Genomic Characterization of Selected Multidrug-Resistant Escherichia coli Isolates from Healthy Dogs in Chile Reveals...

Companion animals are increasingly recognized as carriers of antimicrobial-resistant Escherichia coli, yet genomic data from clinically healthy dogs in Latin America remain scarce. We characterized 13 genetically non-redundant multidrug-resistant E. coli isolates selected from 224 resistant E. coli isolates recovered in a previous surveillance study of 600 clinically healthy household dogs in the Metropolitan Region of Chile (2021-2022). Antimicrobial susceptibility testing was performed using VITEK2 and interpreted according to Clinical and Laboratory Standards Institute criteria, and whole-genome sequencing was used to identify resistance genes, virulence-associated traits, plasmid replicons, phylogroups, sequence types, and ST131 subclades. All isolates were multidrug resistant and showed high resistance to ampicillin and cephalexin (13/13, 100%), ciprofloxacin (13/13, 100%), cefpodoxime (11/13, 84.6%), cefovecin (10/13, 76.9%), and ceftiofur (10/13, 76.9%). An extended-spectrum β-lactamase phenotype was observed in 9/13 isolates (69.2%). bla_CTX-M genes were detected in 7/13 isolates (53.8%) and bla_CMY-2 in 3/13 isolates (23.1%), whereas IncF-associated plasmid replicons predominated. The isolates belonged to diverse lineages, including ST131, ST744, ST1196, and ST1011. The two ST131 isolates belonged to phylogroup B2, carried bla_CTX-M variants, and were assigned to the C2/H30Rx and C1-M27 subclades. These findings support further consideration of companion animals in genomic antimicrobial resistance surveillance under a One Health framework.