Author:
Chaguza Chrispin,Chibwe Innocent,Chaima David,Musicha Patrick,Ndeketa Latif,Kasambara Watipaso,Mhango Chimwemwe,Mseka Upendo L.,Bitilinyu-Bangoh Joseph,Mvula Bernard,Kipandula Wakisa,Bonongwe Patrick,Munthali Richard J.,Ngwira Selemani,Mwendera Chikondi A.,Kalizang’oma Akuzike,Jambo Kondwani C.,Kambalame Dzinkambani,Kamng’ona Arox W.,Steele A Duncan,Chauma-Mwale Annie,Hungerford Daniel,Kagoli Matthew,Nyaga Martin M.,Dube Queen,French Neil,Msefula Chisomo L.,Cunliffe Nigel A.,Jere Khuzwayo C.
Abstract
AbstractMalawi is experiencing its deadliestVibrio cholerae(Vc) outbreak following devastating cyclones, with >58,000 cases and >1,700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022– 2023Vcoutbreak isolates. Our results demonstrate the predominance of ST69 seventh cholera pandemic El Tor (7PET) strains expressing O1 Ogawa (∼80%) serotype followed by Inaba (∼16%) and typical non-outbreak-associated non-O1/non-ST69 serotypes (∼4%). Phylogenetic reconstruction of the current and historicalVcisolates from Malawi, together with globalVcisolates, suggested the Malawi outbreak strains originated from Asia. The unique antimicrobial resistance and virulence profiles of the 2022–2023 isolates, notably the acquisition of ICEGEN/ICEVchHai1/ICEVchind5 SXT/R391-like integrative conjugative elements and a CTXφ prophage, which causedctxB3toctxB7genotype shift, support the importation hypothesis. These data suggest that the recent importation ofctxB7O1 strains, coupled with climatic changes, may explain the magnitude of the cholera outbreak in Malawi.
Publisher
Cold Spring Harbor Laboratory