nadine; Cantos, Valeria D.; Pinto, Jorge; Cahn, Pedro E.; Manentsa, Mmatsie; Makhema, Joseph; Samaneka, Wadzanai; Bhondai-Mhuri, Muchaneta; Stranix-Chibanda, Lynda; Losso, Marcelo H.; Garcia, Edgar Antonio Ramirez; Innes, Craig; Chinula, Lameck; Lama, Javier R.; Gallardo-Cartagena, Jorge A.; Kabengele, Chishiba; Chilengi, Roma; Nchabeleng, Maphoshane; Tieu, Hong-Van; Hoagland, Brenda; Grinsztejn, Beatriz; Brumskine, William L.; Ahmed, Khatija; Wallis, Carole L.; Greninger, Alexander L.; Corey, Lawrence; Hyrien, Ollivier (Nature Research, 2026-06-17)
BACKGROUND : It is challenging to assess SARS-CoV-2 viral kinetics amidst viral variant evolution and changes in population-level immunity. However, understanding the relationship between host factors and viral replication deepens our understanding of viral fitness. METHODS : In CoVPN 5001, we enrolled N = 953 adults diagnosed with acute SARS-CoV-2 from July 2020 to July 2022 across 51 sites. We confirmed SARS-CoV-2 infection by RT-PCR and identified the variant via viral genome sequencing. Using multivariable linear regression and median regression, we studied the association between host factors and either observed peak viral load (VL) or clinical viral shedding, respectively, accounting for viral variant effects in a demographically and clinically diverse longitudinal cohort. RESULTS : In this observational study, we determine that while host factors, including age, BMI, sex, medical comorbidities, and HIV, have no significant associations with either observed peak VL or clinical viral shedding in the nasopharynx, viral variant is significantly associated with observed peak VL and clinical viral shedding. We show that neither observed peak VL nor shedding duration predict evolutionary success since the dominant variants in the SARS-CoV-2 pandemic did not all align with the variants with the highest peak and longest shedding duration. CONCLUSIONS : Altogether, our work shows that observed peak VL and shedding duration should be cautiously interpreted as predictors of viral fitness. PLAIN LANGUAGE SUMMARY : Over time the virus causing COVID has changed, with these different viruses described as viral variants that have started in specific geographic regions. Many studies of COVID have involved small numbers of people infected with only one or two viral variants. We undertook a study of a large number of people across the USA, Southern Africa, and South America who acquired COVID between 2020 and 2022, a period during which many different viral variants were present. Different viral variants resulted in different amounts of virus being present in the upper-airways. However, a large amount of virus being present did not predict that a variant would outcompete other variants. Better understanding of the impact of viral variants offers potential improvements for public health policy and insight into the COVID pandemic to date
Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa : a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance
Foster-Nyarko, Ebenezer; Able-Thomas, Shola; Adade, Nana Eghele; Adade, Rexford; Anne, Jean Claude Blessa; Antwi, Loretta; Bah, Yaya; Boateng, Gifty; Carleton, Heather; Chaima, David; Chilengi, Roma; Coulibaly, Kalpy Julien; Derra, Firehiwot Abera; Didon, Dwayne; Dimuna, Cheelo; Dosso, Mireille; Drammeh, Momodou M.; Ferjani, Sana; Holt, Kathryn E.; Jatta, Rohey; Kalule, John Bosco; Kanteh, Abdoulie; Kette, Hortense Faye; Khan, Dam; Kouadio, N’da Kouame Nazaire; Lee, Christine; Mantina, Hamakwa; Mulenga, Gillan; Mwaba, John; Nyang, Fatou; Owusu-Okyere, Godfred; Rowland, Jessica; Seck, Aissatou; Sesay, Abdul Karim; Smith, Anthony Marius; Smith, Peyton; Soma, Djifahamaï; Tau, Nomsa; Tchuinte, Pierrette Landrie Simo; Tientcheu, Peggy-Estelle Maguiagueu; Sokoni, Chalwe; Vakou, Sabine N'dri; Vubil, Delfino (Microbiology Society, 2025-12-10)
OBJECTIVES : Vibrio cholerae remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of V. cholerae isolates from Côte d’Ivoire, Ghana, Zambia and South Africa to assess genomic diversity, AMR profiles and virulence, demonstrating the utility of WGS for enhanced surveillance within the PulseNet Africa network. METHODS : We analysed Vibrio isolates from clinical and environmental sources (2010–2024) using Oxford Nanopore sequencing and hybracter assembly. Phylogenetic analysis, MLST, virulence and AMR gene detection were performed using Terra, Pathogen watch and Cloud Infrastructure for Microbial Bioinformatics platforms, with comparisons against 118 global reference genomes for broader genomic context. RESULTS : Of 79 high-quality assemblies, 67 were confirmed as V. cholerae, with serogroup O1 accounting for the majority (43 out of 67, 67%). ST69 accounted for 60% (40 out of 67) of isolates, with 8 sequence types identified overall. Thirty-seven isolates formed distinct sub-clades within AFR12 and AFR15 O1 lineages, suggesting local clonal expansions. AMR gene analysis revealed genes associated with resistance to trimethoprim in 96% of isolates and genes associated with resistance to quinolones in 83%, while genes associated with resistance to azithromycin, rifampicin and tetracycline remained low (≤7%). A significant proportion of the serogroup O1 isolates (41 out of 43, 95%) harboured resistance genes in at least 3 antibiotic classes. CONCLUSIONS : This study highlights significant genetic diversity and AMR prevalence in African V. cholerae isolates, with expanding AFR12 and AFR15 clades in the region. The widespread presence of genes associated with resistance to trimethoprim and quinolones raises concerns for treatment efficacy, although azithromycin and tetracycline remain viable options. WGS enables precise identification of species and genotyping, reinforcing PulseNet Africa’s pivotal role in advancing genomic surveillance and enabling timely public health responses to cholera outbreaks.
Asymptomatic Chlamydia trachomatis and Neisseria gonorrhoeae infection in men who have sex with men living with HIV
Peters, Remco P.H.; Manis, Derek; Jung, Hyunsul; De Vos, Lindsey; Mukomana, Freedom; Mahlobisa, Buntu; Molaoa, Renilwe; Metula, Aphiwe; Bongo, Cikizwa; Radebe, Oscar; Struthers, Helen; Daniels, Joseph (AOSIS, 2026-05-31)
BACKGROUND : South Africa faces overlapping epidemics of HIV and sexually transmitted infections (STIs), particularly among men who have sex with men (MSM). Data on asymptomatic Chlamydia trachomatis and Neisseria gonorrhoeae infections in MSM living with HIV are limited. OBJECTIVES : To determine the prevalence and incidence of asymptomatic C. trachomatis and N. gonorrhoeae infections among MSM living with HIV. METHOD : We conducted a pilot randomised controlled trial of the HIV coping and disclosure management intervention among 88 MSM living with HIV in Buffalo City, South Africa. Sexually transmitted infection screening for C. trachomatis and N. gonorrhoeae was performed at baseline and at a 17-week follow-up using nucleic acid amplification testing of urine and rectal swabs. Univariable logistic regression models were used to examine the relationship between conceptually important individual-level variables and any STI at baseline and week 17 of follow-up. RESULTS : Mean age was 30 years in the intervention arm and 33 years in the control arm. At enrolment, most participants had an undetectable HIV viral load (79.1% intervention vs 80.0% control). Syphilis positivity was higher in the intervention arm (9.3% vs 2.3%). Baseline prevalence of STIs was high, including urethral and rectal C. trachomatis and N. gonorrhoeae infections. At week 17, STI prevalence was similar between arms (27.9% intervention vs 28.9% control). Univariable analyses did not identify any factors associated with STI at follow-up in either group. CONCLUSION : Asymptomatic STIs are highly prevalent and incident among MSM living with HIV in South Africa. Findings highlight the need to strengthen STI prevention, treatment and care services, and to innovative interventions.
A bibliometric analysis of the literature on Mycoplasma and Ureaplasma infections
Ramaloko, Winnie T.; Malgwi, Samson A.; Yakobi, Sinethemba H.; Adeleke, Matthew A.; Abbai, Nathlee S.; Osei Sekyere, John; Maningi, Nontuthuko E. (AOSIS, 2026-04-03)
BACKGROUND : Mycoplasma and Ureaplasma species are understudied opportunistic pathogens that infect humans, animals and plants. These infections are often asymptomatic, which, together with fastidious growth requirements, makes them challenging to detect. AIM : The review aimed to provide a bibliometric analysis of available literature to reflect and assess trends, progress and knowledge gaps in this field. SETTING : This article is a literature review. METHOD : A bibliometric analysis of 19 486 documents from 1992 to 2022 was conducted using the Web of Science database and in-depth analyses on RStudio. RESULTS : China and the United States produced a high number of publications and citations. South Africa, the first most-cited African country, contributed 685 publications, ranking 24th globally with 2031 citations. Veterinary Microbiology was the highest performing journal with 448 papers and 10 036 citations. The most frequent keywords were ‘infection’ and ‘Ureaplasma urealyticum’. CONCLUSION : Research on Mycoplasma and Ureaplasma infections has progressed over time, but mainly in developed countries. The restricted publications and moderate citations in South Africa suggest research gaps in understanding the true burden and impacts of these infections. CONTRIBUTION : This study provides a comprehensive bibliometric overview of Mycoplasma and Ureaplasma infections and reports the global and local progress in this field. The overall moderate, steady growth highlights the need for broader international collaboration and expanded research efforts in low-resource countries to address existing research gaps. This expansion is essential, particularly in clinical research, for strengthening both surveillance and treatment guidelines.
Prevalence, pattern of disease and antimicrobial susceptibility of Candidozyma auris in the Pretoria from 2021 to 2024
Moola, Abdullah; Thom, Marko G.; Finlay, Jonah M.; Rule, Roxanne; Said, Mohamed (AOSIS, 2026-05-06)
BACKGROUND : Candidozyma auris has emerged as a nosocomial pathogen in South Africa, characterised by multidrug resistance and environmental persistence. OBJECTIVES : This study aimed to describe the prevalence, disease patterns, and antifungal susceptibility patterns of C. auris isolates recovered from public-sector healthcare facilities in the greater Pretoria region from 2021 to 2024. METHOD : A retrospective laboratory-based surveillance study was conducted using data from the National Health Laboratory Service Tshwane Academic Division laboratory. Isolates were classified as invasive or non-invasive based on specimen source. Temporal trends in antifungal minimum inhibitory concentrations (MICs) were analysed using interval-censored regression. RESULTS : A total of 592 C. auris isolates were identified. Blood cultures were the most frequent specimen source overall, comprising 237 isolates (40.03%). Intravascular catheter tip isolates predominated in 2023 and 2024, with 48 and 72 isolates, respectively. The proportion of invasive isolates declined from 56.8% to 40.8% over the study period. Among tested isolates, fluconazole resistance exceeded 99%. Resistance to amphotericin B and echinocandins was uncommon, with eight total isolates identified. Decreasing MIC trends were observed for amphotericin B (β = −0.059 per year; p = 0.012) and micafungin (β = −0.081 per year; p = 0.026). CONCLUSION : Candidozyma auris remains established in the public-sector within the greater Pretoria region. There is a shift from invasive bloodstream infections towards non-invasive, device-associated isolates. Fluconazole resistance remained high while amphotericin B and echinocandins retained good in vitro activity. CONTRIBUTION : This study contributes to the knowledge of C. auris in the greater Pretoria region, providing insight into epidemiology and antifungal susceptibility.
The TyphiNET data visualisation dashboard : unlocking salmonella Typhi genomics data to support public health
Dyson, Zoe A.; Cerdeira, Louise; Sharma, Vandana; Carey, Megan E.; Holt, Kathryn E.; Aanensen, David M.; Abbas, Ali H.; Fayad, Antoine Abou; Afolayan, Ayorinde O.; Ahmed, Niyaz; Ahmed, Irshad; Amir, Afreenish; Andleeb, Saadia; Argimón, Silvia; Aseffa, Abraham; Ashton, Philip M.; Aworh, Mabel K.; Bavdekar, Ashish R.; Chattaway, Marie A.; Chew, Ka Lip; Crump, John A.; Darton, Thomas C.; Diaz, Paula L.; Dolecek, Christiane; Feasey, Nicholas A.; Greenhill, Andrew R.; Gupta, Madhu; Hatta, Mochammad; Hendriksen, Rene S.; Heyderman, Robert S.; Ikhimiukor, Odion O.; Ikram, Aamer; Ingle, Danielle J.; Kapil, Arti; Keane, Jacqueline A.; Keddy, Karen Helena; Kingsley, Robert A.; Levine, Myron M.; MacLennan, Calman A.; Maes, Mailis; Mahindroo, Jaspreet; Mashe, Tapfumanei; Morita, Masatomo; Mylona, Elli; Nagaraj, Geetha; Nair, Satheesh; Naseri, Take K.; Njamkepo, Elisabeth; Octavia, Sophie; Okeke, Iruka N.; Owusu, Michael; De la Gandara, Maria Pardos; Pollard, Andrew J.; Rahman, Sadia I.A.; Rahman, Saikt; Rasko, David A.; Redwan, Elrashdy M.; Rokney, Assaf; Rupali, Priscilla; Rutanga, Jean Pierre; Shakya, Jivan; Saha, Senjuti; Sikorski, Michael J.; Smith, .Anthony M.; Tagg, Kaitlin A.; Taneja, Neelam; Tamrakar, Dipesh; Turner, Paul; Ussher, James E.; Van Puyvelde, Sandra; Vandelannoote, Koen; Weill, François-Xavier; Wong, Vanessa K.; Wright, Jackie (BioMed Central, 2025-05-09)
BACKGROUND : Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed typhoid conjugate vaccines (TCVs). National immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high, and the Gavi vaccine alliance has provided financial support for their introduction. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance. RESULTS : We developed TyphiNET (https://www.typhi.net), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n = 11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers. CONCLUSIONS : The TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience.
Typhi mykrobe : fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi
Ingle, Danielle J.; Hawkey, Jane; Hunt, Martin; Iqbal, Zamin; Keane, Jacqueline A.; Afolayan, Ayorinde O.; Ahmed, Niyaz; Andleeb, Saadia; Ashton, Philip M.; Bogoch, Isaac I.; Carey, Megan E.; Chattaway, Marie Anne; Crump, John A.; Guevara, Paula Diaz; Howden, Benjamin P.; Izumiya, Hidemasa; Jacob, Jobin John; Judd, Louise M.; Kapil, Arti; Keddy, Karen Helena; Kim, Justin Y.; Levine, Myron M.; Morita, Masatomo; Nair, Satheesh; Octavia, Sophie; Okeke, Iruka N.; Osadebamwen, Precious E.; Rahman, Sadia Isfat Ara; Rokney, Assaf; Rasko, David A.; Shamanna, Varun; Sikorski, Michael J.; Smith, .Anthony M.; Sunmonu, Gabriel T.; Tagg, Kaitlin A.; Wick, Ryan R.; Dyson, Zoe A.; Holt, Kathryn E.; Global Typhoid Genomics Consortium (BioMed Central, 2025-10-24)
BACKGROUND : Typhoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial-resistant (AMR) Typhi lineages have emerged and become established in many parts of the world. Knowledge of local pathogen populations informed by genomic surveillance, including of lineages (defined by the GenoTyphi scheme) and AMR determinants, is increasingly used to inform local treatment guidelines and to inform vaccination strategy. Current tools for genotyping Typhi require multiple read alignment or assembly steps and have not been validated for analysis of data generated with Oxford Nanopore Technologies (ONT) long-read sequencing devices. Here, we introduce Typhi Mykrobe, a command line software tool for rapid genotyping of Typhi lineages, AMR determinants, and plasmid replicons direct from sequencing reads. RESULTS : We validated Typhi Mykrobe lineage genotyping by comparison with the current standard read mapping-based approach and demonstrated 99.8% concordance across nearly 13,000 genomes sequenced with Illumina platforms. For the few isolates with discordant calls, we show that Typhi Mykrobe results are better supported by the evidence from raw sequence read data than the results generated using the mapping-based approach. We also demonstrate 99.9% concordance for detection of AMR determinants compared with the current standard assembly-based approach, with similar results for plasmid marker detection. Typhi Mykrobe predicts clinical resistance categorization (S/I/R) for eight drug classes, and we show strong agreement with phenotypic categorizations generated from reference laboratory minimum inhibitory concentration (MIC) data for n = 1572 Illumina-sequenced isolates (> 99% agreement within one doubling dilution). We show strong concordance (> 96% for genotype and > 98% for AMR and plasmid) between calls made from ONT reads and those made from Illumina reads for isolates sequenced on both platforms (n = 93 genomes). Typhi Mykrobe takes less than a minute per sample and is available at https://github.com/typhoidgenomics/genotyphi. CoONCLUSIONS : Typhi Mykrobe provides rapid and sensitive genotyping of Typhi genomes direct from Illumina and ONT reads, although lower accuracy was observed for R9 ONT data. It demonstrated accurate assignment of GenoTyphi lineage, detection of AMR determinants and prediction of corresponding AMR phenotypes, and identification of plasmid replicons.
Plasmid diversity, antibiotic resistance and virulence genes associated with Staphylococcus aureus isolates from private hospitals in Gauteng, South Africa
Ngoie, Kazadi; Kingsburgh, Chanel; Hamiwe, Thabo; Ehlers, Marthie Magdaleen (Springer, 2026-04)
This study investigated the association between plasmid diversity, antibiotic resistance and virulence genes of Staphylococcus aureus (S. aureus) isolates from private hospitals in Gauteng, South Africa. Automated antibiotic susceptibility testing was done on 100 S. aureus isolates. Plasmid extraction and polymerase chain reaction (PCR)-based replicon typing were done on all isolates, followed by a multiplex-PCR assay screening for virulence genes in plasmid-positive isolates. Whole genome sequencing (WGS) was conducted on ten representative isolates selected based on the presence and number of plasmids, replicon gene profiles and antibiotic susceptibility patterns. Resistance to erythromycin (29%; 29/100), clindamycin (26%; 26/100) and ciprofloxacin (15%; 15/100) was observed. Plasmids were detected in 60% (60/100) of isolates, with pN315 (70%; 7/10) and pSaaS6159 (50%; 5/10) predominating among representative isolates and carrying antibiotic resistance genes (ARGs). Specific rep–ARG associations included rep7a (pS0385p1) with tetK, rep7a (pTZ4) with cat, rep10a (pDLK1) with ermC and rep5a (pN315) and rep16 (pSaaS6159) with blaZ. No virulence gene was specifically linked to any rep gene. Sequence types identified by WGS included ST22, ST35 and ST5 among MRSA isolates and ST152, ST5, ST6, ST1 and ST45 among MSSA isolates. These findings highlight an association between specific plasmids (pS0385p1, pTZ4, pDLK1, pN315 and pSaaS6159) and ARGs. The lack of association between replicon type and virulence gene carriage suggests that plasmid-borne traits in S. aureus are more strongly driven by antimicrobial selection than by virulence factors, with most virulence genes residing on the chromosome. Enhanced surveillance programs targeting these plasmids may improve understanding of ARG dissemination in healthcare settings.
From crisis to control : a study of Typhoid conjugate vaccine efficacy in Harare, Zimbabwe (2017-2024)
Bvochora, Talent; Manyara, John; Thilliez, Gaetan; Vere, Michael; Mukeredzi, Innocent; Nhamo, Denford; Chitiyo, Farai; Muzondo, Augustine; Juru, Agnes; Chonzi, Prosper; Phiri, Isaac; Smith, Anthony Marius; Chaibva, Blessmore V.; Mapingure, Munyaradzi; Fuller, Walter; Shrestha, Pramila; Nair, Parvati; Kingsley, Robert A.; Laxminarayan, Ramanan; Musuka, Godfrey; Mashe, Tapfumanei (Oxford University Press, 2026-03)
BACKGROUND : Typhoid fever remains a public health concern in Harare City, Zimbabwe. Recurrent outbreaks are driven by inadequate water, sanitation, and hygiene infrastructure. In 2019, the typhoid conjugate vaccine (TCV) was introduced. The TCV impact on typhoid epidemiology, antimicrobial resistance (AMR), Salmonella Typhi population, and effectiveness across districts and age groups remains understudied. METHODS : Data from 3401 typhoid cases during 2017–2024 were analyzed. Attack rates, risk ratios, AMR, and vaccine effectiveness across prevaccine (2017–2019) and postvaccine (2020–2024) periods were compared. Analysis was stratified by district, vaccination coverage, and age groups. Genomic characteristics of Salmonella Typhi strains isolated postvaccination were investigated and compared to prevaccine populations. RESULTS : Attack rates for the Western district, which reported 70.8% of cases, decreased from 1373/100 000 before TCV to 341/100 000 after (risk ratio: 0.40, P ≤ .0001). Subdistricts had attack rates of 1783 (Glen View), 1687 (Mufakose), and 1145 (Budiriro) per 100 000 before vaccination and 223, 33, and 364/100 000, respectively, after (risk ratio: 0.22, 0.03, 0.48, respectively, P < .0001). The 0–15 age group showed vaccine effectiveness of 81.2% (95% confidence interval, 71.2–88.8), compared to 61.4% (95% confidence interval, 54.3–68.1) across all ages. Genomic comparison of Salmonella Typhi isolates pre- and postvaccination did not indicate changes in bacterial population. AMR phenotypic data and genomic prediction indicated lower resistance to antibiotics postvaccination. CONCLUSIONS : TCV reduced typhoid incidence, particularly in high-burden areas and children. No shift in the Salmonella Typhi population was observed. Ongoing transmission underscores need for integrated measures, including human-resource capacity, improved water, sanitation, and hygiene infrastructure, research on vaccine performance variability, and refined multisectoral interventions.
Evaluation of a novel point-of-care lateral flow assay screening for Neisseria gonorrhoeae infection among pregnant women in Zimbabwe
Martin , Kevin; Dauya, Ethel; Chikwari, Chido Dziva; Mackworth-Young, Constance R.S.; Simms, Victoria; Bandason, Tsitsi; Makamure, Beauty; Martin, Janice; Makoga, Forget; Machiha, Anna; Peters, Remco P.H.; Mazzola, Laura T.; Blumel, Benjamin; Gleeson, Birgitta; Marks, Michael; Kranzer, Katharina; Ferrand, Rashida A.; Ferreyra, Cecilia (Public Library of Science, 2025-02-11)
Affordable, easy-to-use and rapid diagnostics may support a move away from syndromic management for sexually transmitted infections (STIs) in resource-constrained settings. A lateral flow assay for Neisseria gonorrhoeae (NG-LFA) has shown high sensitivity and specificity (>90%) in symptomatic individuals. We investigated the performance and acceptability of this assay as a screening tool for NG among pregnant women. This evaluation was embedded within a prospective study evaluating point-of-care STI screening in pregnant women attending antenatal care (ANC) in Harare, Zimbabwe. Participants were included regardless of symptom status, ANC visit number, or gestational age. Nurse-collected vaginal swabs were tested on-site using the NG-LFA and the Xpert CT/NG assay (Xpert) (reference test). The implementation team members (n=4) were interviewed to assess acceptability and usability of NG-LFA. Of 912 participants, 4.8% (44/912) self-reported presence of abnormal vaginal discharge. Xpert NG prevalence was 4.2% (38/912); 81.6% (31/38) of infections were asymptomatic. The sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of the NG-LFA were 65.8% (25/38; 95% CI 48.6%-80.4%), 99.2% (867/874; 95% CI 98.4-99.7%), 78.1% (25/32; 95% CI 60.0-90.7%), and 98.5% (867/880; 95% CI 97.5-99.2%). The NG-LFA was considered easy-to-use and interpret but discordant results led to issues of trust in the NG-LFA results. Among predominantly asymptomatic pregnant women, the NG-LFA had high specificity, but relatively low sensitivity meaning one in three cases of gonorrhoea were not detected. Further studies are warranted to assess the clinical performance and cost-effectiveness of the NG-LFA in other settings and populations.
Antibacterial resistance in urinary samples from long-term care-facility and community-dwelling older people in Gauteng, South Africa
Labuschagne, Olivia; Leigh, Stephanie; Kingsburgh, Chanel; Williams, Christopher David (Elsevier, 2026-03)
OBJECTIVE : Older populations (≥ 60 years) are frequent users of health care services, often vulnerable to infections and antimicrobial resistance (AMR). Urinary tract infection is often diagnosed in this cohort based on non-specific or atypical symptoms, yet empirical therapy seldom considers the potential influence of residential setting on resistance patterns. This study therefore aimed to quantify and compare the in vitro AMR profiles of urinary pathogens from these two settings and assessed temporal resistance trends to inform antimicrobial stewardship priorities. METHODS : A retrospective analysis was conducted using anonymised microbiology data from Ampath Laboratories in Gauteng. Urine cultures collected from older adults (≥60 years) between 2015 and 2023 were included. The five most common uropathogens were analysed. Resistance differences between long-term care facility (LTCF) and community samples were assessed using univariate and multivariable logistic regression models adjusting for age, sex, inpatient status, and sampling year. Temporal trends were evaluated using Kendall tau-b. RESULTS : A total of 50 704 urine cultures were analysed, of which 18.81% were from LTCFs. Escherichia coli and P. mirabilis showed consistently higher resistance in LTCF isolates. In E. coli, LTCF residence was associated with increased resistance to ciprofloxacin (adjusted OR 1.26; 95% CI 1.18–1.34), nitrofurantoin (1.55; 1.38–1.75), ceftriaxone (1.24; 1.14–1.34), amoxicillin/clavulanic acid (1.11; 1.05–1.19), and co-trimoxazole (1.10; 1.03–1.18). P. mirabilis showed similar patterns, with higher resistance to ciprofloxacin (2.16), gentamicin (1.64), fosfomycin (1.72) and co-trimoxazole (1.49). Trend analysis showed increasing fosfomycin resistance from E. coli isolates in both LTCFs (3.74% to 6.18%) and community settings (2.75% to 3.74%) and rising ceftriaxone resistance in community isolates (13.32% to 17.60%). CONCLUSIONS : LTCF residence was independently associated with higher AMR in several common urinary pathogens. These findings suggest that empirical urinary tract infection regimens commonly used in community-dwelling older adults may be inadequate for LTCF residents. Setting-specific antibiograms, improved diagnostic stewardship, and strengthened antimicrobial stewardship interventions are needed to support appropriate prescribing. Further studies incorporating patient-level clinical factors are warranted to refine empirical treatment recommendations for older adults across care settings. HIGHLIGHTS • Urinary tract infections are a common clinical diagnosis in older people. • Antibiotics are used excessively in older populations. • Where a patient resides has an impact on antimicrobial resistance. • Long-term care facility residents have higher antimicrobial resistance rates and require an enhanced approach to infection prevention and control.
Identification of multidrug-resistant monophasic Salmonella typhimurium ST34 and other NTS from animal-environmental origins in South Africa
Ogundare, Samuel Tolulope; Thilliez, Gaetan; Bawn, Matt; Makumbi, John-Paul; Hamiwe, Thabo; Fasina, Folorunso Oludayo; Smith, .Anthony M.; Van der Zel, Gerbrand A.; Kock, Marleen M.; Geertsma, Peter F.; Ehlers, Marthie Magdaleen (Nature Research, 2025-11-03)
Non-typhoidal Salmonella (NTS) causes approximately 155 000 deaths annually and poses significant risks to both human and animal health. Antimicrobial resistance (AMR) in NTS is a growing global public health threat. Using a One Health approach, this study investigated NTS in swine, poultry, and wastewater in Gauteng Province, South Africa. From May 2019 to August 2020, 507 samples were collected, including animal faeces (n = 388), hand swabs (n = 104), abattoir and farm run-off (n = 10), and hospital (n = 1) and municipal wastewater (n = 4). Whole genome sequencing of recovered isolates revealed a 2.37% (12/507) NTS prevalence, identifying four serovars: Salmonella Enteritidis sequence type (ST) 11 (n = 3), S. Infantis ST32 (n = 4), S. Irumu ST2026 (n = 2), and multidrug-resistant S. Typhimurium monophasic variant 1,4,[5],12:i:- ST34 (n = 3). The ST34 strains, detected in swine, exhibited ASSuT (ampicillin, streptomycin, sulfamethoxazole, tetracycline) resistance pattern and marked the first detection of ST34 from an animal source in Africa. The strains harboured a novel sopE-phage (AmTI) and SGI-4. Phylogenetic analysis linked these strains to human cases in South Africa and the UK, which could indicate transmission of MDR S. Typhimurium between animals and humans, underscoring the importance of enhanced AMR surveillance using a One Health approach.
Plasmid-borne mcr-1 and replicative transposition of episomal and chromosomal blaNDM-1, blaOXA-69, and blaOXA-23 carbapenemases in a clinical Acinetobacter baumannii isolate
Mmatli, Masego; Mbelle, Nontombi Marylucy; Osei Sekyere, John (American Society for Microbiology, 2025-03)
A multidrug-resistant clinical Acinetobacter baumannii isolate with resistance to most antibiotics was isolated from a patient at an intensive care unit. The genetic environment, transcriptome, mobile, and resistome were characterized. The MicroScan system, disc diffusion, and broth microdilution were used to determine the resistance profile of the isolate. A multiplex PCR assay was also used to screen for carbapenemases and mcr-1 to -5 resistance genes. Efflux-pump inhibitors were used to evaluate efflux activity. The resistome, mobilome, epigenome, and transcriptome were characterized. There was phenotypic resistance to 22 of the 25 antibiotics tested, intermediate resistance to levofloxacin and nalidixic acid, and susceptibility to tigecycline, which corresponded to the 27 resistance genes found in the genome, most of which occurred in multiple copies through replicative transposition. A plasmid-borne (pR-B2.MM_C3) mcr-1 and chromosomal blaPER-7, blaOXA-69, blaOXA-23 (three copies), blaADC-25, blaTEM-1B, and blaNDM-1 were found within composite transposons, ISs, and/or class 1 and 2 integrons on genomic islands. Types I and II methylases and restriction endonucleases were in close synteny to these resistance genes within the genomic islands; chromosomal genomic islands aligned with known plasmids. There was a closer evolutionary relationship between the strain and global strains but not local or regional strains; the resistomes also differed. Significantly expressed/repressed genes (6.2%) included resistance genes, hypothetical proteins, mobile elements, methyltransferases, transcription factors, and membrane and efflux proteins. The genomic evolution observed in this strain explains its adaptability and pandrug resistance and shows its genomic plasticity on exposure to antibiotics. IMPORTANCE : A pandrug-resistant pathogen that was susceptible to only a single antibiotic, tigecycline, was isolated from a middle-aged patient in an ICU. This pathogen contained two plasmids and had a chromosome that contained portions that were integrated externally from plasmids. These genomic islands were rich with resistance genes, mobile genetic elements, and restriction-modification systems that protected the pathogen and facilitated gene regulation. The strain contained 35 resistance genes and 12 virulence genes. The strain was of closer evolutionary distance to several international strains suggesting that it was imported into South Africa. However, its resistome was unique, suggesting an independent evolution on exposure to antibiotic therapy mediated by epigenomic factors and MGE transposition events. The varied mechanisms available to this strain to overcome antibiotic resistance and spread to other areas and/or transfer its resistance determinants are worrying. This is ultimately a risk to public health, evincing the need for antibiotic stewardship.
Rectal carriage of sequence type 307 Klebsiella pneumoniae high-risk clone harboring multiple carbapenemase genes in community hospitals Gauteng, South Africa
Salvador-Oke, Kafilat Taiwo; Pitout, Johann D.D.; Peirano, Gisele; Strydom, Kathy-Anne; Kingsburgh, Chanel; Ehlers, Marthie Magdaleen; Kock, Marleen M. (Wiley, 2025-11)
Asymptomatic rectal carriers are recognized as reservoirs of carbapenem-resistant Klebsiella pneumoniae (CRKp), which can spread epidemic high-risk clones [e.g., sequence types (ST)-307] and plasmids [incompatibility group (Inc)-X3] in hospitals, with possible transmission into the community. This study investigated the epidemiology and characteristics of CRKp high-risk clones ST307 among rectal carriage isolates from community hospitals. A carbapenemase positivity rate of 24% was observed for all rectal screening performed during hospital admission (February to August 2021) in Gauteng, South Africa; 252 CRKp isolates were characterized. Antimicrobial susceptibility was performed using the VITEK 2 automated system, and polymerase chain reaction assays were used to detect K. pneumoniae ST307, carbapenemase genes, and associated mobile genetic elements (MGEs e.g., IncX3, IS3000). Of the 252 isolates, 25% (64/252) were ST307 positive and 75% (188/252) were non-ST307. Among the 64 ST307, 45% (29/64) harbored blaOXA-181 on IncX3 plasmids. Occurrence of blaOXA-181 among ST307 (69%; 44/64) when compared to non-ST307 (48%; 91/188) was statistically significant (p-value = 0.002). Fourteen isolates, including two ST307, harbored double carbapenemase genes. Carbapenemase gene combinations include six blaNDM+blaOXA-48-like, four blaNDM +blaOXA-181, three blaKPC+blaOXA-181, and one blaOXA-181+blaVIM. One ST307 isolate harbored three carbapenemase genes (blaNDM+blaOXA-48+blaOXA-181). Level of antimicrobial resistance was significantly (p-value < 0.001) associated with the occurrence of ST307, comprising 73% (47/64) extensively drug resistant. This study highlights the need for rectal screening of XDR clones and plasmids using simple and cost-effective genomic methodologies suitable for low- and middle-income countries for local risk management and control of infectious diseases in hospitals.
Next-generation sequencing in infectious-disease diagnostics : economic, regulatory, and clinical pathways to adoption
Osei Sekyere, John (Wiley, 2025-11)
Next‐generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well‐established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS‐based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole‐genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent‐only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130–600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near‐term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious‐disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype–phenotype limits while leveraging multiplexing and centralized reference workflows.
Evaluation of six commercial and noncommercial colistin resistance diagnostics
Leshaba, Tumisho Mmatumelo Seipei; Mmatli, Masego; Mbelle, Nontombi Marylucy; Osei Sekyere, John (Wiley, 2025-08)
Resistance to colistin, a last-reserve antibiotic used for treating drug-resistant infections, is rising globally. We compared six commercial and in-house diagnostics-ComASP colistin, CHROMagar COL-APSE, rapid polymyxin NP (Nordmann/Poirel) test, Sensititre, MicroScan, and Vitek 2-against ISO-standard broth microdilution (BMD) using 142 Gram-negative isolates. The isolates (Enterobacterales = 110, Acinetobacter baumannii = 21, Pseudomonas aeruginosa = 11) underwent BMD and conventional multiplex PCR screening for mcr-1-mcr-5. Sensitivity, specificity, categorical agreement (CA), major error (ME), and very major error (VME) were calculated for each test. Vitek 2 and sensititre yielded the highest CA (≥ 98%) and the lowest VME (≤ 0.0%) across taxa. ComASP showed excellent performance for A. baumannii (100% sensitivity/specificity) but slightly lower CA for P. aeruginosa (73%). CHROMagar COL-APSE demonstrated acceptable sensitivity (92%) but low specificity (69%) in Enterobacterales. MicroScan had reduced specificity in Enterobacterales (87.80%). The CHROMAgar COL-APSE efficiently identified the species with their unique colours but was the least specific (68.63%), with the highest ME in Enterobacterales. The rapid NP test provided rapid results within 4 h but showed a relatively high VME (7.84%), despite maintaining an acceptable sensitivity (92.16%) and specificity (96.08%). For laboratories with automated platforms, Vitek 2 remains optimal for colistin MIC testing; Sensititre and ComASP are suitable low-cost BMD alternatives. The Rapid NP test provides a same-day screen, but confirmatory MIC testing is advised. CHROMagar COL-APSE should be used with a ≤ 1 CFU mL⁻¹ inoculum to minimise false resistance calls. Knowing the comparative performance of these different tests will assist in choosing the best test for every species, improving on efficient diagnosis and healthcare outcomes.
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.

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