Nature Communications (Jul 2024)
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,
- Khuzwayo C. Jere
Affiliations
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University
- Innocent Chibwe
- Public Health Institute of Malawi, Ministry of Health
- David Chaima
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences
- Patrick Musicha
- Parasites and Microbes Programme, Wellcome Sanger Institute
- Latif Ndeketa
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- Watipaso Kasambara
- Public Health Institute of Malawi, Ministry of Health
- Chimwemwe Mhango
- Malawi-Liverpool-Wellcome Research Programme
- Upendo L. Mseka
- Malawi-Liverpool-Wellcome Research Programme
- Joseph Bitilinyu-Bangoh
- Public Health Institute of Malawi, Ministry of Health
- Bernard Mvula
- Public Health Institute of Malawi, 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
- Department of Psychiatry, University of British Columbia
- Selemani Ngwira
- Public Health Institute of Malawi, Ministry of Health
- Chikondi A. Mwendera
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- Akuzike Kalizang’oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London
- Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Research Programme
- Dzinkambani Kambalame
- Public Health Institute of Malawi, 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
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University
- Annie Chauma-Mwale
- Public Health Institute of Malawi, Ministry of Health
- Daniel Hungerford
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- Matthew Kagoli
- Public Health Institute of Malawi, Ministry of Health
- Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State
- Queen Dube
- Malawi Ministry of Health
- Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- Chisomo L. Msefula
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences
- Nigel A. Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- Khuzwayo C. Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
- DOI
- https://doi.org/10.1038/s41467-024-50484-w
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 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.
