Metagenomic evidence of the prevalence and distribution patterns of antimicrobial resistance genes in dairy agroecosystems

Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment via manure and to this end we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with18 antibiotic resistances classes across all samples; however, the most abundant genes were those encoding for multi-drug resistance (MDR) efflux systems (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%) and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms; farm 09 was categorized as a high risk farm as a greater proportion of AR genes were common to at least three sectors, suggesting possible transfer of organism(s)/horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.