Characterization of the oral microbiota and antimicrobial resistance genes in shelter dogs in Japan.

Companion animals can serve as reservoirs of antimicrobial resistance genes and zoonotic microorganisms, yet information on shelter dogs remains limited. This study characterized the oral microbiota and screened for antimicrobial resistance genes in shelter dogs in Japan. Oral swabs were collected from 81 dogs, microbial genomic DNA was extracted, bacterial communities were profiled by 16S rRNA gene amplicon sequencing, and antimicrobial resistance genes were screened by PCR. We detected genes conferring resistance to several antimicrobial classes, including β-lactams, tetracyclines, macrolide-lincosamide-streptogramin B, phenicols, and sulfonamides. cfxA was detected in all 81 samples, followed by sul1 (66/81), tet(M) and sul2 (65/81), floR (39/81), mecA (17/81), and erm(B) (15/81). We identified potentially pathogenic genera including Capnocytophaga, Pasteurella, Fusobacterium, Campylobacter and Corynebacterium. Microbiome analysis revealed that at the phylum level, Pseudomonadota and Bacteroidota were the most dominant, while Porphyromonas, Frederiksenia and Moraxella were the most prevalent genera. Our findings highlight that (i) the oral microbiota of shelter dogs broadly resembles that reported in companion dogs and (ii) shelter dogs represent an overlooked reservoir of clinically relevant antimicrobial resistance genes and potentially zoonotic bacteria. Therefore, it is necessary to include shelter animals in antimicrobial resistance surveillance programs to capture any potential gaps in the antimicrobial resistance prevalence in companion animals and prevent dissemination of resistant bacteria to humans following adoption of shelter dogs and cats.