Regional sequencing collaboration reveals persistence of the T12 <i>Vibrio cholerae</i> O1 lineage in West Africa.

Abstract

Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of <i>Vibrio cholerae</i> in the areas most affected may reveal transmission patterns important for cholera control. During a regional sequencing workshop in Nigeria, we sequenced 46 recent <i>V. cholerae</i> isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the <i>V. cholerae</i> bacterium circulating in these three countries. From these isolates, we generated 44 whole <i>Vibrio cholerae</i> O1 sequences and analyzed them in the context of 1280 published <i>V. cholerae</i> O1 genomes. All sequences belonged to the T12 <i>V. cholerae</i> seventh pandemic lineage. Phylogenetic analysis of newly generated and previously published <i>V. cholerae</i> genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts. Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.