National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, China.
Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
Nat Commun. 2023 Aug 12;14(1):4868. doi: 10.1038/s41467-023-40587-1.
Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.
呼吸系统疾病及其治疗在养猪业和人类健康中都受到高度关注。然而，猪下呼吸道微生物组中抗生素耐药基因（ARGs）的组成和分布尚不清楚。ARGs 与移动遗传元件（MGEs）和肺部健康之间的关系也不清楚。在这里，我们使用来自 675 头实验猪的 745 个宏基因组，对包含 1228 个开放阅读框的猪下呼吸道微生物组的抗生素耐药组进行了特征描述，这些开放阅读框属于 372 个 ARGs。12 个赋予四环素抗性的 ARGs 与 MGE Tn916 家族有关，多种类型的 ARGs 与转座酶基因 tnpA 有关。ARGs 和 MGE 之间的大多数连锁复合物（Tn916 家族和 tnpA）也存在于猪肠道微生物组和人类肺部微生物组中，这表明这些 MGE 介导 ARG 向人类和猪健康转移的风险很高。γ-变形菌是主要的 ARG 携带者，其中大肠杆菌携带超过 50 个 ARGs 和超过 10 个 MGEs。尽管微生物组成决定了 ARG 的组成，但我们确定了 73 个 ARG，它们的相对丰度与肺部病变的严重程度显著相关。我们的研究结果提供了猪下呼吸道微生物组中 ARG 图谱的首次概述。
