<p>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.</p>
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