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

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 A. Mwendera, Akuzike Kalizang’oma, Kondwani C. 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 L. Msefula, Nigel A. Cunliffe and Khuzwayo C. Jere ()
Additional contact information
Chrispin Chaguza: Yale University
Innocent Chibwe: Ministry of Health
David Chaima: Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences
Patrick Musicha: Wellcome Sanger Institute
Latif Ndeketa: University of Liverpool
Watipaso Kasambara: Ministry of Health
Chimwemwe Mhango: Malawi-Liverpool-Wellcome Research Programme
Upendo L. Mseka: Malawi-Liverpool-Wellcome Research Programme
Joseph Bitilinyu-Bangoh: Ministry of Health
Bernard Mvula: Ministry of Health
Wakisa Kipandula: Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences
Patrick Bonongwe: Ministry of Health, Balaka District Hospital
Richard J. Munthali: University of British Columbia
Selemani Ngwira: Ministry of Health
Chikondi A. Mwendera: University of Liverpool
Akuzike Kalizang’oma: University College London
Kondwani C. Jambo: Malawi-Liverpool-Wellcome Research Programme
Dzinkambani Kambalame: Ministry of Health
Arox W. Kamng’ona: Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences
A. Duncan Steele: Sefako Makgatho Health Sciences University
Annie Chauma-Mwale: Ministry of Health
Daniel Hungerford: University of Liverpool
Matthew Kagoli: Ministry of Health
Martin M. Nyaga: University of the Free State
Queen Dube: Malawi Ministry of Health
Neil French: University of Liverpool
Chisomo L. Msefula: Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences
Nigel A. Cunliffe: University of Liverpool
Khuzwayo C. Jere: University of Liverpool

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-50484-w

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