Vibrio cholerae lineage and pangenome diversity vary geographically across Bangladesh over 1 year

Cholera is an acute diarrhoeal disease caused by Vibrio cholerae . It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae , namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae , we long-read sequenced 273 V . cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three…