Comparative genomic analysis of antimicrobial resistance and virulence in Escherichia coli isolated from pigeons and chickens in live poultry markets, Guiyang, China.

The transmission risk of multidrug-resistant (MDR) Escherichia coli (E. coli) in poultry production has grown increasingly severe, and the mixed selling model in live poultry markets further elevates the threat of cross-species pathogen spread. In this study, we integrated phenotypic resistance and virulence profiling with whole-genome sequencing to characterize two MDR E. coli isolates from pigeons and chickens. Two MDR E. coli strains were recovered, belonging to different MLST genotypes and serotypes, with the pigeon-origin strain exhibiting markedly higher virulence. Genomic sizes were similar between the two isolates, but the pigeon isolate harbored more genomic islands and three plasmids (none carrying resistance genes), whereas the chicken isolate carried two plasmids bearing blaTEM-1 and tet(A). Both strains relied mainly on efflux pumps and target modification, yet fluoroquinolone susceptibility differed strikingly: in the pigeon-origin strain, amino acid mutations at positions 247 and 249 of gadX altered the protein secondary structure, likely driving its high-level ciprofloxacin resistance (MIC = 128 μg/mL). Although the pigeon-origin strain had fewer total virulence genes, it possessed unique functional categories related to immune modulation (gtrB) and biofilm formation (cah) that were absent in the chicken isolate. Host-pathogen interaction analysis revealed divergent strategies: pigeon-specific virulence genes interacted with host apoptosis and stress response pathways, while those of chicken origin were mainly associated with inflammatory signaling. This study demonstrates the ongoing evolution of antibiotic resistance among commensal E. coli, underscoring the need for stricter management of live poultry markets and regular surveillance of antibiotic resistance to reduce public health risks.