Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

Animal feces from livestock farming can be a major source of antibiotic
resistance to the environment, but a clear gap exists on how the
resistance reservoir in feces alters as farming activities intensify.
Here, we sampled feces from eight Chinese farms, where yak, sheep, pig,
and horse were reared under free-range to intensive conditions, and
determined fecal resistance using both genotype and phenotype approaches.
Animals reared intensively exhibited increased
diversity of antibiotic resistance genes (ARGs) and greater
resistance phenotypes in feces, which were cross-correlated. Furthermore,
at the metagenome contig level, ARGs were
co-located with mobile genetic elements at a higher frequency
(27.38%) as farming intensified, with associated resistance
phenotypes being less coupled with bacterial phylogeny. Intensified
farming also expanded the multidrug resistance preferentially carried on
pathogens in fecal microbiomes. Overall, farming intensification
can increase antibiotic resistance genotypes and phenotypes in
domestic animal feces, with implications for environmental health.