Genomic Characterization of Selected Multidrug-Resistant Escherichia coli Isolates from Healthy Dogs in Chile Reveals Diverse Lineages Including ST131

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%). blaCTX-M genes were detected in 7/13 isolates (53.8%) and blaCMY-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 blaCTX-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.