Use of whole-genome sequencing of Vibrio cholerae O1 isolates to assist the epidemiological investigation of a cholera outbreak in Zimbabwe, 2018

We used whole-genome sequencing (WGS) to investigate Vibrio cholerae O1 isolates associated with a cholera outbreak in Zimbabwe which started around September 2018. Identification of isolates was confirmed as toxin-producing V. cholerae O1 Ogawa. Isolates showed multidrug resistance including the presence of extended-spectrum ß-lactamase (ESBL) activity. Analysis of WGS data showed the isolates were all highly related and showed the presence of several antibiotic resistance genes including the ESBL gene CTX-M15. WGS data of isolates was compared against a global collection of cholera isolates, with phylogenetic analysis showing that the Zimbabwe isolates belonged to the T13 sublineage, the most recent cholera lineage introduced into Africa.