Comprehensive genomic characterization and public health implications of multidrug-resistant Escherichia coli from poultry in Noakhali, Bangladesh

Poultry chickens and their farming environments serve as reservoirs for multi-drug resistant (MDR) pathogenic Escherichia coli (E. coli) that can spread to other species, including humans. In response to this, the study was conducted to assess the antibiotic resistance profile, virulence capabilities, and zoonotic potential of isolates obtained from poultry chickens in Noakhali, Bangladesh. E. coli isolates were identified through biochemical and molecular methods, including 16S rRNA sequencing. After antibiotic susceptibility testing and multiple antibiotic resistance index (MARI) profiling, two strains out of twenty-four underwent whole-genome Illumina sequencing. For the genetic characterization of these two isolates, genome annotation, serotyping, multilocus sequence typing (MLST), fimbrial typing, plasmid profiling, identification of resistance and virulence genes, detection of mobile genetic elements (MGEs), pan-genome analysis, and phylogenetic comparison were performed. The two sequenced strains (one lactose-negative and the other lactose-positive) exhibited resistance to nearly all of the 17 tested antibiotics, with a MAR index of 0.82. Both strains contained ~ 58 AMR genes, including significant genes like blaTEM-1B, qnrS1, aac(3)IId, tet(A), dfrA1, and sul3. Each strain carried six plasmids, including a novel one, along with multiple metal resistance genes (MRGs) that conferred tolerance to arsenic, tellurium, copper, and silver, indicating their ability to survive in metal-rich environments. Pathogenicity prediction suggested a 91.4% probability of causing human infection. Virulence genes related to adhesion, biofilm formation, and immune evasion were identified. Comparative genomics showed similarity to clinical strains. Although zoonotic transmission was not directly evaluated, genomic similarity and the presence of human-associated virulence and AMR genes suggest a potential public health risk from poultry strains. These findings highlight the zoonotic threat posed by MDR bacteria in poultry farms. Regular monitoring of antibiotic use in poultry, along with genomic surveillance of MDR isolates, is crucial to mitigate this emerging public health concern.