动物和人类粪便传播抗生素耐药性的风险是一个迫切的公共问题。在本研究中，我们试图建立流程解释抗生素抗性基因（ARG）的组装，以研究ARG及其相关遗传片段。在装配的基因组片段中发现的遗传元件包括流动性遗传因子（MGE）和金属抗性基因（MRG）。然后，我们研究了这些抗性基因的宿主以及猪，鸡和人类粪便样品的共同抗体组。在这些粪便样品中发现高水平的四环素，多药物，红霉素和氨基糖苷类抗性基因。尤其是成年鸡鸡粪检测到高水平的ARG（7762×/ Gb），表明ARG污染水平高于其他粪便样本。发现许多ARGs复合基因（例如，macA-macB和tetA-tetR）在鸡，猪和人粪便都有存在。另外，在鸡粪的重组片段上鉴定出人类病原体携带的aadA5-dfrA17的1型整合子等MGEs。差异覆盖率分析显示成年鸡粪中ARG富集显着。基因组草案，注释为多重耐药性大肠杆菌，从鸡粪便宏基因组中检索，并确定携带不同的ARG（多药，吖啶黄和大环内酯）。目前的研究确定了ARG宿主和宏基因组数据集共享基因组，并成功建立了ARGs，宿主和环境之间的关系。 这种基于宏基因组装的ARG注释流程将有助于弥合与宏基因组数据集有关的ARG相关基因和ARG宿主的知识空白。 此外，这一途径将有助于评估ARG遗传背景下的环境风险。

      The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs. 

http://pubs.acs.org/doi/abs/10.1021/acs.est.5b03522