Genomic and Plasmid Distribution of Clinically Relevant Antibiotic Resistance Genes in Pets and Free-Roaming Dogs in an Urban Area of Central Mexico

Dogs, especially as pets but also an increasing number of stray dogs, share environments with humans, facilitating the transfer of antibiotic resistance genes (ARGs) between genetic compartments, with zoonotic and public health implications that must be addressed within One Health. In this cross-sectional comparative study, we explored the distribution of seven selected clinically relevant ARGs in both genomic DNA (gDNA) and plasmid DNA (pDNA), and the phenotypic resistance profile of the cultivable microbiota, between pet dogs (PeDs, n = 12) and free-roaming dogs (FRDs, n = 10) in Mexico. Tetracycline resistance genes (tetQ, tetW, and tetM) predominated in both compartments (40% to 100%), suggesting the presence of a core tetracycline-associated resistome. In contrast, plasmid-associated differences were group-specific: in pDNA cfxA was enriched in FRDs (90%) and tetK in PeDs (42%), whereas blaTEM-1 and ermC were absent in two dog populations. Cultivable bacteria from both groups exhibited phenotypic multidrug resistance, particularly by β-lactams, macrolides, lincosamides, and tetracyclines. FRDs also harbored pathogenic–zoonotic bacteria such as Yersinia enterocolitica, Campylobacter jejuni, and Enterococcus faecalis. Our findings indicated that FRDs and PeDs harbor substantial resistomes, with differences in plasmid-associated ARGs, revealing a transfer potential related to environmental exposure.