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

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 SteeleAnnie Chauma-Mwale, Daniel Hungerford, Matthew Kagoli, Martin M. Nyaga, Queen Dube, Neil French, Chisomo L. Msefula, Nigel A. Cunliffe, Khuzwayo C. Jere^*

^*Corresponding author for this work

Virological Pathology

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	6291
Journal	Nature Communications
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-50484-w
Publication status	Published - Dec 2024

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Chaguza, C., Chibwe, I., Chaima, D., Musicha, P., Ndeketa, L., Kasambara, W., Mhango, C., Mseka, U. L., Bitilinyu-Bangoh, J., Mvula, B., Kipandula, W., Bonongwe, P., Munthali, R. J., Ngwira, S., Mwendera, C. A., Kalizang’oma, A., Jambo, K. C., Kambalame, D., Kamng’ona, A. W., ... Jere, K. C. (2024). Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi. Nature Communications, 15(1), Article 6291. https://doi.org/10.1038/s41467-024-50484-w

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title = "Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi",

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.",

author = "Chrispin Chaguza and Innocent Chibwe and David Chaima and Patrick Musicha and Latif Ndeketa and Watipaso Kasambara and Chimwemwe Mhango and Mseka, {Upendo L.} and Joseph Bitilinyu-Bangoh and Bernard Mvula and Wakisa Kipandula and Patrick Bonongwe and Munthali, {Richard J.} and Selemani Ngwira and Mwendera, {Chikondi A.} and Akuzike Kalizang{\textquoteright}oma and Jambo, {Kondwani C.} and Dzinkambani Kambalame and Kamng{\textquoteright}ona, {Arox W.} and Steele, {A. Duncan} and Annie Chauma-Mwale and Daniel Hungerford and Matthew Kagoli and Nyaga, {Martin M.} and Queen Dube and Neil French and Msefula, {Chisomo L.} and Cunliffe, {Nigel A.} and Jere, {Khuzwayo C.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = dec,

doi = "10.1038/s41467-024-50484-w",

language = "English",

volume = "15",

journal = "Nature Communications",

issn = "2041-1723",

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Chaguza, C, Chibwe, I, Chaima, D, Musicha, P, Ndeketa, L, Kasambara, W, Mhango, C, Mseka, UL, Bitilinyu-Bangoh, J, Mvula, B, Kipandula, W, Bonongwe, P, Munthali, RJ, Ngwira, S, Mwendera, CA, Kalizang’oma, A, Jambo, KC, Kambalame, D, Kamng’ona, AW, Steele, AD, Chauma-Mwale, A, Hungerford, D, Kagoli, M, Nyaga, MM, Dube, Q, French, N, Msefula, CL, Cunliffe, NA & Jere, KC 2024, 'Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi', Nature Communications, vol. 15, no. 1, 6291. https://doi.org/10.1038/s41467-024-50484-w

TY - JOUR

T1 - Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi

AU - Chaguza, Chrispin

AU - Chibwe, Innocent

AU - Chaima, David

AU - Musicha, Patrick

AU - Ndeketa, Latif

AU - Kasambara, Watipaso

AU - Mhango, Chimwemwe

AU - Mseka, Upendo L.

AU - Bitilinyu-Bangoh, Joseph

AU - Mvula, Bernard

AU - Kipandula, Wakisa

AU - Bonongwe, Patrick

AU - Munthali, Richard J.

AU - Ngwira, Selemani

AU - Mwendera, Chikondi A.

AU - Kalizang’oma, Akuzike

AU - Jambo, Kondwani C.

AU - Kambalame, Dzinkambani

AU - Kamng’ona, Arox W.

AU - Steele, A. Duncan

AU - Chauma-Mwale, Annie

AU - Hungerford, Daniel

AU - Kagoli, Matthew

AU - Nyaga, Martin M.

AU - Dube, Queen

AU - French, Neil

AU - Msefula, Chisomo L.

AU - Cunliffe, Nigel A.

AU - Jere, Khuzwayo C.

PY - 2024/12

Y1 - 2024/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85199764271&partnerID=8YFLogxK

U2 - 10.1038/s41467-024-50484-w

DO - 10.1038/s41467-024-50484-w

M3 - Article

C2 - 39060226

AN - SCOPUS:85199764271

SN - 2041-1723

VL - 15

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 6291

ER -

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

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