Genomic evolution and climate related drivers of cholera surges in Dhaka Bangladesh between 1996 and 2024

BACKGROUND: Cholera, a climate-associated diarrhea occurs endemically in Dhaka city, Bangladesh, often turning into large epidemics. In 2022, a massive outbreak struck Dhaka city, resulting in a very high number of cholera cases. Although extensive studies have focused on climate and cholera, including genomic evolution of the causative agent, Vibrio cholerae, their association with the case surges remains poorly understood. METHODS: We analyzed cholera data between 1996 and 2024 from the Diarrheal Disease Surveillance System (DDSS) of icddr,b, and also conducted a follow up genomic analysis of V. cholerae O1 El Tor by including newly sequenced and archived sequence data. Integrated analyses of genomic, climatic, and cholera surveillance data investigated the role of different factors on yearly case surges in Dhaka city. RESULTS: Analysis of DDSS data shows temporal changes of cholera cases across Dhaka city, and genomic analysis shows continuous evolution of V. cholerae. Association analysis of cholera case data against the genomic data reveals that co-circulation of multiple lineages/sub lineages of V. cholerae, as well as their flux between the years with newly introduced or re-emerged lineages, are significantly (p-value <= 0.05) associated with the yearly cholera cases in Dhaka city. Integrated statistical association analysis of cholera cases with the climate and genomic evolutionary factors also reveals a significant association. CONCLUSIONS: This study associates climate factors and the V. cholerae genome evolutionary events with interannual variation, such as high and low cholera, including surges of the disease in Dhaka city.