摘要
      畜牧业产生的动物粪便可能是对环境产生抗生素耐药性的主要来源，但随着农业活动的加强，粪便中的耐药性库是如何变化的，这方面存在着明显的差距。在这里，我们对八个中国农场的粪便进行了采样，这些农场的牦牛、绵羊、猪和马都是在自由放养到集约饲养的条件下饲养的，并使用基因型和表型方法确定了粪便耐药性。集中饲养的动物表现出抗生素耐药性基因的多样性增加和粪便中更大的耐药性表型，这是相互关联的。此外，在宏基因组重叠群水平上，随着农业的加强，抗生素抗性基因与可移动遗传元件的共同定位频率更高（27.38%），相关的抗性表型与细菌系统发育的耦合程度较低。集约化养殖也扩大了粪便微生物群中病原体优先携带的多药耐药性。总的来说，集约化养殖会增加家畜粪便中的抗生素抗性基因型和表型，对环境健康有影响。
Abstract
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.

https://www.nature.com/articles/s43247-023-00790-w