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

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Abstract
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, Pathogenwatch 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.
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