Whole genome sequencing (WGS) was carried out on 78 V. cholerae clinical isolates characterized phenotypically and associated with cholera in eastern provinces of the Democratic Republic of Congo between 2014 and 2017

Whole genome sequencing (WGS) was carried out on 78 V. cholerae clinical isolates characterized phenotypically and associated with cholera in eastern provinces of the Democratic Republic of Congo between 2014 and 2017. 73/78 isolates were O1 biotype El Tor and harbored the CTX-3 prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T) 10 in East Africa. These isolates clustered in two sub-clades corresponding to two Multiple Locus Sequence Types (MLST) profiles: ST69 and the first-time reported ST515 displaying a higher genetic diversity compared to ST69. The two sub-clades had a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin whereas ST515 isolates were disseminated along the Albertine Rift. 5/78 isolates were non-O1/non-O139 and did not harbor any CTX prophage.