Whole genome sequencing and transmission analysis of Vibrio cholerae isolates from Eastern and Southern Africa: a genomic epidemiology study
Abstract
BACKGROUND: Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region, so this study uses genomic epidemiology to identify disease transmission patterns in Southern and Eastern Africa. METHODS: To better characterize regional transmission, we performed whole genome sequencing on 142 Vibrio cholerae samples of different sample types, each collected between 2007-2019 from five different countries in Southern and Eastern Africa. We obtained 114 high quality V. cholerae genomes that we combined with 1385 previously published genomes to conduct phylogenetic and other analyses used to better understand cholera transmission and circulation in Southeastern Africa. FINDINGS: We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. INTERPRETATIONS: Our findings suggest that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.
