The future of cholera genomics through the lens of clinical, public health, and research practitioners in Africa.

Cholera remains a persistent public health threat, complicating efforts to track transmission across borders and undermining control measures. Surveillance systems often remain fragmented and reactive, and many aspects of Vibrio cholerae evolution continue to be challenging, restricting the development of effective, data-driven interventions. Although genomics is increasingly transforming our understanding of cholera by revealing new insights into pathogen biology, transmission dynamics, and evolution, its routine integration into public health practice remains low. In this Personal View, we present the perspectives of those working at the frontline of cholera control in Africa (clinicians, public health practitioners, and researchers) who are rarely heard from, yet who actively shape strategies, navigate technological hurdles, and address system-level challenges to incorporate genomics into routine practice. These insights emerged through the Vibriowatch and Cholera Genomics Course, funded by the Gates Foundation and hosted by the Centre for Infectious Disease Research in Zambia in Lusaka, Zambia, on Feb 9-14, 2025. The course convened 36 participants from 18 African countries to exchange practical experience on how genomic data can be translated into public health decision making. A key outcome of this convening was the establishment of the Community of Practice for Cholera Genomics, which has since evolved into a sustained and structured platform for collaboration, peer learning, and collective problem solving, bringing together practitioners working across cholera surveillance, genomics, and response systems, ensuring that genomic approaches are grounded in local realities and appropriately embedded within cholera-control approaches. The thematic workstreams of the Community of Practice for Cholera Genomics meet regularly to deliver defined technical priorities, with seminar sessions bringing the whole community together to review progress, align priorities, and engage external experts. Accountability is embedded through shared ownership of workplans within each thematic team, with members jointly responsible for tracking progress. Grounded in real-world experience, in this Personal View, we offer timely, policy-relevant recommendations to strengthen genomic approaches, centring African leadership, equity, and long-term sustainability.