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Background Despite the advancement in our understanding of cholera and its etiological agent, V. cholerae, the prevention and treatment of the disease are often hindered due to rapid changes in drug response pattern, serotype, and the major genomic islands namely, the cholera toxin phage, and related genetic characteristics. In the present study, V. cholerae (n = 172) associated with endemic cholera in Dhaka during the years 2015–2021 were analyzed for major phenotypic and genetic characteristics, including drug resistance patterns. Results Results revealed that the V. cholerae strains belonged to serogroup O1 biotype El Tor carrying El Tor -specific genes rtxC, tcpA El Tor, and hlyA El Tor, but possessed classical-biotype cholera toxin. Serotypes of V. cholerae strains differed temporally in predominance with Inaba during 2015–2017, and again in 2020–2021, while Ogawa was the predominant serotype in 2018–2019. Also, ctxB1 was predominant in V. cholerae associated with cholera during 2015–2017, while ctxB7 was predominant in 2018, and in the subsequent years, as observed until 2021. V. cholerae strains differed in their antibiotic resistance pattern with a majority (97%) being multi-drug resistant (MDR) and belonging to eight sub-groups. Notably, one of these MDR strains was resistant to eleven of the eighteen antibiotics tested, with resistance to fourth-generation cephalosporin (cefepime), and aztreonam. This extreme drug resistant (XDR) strain carried resistance-related genes namely, extended-spectrum β-lactamases (ESBL), blaOXA-1 and blaPER-3. Conclusion The observed temporal switching of serotypes, as well as the ctxB genotype, and the emergence of MDR/XDR V. cholerae and their association with endemic cholera in Dhaka underscore the need for routine monitoring of the pathogen for proper patient management.

Bangladesh is currently experiencing one of the worst cholera outbreaks in its history. The icddr,b hospital has treated a record number of patients, more than 1400 per day and ca. 40,000 diarrheal cases from the end of March through April 20221. A recent genomic study showed temporal progression of two lineages, BD-1 and BD-2, with the former linked to the 7th pandemic wave-3 global clade and the latter predominant in endemic cholera in Dhaka during 2013 and 20172. Here, we present genomic attributes of V. cholerae O1 responsible for the 2022 Dhaka cholera epidemic and genome phylogeny of 960 7th pandemic El Tor strains from 88 countries. Results show the Dhaka cholera etiological agent clustered with the 7th pandemic El Tor wave-3 global clade, but comprises a new subclade, BD-1.2, for which the most recent common ancestor appears to be of the globally distributed sublineage predominantly associated with recent endemic cholera in India. Results also suggest BD-1.2 was present in Bangladesh since 2016. However, it was not until 2018 that strains of the subclade successfully established dominance over the BD-2 during an expansion of the wave-3 global clade. It is concluded that the recent shift in predominant lineage and the observed genetic changes including serotype switch in BD-1.2 from Ogawa to Inaba may explain the increasing number of infections and massive outbreak of cholera during 2022 in Bangladesh.