Diversity of tetracycline- and erythromycin-resistant bacteria in aerosols and manures from four types of animal farms in China

Confined animal feeding operations generate high levels of airborne antibiotic-resistant bacteria, including pathogenic strains that may pollute the local environment or pose a health risk to both animals and workers. However, the communities of airborne antibiotic-resistant bacteria in such operations are not fully understood, especially in fine particles that penetrate deeply into the respiratory system. To address these gaps, manures and aerosols from inside and outside of animal houses were collected, and the characteristics of antibiotic-resistant bacteria were analyzed using Illumina MiSeq sequencing to amplify the V3–V4 region of bacterial 16S rRNA. The results indicated that animal species was the main factor that influenced the bacterial community of both manure and aerosol samples, while antibiotic selection was the major factor that influenced the bacterial community of aerosol samples from the inside of animal houses. An obvious clustering difference was detected between manure and aerosol samples. No significant difference in both alpha- and beta-diversity indices was detected between fine and coarse particles. As a key genus, Staphylococcus was found to drive the difference in the bacterial community of tetracycline-resistant bacteria to total culturable bacteria and erythromycin-resistant bacteria and also the difference in the bacterial community from aerosol to manure samples. Current data would help in evaluating the risk to human and livestock health and tracing the source of airborne antibiotic-resistant bacteria in animal farms.