Genomic insights into a diarrheal outbreak in Bangladesh reveal novel ETEC lineages and expansion of CS23 colonization factor

Enterotoxigenic Escherichia coli (ETEC), a leading cause of diarrhea, is defined by heat-stable (ST) and/or heat-labile (LT) toxins and associated colonization factors (CFs). However, there is still a knowledge gap in understanding ETEC's evolution, particularly in endemic regions like Bangladesh. This study investigates the genomic attributes contributing to the rise of ETEC-associated diarrhea in Bangladesh during 2022–2023. Whole genome sequencing of 325 ETEC isolates (2022–2023), compared with historical strains (1980–2021), revealed significant evolutionary changes. Our findings showed a significant shift in ETEC toxin from LT to ST over the period 2013–2023. The most frequent virulence profile during this period was CFA/I + CS21 compared with previous years (1980–2021). The emergence of CS23-positive ETEC was reported for the first time in Bangladesh, which was considered a less common CF in previous studies. Notably, we report the four novel lineages “L26–L29” in this study through phylogenetic analysis, partly encompassing emergent CS23-positive ETEC strains. Additionally, the high prevalence of multi-drug-resistant ETEC strains and the presence of ESBL-CTX-M-resistant gene during 2022–2023 are a matter of great concern, underscoring the need for preventive measures. The switch of distinct toxin and CF combinations, the rapid emergence of CS23, ESBL-CTX-M resistance, and novel lineages may be the reason behind the increased number of ETEC diarrheal cases between 2022 and 2023. These findings highlight the rapid ETEC evolution that underscores the necessity of continued genomic surveillance to track ongoing changes. IMPORTANCE This study expands on previous evidence, demonstrating a remarkable genomic diversity in ETEC strains from 2022 to 2023, particularly in virulence factors and AMR genes. The combined findings from these studies will be important for mitigating future diarrheal outbreaks by informing preventive measures, including future vaccine targets, and implementing antibiotic stewardship programs against ETEC infection. Importantly, this research underscores the necessity of continued genomic surveillance to track ongoing changes in ETEC. Such monitoring is essential for understanding the pathogen's evolving population structure, transmission dynamics, and resistance mechanisms.