摘要

       与从动物和人类粪便传播的抗生素耐药性相关的风险是一个紧迫的公共问题。在本研究中，我们试图建立一个基于宏基因组组装注释抗生素抗性基因 (ARG) 的管道，以研究 ARG 及其与相关遗传元件的共存。在组装的基因组片段上发现的遗传元件包括移动遗传元件 (MGE) 和金属抗性基因 (MRG)。然后我们探索了这些抗性基因的宿主以及猪、鸡和人类粪便样本的共同抗性组。在这些粪便样本中发现了高水平的四环素、多药、红霉素和氨基糖苷类抗性基因。特别是，在成年鸡粪便中检测到显着高水平的 ARGs (7762 ×/Gb)，表明 ARG 污染水平高于其他粪便样本。许多 ARGs 排列（例如，macA-macB 和 tetA-tetR）被发现由鸡、猪和人类粪便共享。此外，在组装好的鸡粪支架上鉴定了 MGE，例如携带 aadA5-dfrA17 的 1 类整合子，并由人类病原体携带。差异覆盖分箱分析揭示了成年鸡粪便中显着的 ARG 富集。从鸡粪便宏基因组中检索到注释为多药耐药大肠杆菌的基因组草图，并确定携带多种 ARG（多药、吖啶黄和大环内酯）。本研究证明了 ARG 宿主的确定和宏基因组数据集的共享抗性组，并成功建立了 ARG、宿主和环境之间的关系。这种基于宏基因组组装的 ARG 注释管道将有助于弥合有关 ARG 相关基因和 ARG 宿主与宏基因组数据集的知识差距。此外，该管道将有助于在 ARG 的遗传背景下评估环境风险。

       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.

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