Genomic epidemiology of the cholera outbreak in Malawi 2022-2023

Abstract

Abstract Since early 2022, in the aftermath of two extreme weather events, Malawi experienced its largest ever cholera outbreak, with over 58,000 reported cases and 1,761 deaths as of May 2023. We generated 49 high-quality, near-complete Vibrio cholerae genomes in Malawi from isolates collected between December 2022 and March 2023 from all three regions of Malawi. Using phylogenetic methods with 2159 publicly available genomes, we present evidence suggesting that the Malawi outbreak strains originated from the Pakistan outbreak, the estimated most recent ancestor of this lineage, named T15, was during the Pakistan floods, and once introduced into Malawi was exacerbated by major floods between June and October 2022. The extreme weather events and humanitarian crises in Malawi provided the environment for the spread of Vibrio cholerae, and the subsequent movement of large numbers of people may have facilitated its spread to susceptible populations in areas relatively unaffected by cholera for over a decade.