Functional profile reveals distinct risk potential of airborne and fecal antibiotic-resistant pathogen in animal farms

Animal farms serve as reservoirs of antibiotic-resistant pathogenic bacteria (ARPBs), which may pose health risks to both animals and workers. Here, tetracycline- and erythromycin-resistant bacteria were screened from aerosols and fecal samples at four types of animal farms, with their taxonomic and functional profiles determined via 16S rRNA gene sequencing. The results showed that environmental habitat type was the primary driver of beta diversity, with significant differences observed in the taxonomic (R² = 0.104, p < 0.01) and functional (R² = 0.163, p < 0.01) compositions of ARPBs between aerosol and fecal samples. Environmental habitats influenced taxonomic and functional alpha diversity (both Shannon index and richness) differently. Acquired antibiotic resistance may influence the distribution of dominant pathogens across diverse environmental habitats, a trend exemplified by the clinically significant pathogens Staphylococcus spp, which was more abundant in tetracycline-resistant aerosol samples. Functional analysis revealed that antibiotic-resistant communities were enriched with pathogenic bacteria. Specifically, pathogenicity-related functions were elevated by 12.3 % (tetracycline resistance) and 11.6 % (erythromycin resistance) in indoor aerosols compared to fecal samples (p < 0.05). These communities also exhibited distinct metabolic shifts: nitrogen metabolism increased by 25.8 % and 28.7 %, while carbon metabolism concurrently decreased by 30.4 % and 31.3 % for tetracycline and erythromycin resistant strains, respectively. This study reveals the functional and taxonomic profiles of ARPBs in various habitats, emphasizing the importance for multi-dimensional analyses to evaluate the risks potential and ecological roles in AMR pollution hotspots, including but not limited to farming environments.