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.

Methods
We sampled feces from eight Chinese farms, where animals (yak, sheep, pig, and horse) were reared under free range to more intensive conditions, to determine the extent to which intensified farming expands antibiotic resistance in fecal matter, using both genotype and phenotype approaches.The datasets of Ct values from high-throughput qPCR analyses are shown in supplementary Data 1 (*.xlsx). The datasets of TPM values from metagenomic sequencing analyses are shown in Supplementary Data 2 (*.xlsx). All isolated and then identified strains with their sequenced reads are listed in Supplementary Data 3 (*.xlsx). Supplementary Data 4 (*.xlsx) contains all recorded diameters of the inhibition zone (IZD) for these strains tested using the standard disc diffusion assay. Please see the README document for detailed information.