Living Environment Influences Canine Nasal Microbiota and Antimicrobial Resistance Networks

Abstract

The canine nasal cavity serves as a critical defensive barrier and ecological interface between the host and its external environment. This study aimed to compare culturable nasal bacterial colonization and antimicrobial resistance status in a cohort of 18 clinically healthy dogs, categorized by primary living conditions as indoor (n=8) and outdoor (n=10). Nasal swabs obtained from the anterior nares were subjected to aerobic culture and bacterial species were identified using the BD Phoenix™ automated microbiology system. Taxonomic profiling identified 17 distinct bacterial taxa, revealing differences in species composition between the two environmental cohorts. Indoor dogs were characterized by a higher prevalence of human-associated pathobionts, most notably Streptococcus pneumoniae, Kingella kingae, and Rothia mucilaginosa. Conversely, the outdoor group harbored more environmental and opportunistic taxa, including Aeromonas salmonicida and Yersinia kristensenii. Antimicrobial resistance was more pronounced in the indoor cohort, where 71.4% of isolates were resistant to clindamycin. Notably, all Staphylococcus species exhibited an oxacillin-resistant phenotype. Statistical modeling using Spearman's rank correlation and Fisher’s Z-transformation demonstrated that the indoor environment fundamentally reorganizes the resistome architecture, notably strengthening the correlation between enrofloxacin and trimethoprim-sulfamethoxazole resistance. These findings suggest that the "indoor exposome", comprised of human proximity and domestic chemical exposures, may act as a powerful selective force that alters the canine respiratory microbiome and promotes the accumulation of complex resistance determinants. This study provides empirical support for the “Epithelial Barrier Theory” in a veterinary context and underscores the role of companion animals as potential reservoirs for human-derived pathogens, emphasizing the necessity for One Health-oriented antimicrobial stewardship within shared domestic environments.

Keywords

• canine nasal microbiome
• antimicrobial resistance
• indoor exposome
• One Health.

Ethical Statement

Ethical approval was obtained from the Bursa Uludag University Animal Experiments Local Ethics Committee (Approval No: 2025-16/03).

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