基于宏基因组学分析安徽地区畜禽粪便微生物耐药性特征

为深入了解在食用动物生产过程中滥用抗生素，迫使肠道共生细菌成为微生物耐药性（antimicrobial resistance，AMR）重要宿主之一的现象，本研究利用宏基因组学针对食用动物的肠道细菌AMR进行分析。

利用宏基因组学技术对安徽地区猪和鸡粪便中的AMR及可移动遗传元件进行定量和表征，并且在核心抗性基因亚型水平上研究猪和鸡共生细菌群落的耐药性特征。

从抗性基因（antimicrobial resistance gene，ARG）的丰度和多样性来看，鸡肠道共生菌中ARG的多样性和检出率高于猪，而猪肠道共生菌中ARG总丰度高于鸡。大环内酯―林可酰胺―链菌素类抗性基因和四环素抗性基因是所有样本中含量最高的2种ARG，研究也检测到了世界范围内流行的ARG，包括optrA、qnrS、lsaE和tem等，同时，一些可移动遗传元件，包括噬菌体、质粒和插入序列也显示出与ARG存在一定相关性，这揭示了ARG的水平转移潜力。此外，食物链动物的抗性组和微生物组之间在统计学上也被证明存在正相关性。宿主溯源分析表明，在鸡样本中的拟杆菌和大肠埃希菌被检测出含有大量ARG，而在猪的样本中被检测出含有丰富ARG的为瘤胃球菌和罗氏菌。

本研究通过对猪和鸡共生细菌群落中AMR的调查统计，证实肠道微生物群是ARG的重要宿主及传播途径之一，为评价食用动物安全性及后续泛耐药基因数据库的构建提供科学依据，对公共健康具有重要意义。

Macrogenomics-based analysis of microbial resistance of microbes in pig and chicken faeces in Anhui region

ObjectiveIn order to gain insight into the phenomenon that the misuse of antibiotics in the production of food animals has forced intestinal commensal bacteria to become one of the important hosts of antimicrobial resistance (AMR). Therefore, the present study was conducted to analyze the intestinal bacterial AMR in food animals using macrogenomics. MethodsAMR and mobile genetic elements in pig and chicken faeces from Anhui region were quantified and characterised using macrogenomics techniques, and the resistance profiles of the commensal bacterial communities in pigs and chickens were observed at the level of the core resistance gene subtype. ResultsIn terms of the abundance and diversity of antimicrobial resistance gene (ARG), the diversity and detection rate of ARG were higher in chicken intestinal commensal bacteria than in pigs, whereas the total abundance of ARG was higher in porcine intestinal commensal bacteria than in chickens. Macrolide-Lincosamide-Streptozotocin-like resistance genes and Tetracycline resistance genes were the two most abundant ARG in all the samples. The study also detected ARG prevalent worldwide, including optrA, qnrS, lsaE, and tem, etc.. At the same time, a number of removable genetic elements including phage, plasmid and insertion sequences were also shown to have some correlation with ARG, which revealed the horizontal transfer potential of ARG. In addition, a statistically positive correlation was demonstrated between resistance groups and microbiomes of food chain animals. Host traceability analyses showed that Bacteroides and Escherichia coli were detected to contain high levels of ARG in chicken samples, whereas rich ARG were detected in Ruminococcus and Roseburia in pig samples. ConclusionIntestinal microbiota is one of the important hosts and transmission routes of ARG. The study provides a scientific basis for evaluating the safety of food animals and the subsequent construction of a database of pan-resistant genes, which is of great significance for public health.