Vibrio cholerae O1 Genome sequencing and assembly. Vibrio cholerae O1

Seventy-two Vibrio cholerae isolates from outbreaks in 2009/2010, 2016, and 2017/2018 in Zambia were characterized using multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS). Eight MLVA genotypes clustered into three MLVA clonal complexes (CCs). Results from WGS were consistent with the MLVA, each CC was a distinct genetic lineage and had nearest neighbors from other East African countries. In Lusaka, isolates from the same outbreak were more closely related to themselves and isolates from other countries than to isolates from other outbreaks in other years. Our observations are consistent with three separate transmission events of cholera into Lusaka, Zambia.