Multicountry genomic analysis underscores regional cholera spread in Africa

TL;DR

A large genomic study of cholera bacteria in Africa reveals regional spread patterns and highlights the need for coordinated surveillance.

Contribution

The study presents the largest locally generated V. cholerae genomic dataset in Africa, enabling insights into regional transmission dynamics.

Findings

The AFR15 lineage is rapidly spreading across Southern Africa, causing large outbreaks.

Transmission dynamics differ between West and East Africa, but cross-border spread is common.

Antimicrobial resistance genotypes have not significantly changed across lineages.

Abstract

Cholera remains a significant public health burden in many countries in sub-Saharan Africa, though the exact mechanisms of bacterial emergence and spread remain largely undefined. We generated genomic data from 763 Vibrio cholerae O1 isolates predominantly collected between 2019-2024 to create the largest dataset of V. cholerae genomes sequenced locally in Africa. This dataset enabled us to interrogate recent patterns of spread, including the rapid circulation of the AFR15 lineage associated with unusually large outbreaks in Southern Africa. We provide evidence for the movement of the AFR15 lineage into new African Union Member States and confirm previously observed differences in V. cholerae transmission dynamics in West versus East Africa, though cross-border transmission is prevalent on both sides of the continent. Despite observed differences, evolutionary processes are similar across lineages and we find no evidence for significant changes in antimicrobial resistance genotypes. Overall, our findings emphasize the importance of regionally coordinated cross-border surveillance and interventions, while also demonstrating the critical role of locally generated genomic data in understanding the spread of cholera in Africa.

Cholera remains a significant public health burden in sub-Saharan Africa, but the mechanisms of continental and regional spread remain undefined. Here, the authors investigate recent patterns of spread using Vibrio cholerae genomic surveillance data collected by a consortium of seven African Union member states from 2019-2024.

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