Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures. Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types. Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.

中文翻译：

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宾夕法尼亚州常规奶牛场和有机奶牛场中整个农场环境中微生物群落和菌群的分布

抗菌素耐药性是一个严重的问题。尽管抗菌剂在牲畜中的广泛使用加剧了农场环境中抗菌素耐药基因（ARG）的出现和传播，但对抗菌素使用是否会影响ARG在牲畜系统中的分布知之甚少。这项研究比较了不同畜群使用不同抗生素的奶牛群中微生物群落和抵抗组（ARG的集合）的分布。在宾夕法尼亚州的三个常规农场（用于治疗母牛的抗菌药物）和三个有机农场（至少在四年内没有抗菌药物）中采集了来自小母牛，非泌乳和泌乳母牛，粪便存储和土壤的粪便。提取样品中的基因组DNA，进行处理，并在Illumina NextSeq平台上测序，并使用既定程序分析微生物群落和抵抗力谱。在所有农场中，微生物群落和抵抗力概况均按样品类型聚集。总体而言，常规畜群的粪便中ARG的丰度和多样性显着高于有机畜群。与有机牛群相比，常规牛群的粪便样品中对内酰胺，大环内酯-林可酰胺-链霉菌素（MLS）和四环素类药物具有抗性的ARG明显更高。无论农场类型如何，所有粪便存储样品的ARG都具有更大的多样性（尽管丰度较低），从而赋予了对氨基糖苷类，四环素类，MLS，多药耐药性和苯酚的耐药性。与粪便，粪便，和盐水样品，由ARG赋予对氨基糖苷，糖肽和多药的耐药性。ARG的分布可能由相应样品类型中微生物群的组成决定。农场使用抗生素会严重影响粪便中特定的ARG组，但不会影响粪便存储或土壤样品。