Vibrio cholerae circulating throughout a mass vaccination campaign in the Forcibly Displaced Myanmar National population in Cox’s Bazar, Bangladesh

Abstract Over the last decade, the influx of Forcibly Displaced Myanmar Nationals (FDMNs) into Bangladesh has increased the population of Cox’s Bazar. Due to the already high population density coupled with poor living conditions, FDMNs and the host population of Bangladeshi Nationals (BGDNs) were at heightened risk of diarrhoeal disease outbreaks. Due to this, a nationwide sentinel surveillance programme was established, which revealed that there were seasonal localised sporadic cholera outbreaks in Cox’s Bazar. In this study, we aimed to infer the epidemic risk of the Vibrio cholerae strains circulating in the FDMN and BGDN populations, by determining if isolates linked to the current cholera pandemic were responsible for these outbreaks. Further, to better understand the dynamics of cholera before and during the mass oral cholera vaccination campaign conducted in Cox’s Bazar – the largest in the last decades – we also wanted to understand the links between these circulating strains and the current radiation of lineages causing disease in Haiti and Yemen – places in which reactive vaccination campaigns were conducted in response to outbreaks following humanitarian crises. To do this, we sequenced 223 V. cholerae isolates obtained from stool collected from ten intra-district surveillance sites in Cox’s Bazar, sampling both the FDMN and BGDN subpopulations over a period spanning the pre-and post-vaccination campaign (2014–2019). Phylogenetic analysis of these genomes showed that all isolates belonged to the epidemic “7PET” lineage – responsible for the current cholera pandemic – branching alongside V. cholerae that were circulating in Dhaka and Kolkata between 2014 and 2018. Two distinct sublineages of V. cholerae were present in Cox’s Bazar during the study period; one lineage (PG 1.3) that had radiated globally, and another lineage (PG 1.5) that was restricted to Asia and the Middle East. PG 1.3 was associated with a shorter duration of diarrhoea and lower relative risk of rice watery stool compared to PG 1.5. Given the nature and diversity of the V. cholerae isolated from the BGDN and FDMN subpopulations in Cox’s Bazar, without a vaccine intervention, the risk of local or widespread epidemics or even a pandemic was very high.