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 and greater resistance phenotypes in feces, which were cross-correlated. Furthermore, at the metagenome contig level, antibiotic resistance genes 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.