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

Chaguza, Chrispin, Chibwe, Innocent, Chaima, David, Musicha, Patrick, Ndeketa, Latif, Kasambara, Watipaso, Mhango, Chimwemwe, Mseka, Upendo L., Bitilinyu-Bangoh, Joseph, Mvula, Bernard, Kipandula, Wakisa, Bonongwe, Patrick, Munthali, Richard J., Ngwira, Selemani, Mwendera, Chikondi A., Kalizang’oma, Akuzike, Jambo, Kondwani ORCID: https://orcid.org/0000-0002-3195-2210, Kambalame, Dzinkambani, Kamng’ona, Arox W., Steele, A. Duncan, Chauma-Mwale, Annie, Hungerford, Daniel, Kagoli, Matthew, Nyaga, Martin M., Dube, Queen, French, Neil, Msefula, Chisomo L., Cunliffe, Nigel A. and Jere, Khuzwayo C. (2024) 'Genomic insights into the 2022–2023 Vibrio cholerae outbreak in Malawi'. Nature Communications, Vol 15, Issue 1, e6291.

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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 ICEGEN/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.

Item Type:	Article
Subjects:	QU Biochemistry > Genetics > QU 460 Genomics. Proteomics WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 262 Cholera
Faculty: Department:	Clinical Sciences & International Health > Clinical Sciences Department
Digital Object Identifer (DOI):	https://doi.org/10.1038/s41467-024-50484-w
SWORD Depositor:	JISC Pubrouter
Depositing User:	JISC Pubrouter
Date Deposited:	07 Aug 2024 14:26
Last Modified:	07 Aug 2024 14:26
URI:	https://archive.lstmed.ac.uk/id/eprint/25012

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