Short- and long-read metagenomics insight into the genetic contexts an hosts of mobile antibiotic resistome in Chinese swine farms
Short- and long-read metagenomics insight into the genetic contexts an hosts of mobile antibiotic resistome in Chinese swine farms
复制标题
通过短读和长读宏基因组学深入了解中国养猪场移动抗生素抗性组的遗传背景和宿主
DOI：
10.1016/j.scitotenv.2022.154352
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发表时间：
2022-03-11
影响因子：
9.8
通讯作者：
Shi, Lei
中科院分区：
文献类型：
--
作者：
Li, Lili;Xiao, Yawen;Shi, Lei
抗生素耐药基因（ARGs）是对公众健康构成威胁的新兴环境污染物。集约化养猪场被认为是抗生素耐药基因（ARGs）的热点。然而，抗生素抵抗组及其遗传背景、宿主和在中国养猪场的可转移性在很大程度上仍未被探索。在这里，我们使用Illumina和Oxford Nanopore宏基因组测序研究了中国14个遥远的大型（每年10,000头）商业养猪场的抗生素抗性组背景。我们在所有样本中发现了丰富多样的ARGs（609,966.8种，1433种类型，属于38种不同的抗生素类别），包括对临床关键重要抗生素（如mcr， tetX, optrA, poxtA， qnr和bla(CTX-M)）产生耐药性的ARGs。检测到的ARGs中约75%是由移动遗传元件（主要是质粒）携带的，这表明它们在接收环境中具有很高的传播潜力。寄主跟踪分析发现，梭菌、prausnitzii粪杆菌和大肠杆菌是移动ARGs的优势寄主。值得注意的是，基因组分箱生成了246个高完整性草图基因组。对多耐药（MDR）基因进行遗传背景分析，发现插入序列（ISs）、整合子和SGI2基因组岛参与其中，提示它们在促进MDR细菌发育中发挥重要作用。总的来说，这些发现大大扩展了我们目前对中国养猪场移动抗生素抗性组的了解，并建议合理管理养猪场的动物粪便，以减少抗生素耐药性对环境的传播。
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and bla(CTX-M)). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.