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Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi

Article scientifique 2024 Anglais

Résumé

Abstract Malawi experienced its deadliest Vibrio cholerae ( Vc ) outbreak following devastating cyclones, with >58,000 cases and >1700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022–2023 Vc outbreak isolates. Our results demonstrate the predominance of ST69 clone, also known as the seventh cholera pandemic El Tor (7PET) lineage, expressing O1 Ogawa (~ 80%) serotype followed by Inaba (~ 16%) and sporadic non-O1/non-7PET serogroups (~ 4%). Phylogenetic reconstruction revealed that the Malawi outbreak strains correspond to a recent importation from Asia into Africa (sublineage AFR15). These isolates harboured known antimicrobial resistance and virulence elements, notably the ICE GEN /ICEVchHai1/ICEVchind5 SXT/R391-like integrative conjugative elements and a CTXφ prophage with the ctxB7 genotype compared to historical Malawian Vc isolates. These data suggest that the devastating cyclones coupled with the recent importation of 7PET serogroup O1 strains, may explain the magnitude of the 2022–2023 cholera outbreak in Malawi.

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Chaguza, C., Chibwe, I., Chaima, D., Musicha, P., Ndeketa, L., Kasambara, W., Mhango, C., Mseka, U., Bitilinyu-Bangoh, J., Mvula, B., Kipandula, W., Bonongwe, P., Munthali, R., Ngwira, S., Mwendera, C., Kalizang’oma, A., Jambo, K., Kambalame, D., Kamng’ona, A., Steele, A., Chauma-Mwale, A., Hungerford, D., Kagoli, M., Nyaga, M., Dube, Q., French, N., Msefula, C., Cunliffe, N., Jere, K. (2024). Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi. https://doi.org/10.1038/s41467-024-50484-w

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Auteur(s)

Chrispin Chaguza Innocent Chibwe David Chaima Patrick Musicha Latif Ndeketa Watipaso Kasambara Chimwemwe Mhango Upendo L. Mseka Joseph Bitilinyu-Bangoh Bernard Mvula Wakisa Kipandula Patrick Bonongwe Richard J. Munthali Selemani Ngwira Chikondi Mwendera Akuzike Kalizang’oma Kondwani Jambo Dzinkambani Kambalame Arox W. Kamng’ona A. Duncan Steele Annie Chauma-Mwale Daniel Hungerford Matthew Kagoli Martin M. Nyaga Queen Dube Neil French Chisomo Msefula Nigel A. Cunliffe Khuzwayo C. Jere

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