The Distribution of Microbiomes and Resistomes Across Farm Environments in Conventional and Organic Dairy Herds in Pennsylvania

Antimicrobial resistance is a serious problem. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial-resistant genes (ARGs) in farm environments, little is known about how antimicrobial use affects distribution of ARGs in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of antimicrobial-resistant genes) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, dry and lactating cows, manure storage, and soils from three conventional and three organic farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on Illumina NextSeq, and analyzed for microbial community and resistome profiles using established procedures. Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARGs in feces was much higher in conventional herds compared to organic herds; however, lactating cows from organic herds had ARGs for rifampins, macrolide-lincosamide-streptogramin (MLS), and tetracyclines carried in commensal bacteria in their feces. Regardless of farm type, all manure storage samples had greater diversity of ARGs than other sample types. Feces were dominated by ARGs conferring resistance to tetracyclines and MLS whereas rifampin, fluoroquinolones, aminoglycosides, tetracyclines, and MLS-resistant ARGs were prevalent in manure storage samples. Soil from organic herds had a greater proportion of fluoroquinolones and aminoglycosides compared to conventional herds, but no significant differences were observed. In conclusion, antimicrobial use on farms influenced specific groups of ARGs in feces but not manure storage or soil samples.