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

doi:10.1038/s41467-024-50484-w

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

Nat Commun. 2024 Jul 26;15(1):6291. doi: 10.1038/s41467-024-50484-w.

Authors

Chrispin Chaguza^#^{1

2

3

4

5}, Innocent Chibwe^#⁶, David Chaima⁷, Patrick Musicha^{8

9}, Latif Ndeketa^{10

9}, Watipaso Kasambara⁶, Chimwemwe Mhango⁹, Upendo L Mseka⁹, Joseph Bitilinyu-Bangoh⁶, Bernard Mvula⁶, Wakisa Kipandula¹¹, Patrick Bonongwe¹², Richard J Munthali¹³, Selemani Ngwira⁶, Chikondi A Mwendera¹⁰, Akuzike Kalizang'oma^{14

9}, Kondwani C Jambo^{9

15}, Dzinkambani Kambalame⁶, Arox W Kamng'ona¹⁶, A Duncan Steele¹⁷, Annie Chauma-Mwale⁶, Daniel Hungerford^{10

18}, Matthew Kagoli⁶, Martin M Nyaga¹⁹, Queen Dube²⁰, Neil French^{10

9}, Chisomo L Msefula⁷, Nigel A Cunliffe^{10

18

21}, Khuzwayo C Jere^{22

23

24

25

26}

Affiliations

¹ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA. chrispin.chaguza@yale.edu.
² Yale Institute for Global Health, Yale University, New Haven, CT, USA. chrispin.chaguza@yale.edu.
³ Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. chrispin.chaguza@yale.edu.
⁴ NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK. chrispin.chaguza@yale.edu.
⁵ Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK. chrispin.chaguza@yale.edu.
⁶ Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi.
⁷ Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi.
⁸ Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
⁹ Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi.
¹⁰ Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
¹¹ Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi.
¹² Ministry of Health, Balaka District Hospital, Balaka, Machinga, Malawi.
¹³ Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada.
¹⁴ NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK.
¹⁵ Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.
¹⁶ Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi.
¹⁷ Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, 0204, Pretoria, South Africa.
¹⁸ NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
¹⁹ Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, 9300, South Africa.
²⁰ Malawi Ministry of Health, Lilongwe, Malawi.
²¹ NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
²² Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK. Khuzwayo.Jere@liverpool.ac.uk.
²³ Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi. Khuzwayo.Jere@liverpool.ac.uk.
²⁴ Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi. Khuzwayo.Jere@liverpool.ac.uk.
²⁵ NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK. Khuzwayo.Jere@liverpool.ac.uk.
²⁶ NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK. Khuzwayo.Jere@liverpool.ac.uk.

^# Contributed equally.

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.

MeSH terms

Cholera* / epidemiology
Cholera* / microbiology
Disease Outbreaks*
Genome, Bacterial / genetics
Genomics
Genotype
Humans
Malawi / epidemiology
Phylogeny*
Prophages / genetics
Serogroup
Vibrio cholerae* / classification
Vibrio cholerae* / genetics