Gerald Mboowa, Nathaniel Lucero Matteson, Collins Kipngetich Tanui, Mpanga Kasonde, Guyguy Kamwiziku, Olusola Anuoluwapo Akanbi, Jucunú Johane Elias Chitio, Mathews Kagoli, René Ghislain Essomba, Alisen Ayitewala, Isaac Ssewanyana, Valentina Josiane Ngo Bitoungui, Adrienne Aziza Amuri, Andrew S Azman, Olajumoke Babatunde, Blaise Akenji, Anaïs Broban, Espoir Bwenge Malembaka, Francis Ongole, Chimaobi Emmanuel Chukwu, Nália Ismael, Otridah Kapona, Osvaldo Laurindo, Placide Kingebeni Mbala, Georges Alain Etoundi Mballa, Imelda Carlos Zulfa Miambo, Alex Mwanyongo, Grace Najjuka, Joseph Mutale, Kunda Musonda, Allan Muruta Niyonzima, Mirriam Ethel Nyenje, Michael Oladotun Popoola, Doreen Mainza Shempela, Christiane Medi Sike, Sofião Manjor Sitoe, Dorcas Wanjohi, Placide Okitayemba Welo, Mtisunge Yelewa, Sebastian Yennan, Lucius Ziba, Valentina Josiane Ngo Bitoungui, Jide Idris, Joseph Bitilinyu-Bangoh, Roma Chilengi, Hamsatou Hadja, Jide Idris, José Paulo Maurício Langa, Daniel Mukadi-Bamuleka, Susan Nabadda, Amanda K. Debes, David A. Sack, Yenew Kebede Tebeje, Shirlee Wohl, Sofonias Kifle Tessema
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.