摘要
      抗生素耐药性基因（ARGs）是新出现的环境污染物，对公众健康构成威胁。集约化养猪场被认为是抗生素抗性基因（ARGs）的热点。然而，中国养猪场的抗生素耐药性及其遗传背景、宿主和可转移性在很大程度上仍未得到探索。在这里，我们使用Illumina和Oxford Nanopore宏基因组学测序来调查中国14个偏远大型（每年10000只动物）商业养猪场的抗生素耐药性情况。我们在所有样本中鉴定了高丰度和多样性的ARGs（609966.8，1433种类型，属于38个不同的抗生素类别），包括那些编码对临床关键重要抗生素（如mcr、tetX、optrA、poxtA、qnr和blaCTX-M）的耐药性的ARGs。检测到的ARGs中，约75%由可移动的遗传元件（主要是质粒）携带，这表明它们在接收环境中具有很高的传播潜力。宿主追踪分析确定梭状芽孢杆菌、粪杆菌和大肠杆菌是移动ARGs的主要细菌宿主。值得注意的是，基因组装箱产生了246个高完整性的基因组草案。对装箱基因组中的耐多药（MDR）基因的遗传背景分析显示，插入序列（IS）、整合素和SGI2基因组岛参与其中，这表明它们在促进耐多药细菌发展中发挥着重要作用。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耐药性的了解，并建议合理管理养猪场的动物粪便，以减少抗生素耐药性向环境的传播。
Abstract
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 blaCTX-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.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722014450