Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance

<b>Objectives.</b> <i>Vibrio cholerae</i> remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of <i>V. cholerae</i> 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.<b>Methods.</b> We analysed <i>Vibrio</i> 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, Pathogenwatch and Cloud Infrastructure for Microbial Bioinformatics platforms, with comparisons against 118 global reference genomes for broader genomic context.<b>Results.</b> Of 79 high-quality assemblies, 67 were confirmed as <i>V. cholerae</i>, 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.<b>Conclusions.</b> This study highlights significant genetic diversity and AMR prevalence in African <i>V. cholerae</i> 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.

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Journal
Microbial Genomics
Published
2025-12-05
DOI
https://doi.org/10.1099/mgen.0.001586
Primary Topic
Vibrio bacteria research studies
Type
article
Field-Weighted Citation Impact
0.00

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article

Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance

Godfred Owusu-Okyere, D Didon, Hortense Faye Kette, Gifty Boateng et al.
Microbial Genomics
Vibrio bacteria research studies
article

Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance

Godfred Owusu-Okyere, D Didon, Hortense Faye Kette, Gifty Boateng, Christine C. Lee, John Mwaba, Aïssatou Seck, Yaya Bah, Nomsa P. Tau, Kalpy Julien Coulibaly, Abdul Karim Sesay, A. Peyton Smith, Momodou M. Drammeh, Nana Eghele Adade, Sabine N’dri Vakou, Ebenezer Foster-Nyarko, Abdoulie Kanteh, John Bosco Kalule, Heather A. Carleton, Mireille Dosso, Hamakwa Mantina, Cheelo Dimuna, Loretta Antwi, Pierrette Landrie Simo Tchuinte, David Chaima, Anthony M. Smith, Gillan Mulenga, Sana Ferjani, Roma Chilengi, Kathryn E. Holt, Firehiwot Abera Derra, Peggy-Estelle Tientcheu, Dam Khan, Delfino Vubil, Djifahamaï Soma, Jean Claude Blessa Anne, Jessica Rowland, Rexford Adade, Shola Able-Thomas, Rohey Jatta, N'da Kouamé Nazaire Kouadio, Fatou Nyang, Chalwe Sokoni
article en

Abstract

<b>Objectives.</b> <i>Vibrio cholerae</i> remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of <i>V. cholerae</i> 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.<b>Methods.</b> We analysed <i>Vibrio</i> 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, Pathogenwatch and Cloud Infrastructure for Microbial Bioinformatics platforms, with comparisons against 118 global reference genomes for broader genomic context.<b>Results.</b> Of 79 high-quality assemblies, 67 were confirmed as <i>V. cholerae</i>, 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.<b>Conclusions.</b> This study highlights significant genetic diversity and AMR prevalence in African <i>V. cholerae</i> 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.

Microbial GenomicsVol. 11(12)
National Health Laboratory Service (ZA), Centers for Disease Control and Prevention (US), Association of Public Health Laboratories (US), Université Joseph Ki-Zerbo (BF), Ministry of Health (ZM), University of Ghana (GH), University of the Witwatersrand (ZA), University Teaching Hospital (ZM), University of Zambia (ZM), London School of Hygiene & Tropical Medicine (GB), Ethiopian Public Health Institute (ET), Centre Pasteur du Cameroun (CM), MRC Unit the Gambia (GM), Manhiça Health Research Centre (MZ), Hôpital Charles-Nicolle (TN), National Public Health Laboratory (NP), Zambia National Public Health Institute (ZM), Institut Pasteur de Côte d'Ivoire (CI), Ministry of Health (SC), Ghana Health Service (GH), Tunis El Manar University (TN), University of Pretoria (ZA), Makerere University (UG)
Association of Public Health Laboratories, London School of Hygiene and Tropical Medicine, Medical Research Charities Group, Centers for Disease Control and Prevention
Openalex Percentile: Top 66%
Vibrio bacteria research studies
DOIOpen Access PDFOpenAlex
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