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

Author

Listed:
  • Chrispin Chaguza

    (Yale University
    Yale University
    University of Liverpool
    University College London)

  • 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
    Malawi-Liverpool-Wellcome Research Programme)

  • Latif Ndeketa

    (University of Liverpool
    Malawi-Liverpool-Wellcome Research Programme)

  • 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
    Malawi-Liverpool-Wellcome Research Programme)

  • Kondwani C. Jambo

    (Malawi-Liverpool-Wellcome Research Programme
    Department of Clinical Sciences, Liverpool School of Tropical Medicine)

  • 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
    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
    Malawi-Liverpool-Wellcome Research Programme)

  • Chisomo L. Msefula

    (Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences)

  • Nigel A. Cunliffe

    (University of Liverpool
    University of Liverpool
    University of Liverpool)

  • Khuzwayo C. Jere

    (University of Liverpool
    Malawi-Liverpool-Wellcome Research Programme
    Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences
    University of Liverpool)

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.

Suggested Citation

  • Chrispin Chaguza & Innocent Chibwe & David Chaima & Patrick Musicha & Latif Ndeketa & Watipaso Kasambara & Chimwemwe Mhango & Upendo L. Mseka & Joseph Bitilinyu-Bangoh & Bernard Mvula & Wakisa Kipandu, 2024. "Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50484-w
    DOI: 10.1038/s41467-024-50484-w
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    References listed on IDEAS

    as
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