Multicountry genomic analysis underscores regional cholera spread in Africa
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.
Authors
- Kunda Musonda
- Blaise Akenji
- Gerald Mboowa (ORCID: https://orcid.org/0000-0001-8445-9414)
- Charles Nnanna Chukwu (ORCID: https://orcid.org/0000-0002-7271-4606)
- Anaïs Broban (ORCID: https://orcid.org/0000-0003-0275-161X)
- Nalia Ismael
- Alisen Ayitewala (ORCID: https://orcid.org/0000-0001-6173-4006)
- Dorcas Wanjohi
- Mathews Kagoli
- Jucunú Johane Elias Chitio
- Olajumoke Babatunde
- Francis Ongole
- Georges Alain Etoundi Mballa
- René Ghislain Essomba (ORCID: https://orcid.org/0000-0003-0435-6680)
- Roma Chilengi
- Michael Oladotun Popoola
- Valentina Josiane Ngo Bitoungui (ORCID: https://orcid.org/0000-0002-2845-8879)
- Guyguy Kamwiziku (ORCID: https://orcid.org/0000-0001-6770-3999)
- Mpanga Kasonde (ORCID: https://orcid.org/0009-0001-4316-7164)
- Collins Kipngetich Tanui (ORCID: https://orcid.org/0000-0002-0421-1708)
- Isaac Ssewanyana (ORCID: https://orcid.org/0000-0001-8605-2001)
- Alex Mwanyongo (ORCID: https://orcid.org/0009-0001-2356-0436)
- Osvaldo Laurindo
- Joseph Bitilinyu-Bangoh
- Placide Okitayemba Welo
- Nathaniel Lucero Matteson
- Imelda Carlos Zulfa Miambo
- Joseph Mutale
- Allan Muruta Niyonzima
- Sofião Manjor Sitoe
- Mtisunge Yelewa
- Lucius Ziba
- Hamsatou Hadja
- Espoir Bwenge Malembaka
- Andrew S Azman
- Jide Idris
- Grace Najjuka
- José Paulo Maurício Langa
- Amanda K. Debes
- Daniel Mukadi-Bamuleka
- Doreen Mainza Shempela
- Mirriam Ethel Nyenje
- Susan Nabadda
- Otridah Kapona
- Shirlee Wohl
- Placide Kingebeni Mbala
- Christiane Medi Sike
- Adrienne Aziza Amuri
- David A. Sack
- Yenew Kebede Tebeje
Institutions
- Brigham and Women's Hospital (US)
- Ministry of Public Health (CD)
- Université de Yaoundé I (CM)
- Johns Hopkins University (US)
- University of Douala (CM)
- Université de Dschang (CM)
- University of Kinshasa (CD)
- Public Health Institute of Malawi (MW)
- Ministry of Health (UG)
- Africa Centres for Disease Control and Prevention (ET)
- University Hospital of Geneva (CH)
- Université Catholique de Bukavu (CD)
- Zambia National Public Health Institute (ZM)
- Instituto Nacional de Saúde (MZ)
- National Institute of Biomedical Research (CD)
- Ministry of Public Health (CM)
- Yaoundé General Hospital (CM)
- Nigeria Centre for Disease Control (NG)
- Churches Health Assoication Of Zambia (ZM)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-02-09
- DOI
- https://doi.org/10.1038/s41467-026-68642-7
- Primary Topic
- Vibrio bacteria research studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00