Genomic Insights and Antimicrobial Resistance Profiling of Diarrheagenic Escherichia coli in Bhutan: A Retrospective Whole-Genome Sequencing Study

Diarrheal disease remains a significant public health concern in Bhutan; however, the genomic epidemiology of the circulating diarrhoeagenic Escherichia coli (DEC) strain remains poorly understood. This study characterized the genomic diversity, antimicrobial resistance (AMR), and virulence determinants of DEC isolates using whole-genome sequencing (WGS). DEC isolates recovered from stool samples and collected through Bhutan’s National Diarrheal Disease Surveillance sentinel hospitals during 2023 were identified by a multiplex polymerase chain reaction, tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion method, and sequenced on the Illumina MiSeq platform. Genomes were analyzed using the Bohra pipeline to determine pathotypes, phylogeny, multilocus sequence types, serotypes, virulence factors, and AMR genes. Of the 29 DEC isolates, 27 were confirmed by WGS and enteropathogenic E. coli (37.0%) and enteroaggregative E. coli (33.3%) were the predominant pathotypes. Isolates exhibited extensive genetic diversity, representing phylogroups A and B1 and 22 serotypes. Phenotypic resistance to β-lactams was common, with 25.9% of isolates carrying blaCTX-M-15. Virulence profiling identified diverse adhesins, toxins, iron acquisition systems, and type III secretion system components. DEC isolates in Bhutan comprise a genetically diverse population with a concerning convergence of virulence determinants and multidrug resistance. The findings underscore the strengthening of sustained genomic surveillance to monitor AMR and genomic epidemiology of bacterial pathogens.