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 resis..., 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. , 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.
 
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畜牧业畜禽粪便可成为环境中抗生素耐药性的重要污染源，但目前针对养殖活动集约化程度提升时，粪便内耐药基因库的变化规律仍存在显著研究空白。本研究采集中国8个养殖场的粪便样本，涵盖牦牛、绵羊、猪、马从散养至集约化养殖的不同模式，通过基因型与表型两种方法测定粪便中的耐药性特征，旨在明确养殖集约化对粪便中抗生素耐药性的扩增程度。结果显示，集约化养殖的动物粪便中抗生素耐药基因（antibiotic resistance genes, ARGs）多样性更高，耐药表型也更强，二者呈现显著相关性。进一步在宏基因组重叠群（metagenome contig）水平分析发现，随着养殖集约化程度提升，抗生素耐药基因与可移动遗传元件共定位的频率升至27.38%，且相关耐药表型与细菌系统发育的关联性减弱。此外，集约化养殖还扩大了粪便微生物组中病原体携带的多重耐药基因的优势丰度。总体而言，养殖集约化可增强粪便中的抗生素耐药性……

高通量定量PCR分析得到的Ct值数据集见补充数据1（*.xlsx）；宏基因组测序分析得到的转录本每百万reads（Transcripts Per Million, TPM）值数据集见补充数据2（*.xlsx）。所有分离并经鉴定的菌株及其测序读段信息详见补充数据3（*.xlsx）。补充数据4（*.xlsx）收录了采用标准纸片扩散法测定的所有菌株的抑菌圈直径（inhibition zone diameter, IZD）记录。详细信息请参阅README文档。