College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
Sci Total Environ. 2022 Apr 10;816:151613. doi: 10.1016/j.scitotenv.2021.151613. Epub 2021 Nov 12.
Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, large-scale investigation on the distribution of antibiotic resistance genes (ARGs) in the microbiomes from most types of ecosystem is still lacking. In this study, we provide a comprehensive characterization of ARGs for 52,515 microbial genomes covering various Earth's ecosystems, and conduct the risk assessment for ARG-carrying species based on further identification of mobile genetic elements (MGEs) and virulence factor genes (VFGs). We identify a total of 6159 ARG-carrying metagenome-assembled genomes (ACMs), and most of them are recovered from human gut and city subway. Our results show that efflux pump is the most common mechanism for bacteria to acquire multidrug resistance genes in Earth's microbiomes. Enterobacteriaceae species are the largest hosts of ARGs, accounting for 14% of total ACMs with 64% of the total ARG hits. Most of ARG-carrying species are unique in the different ecosystem categories, while 33 potential background ARGs are commonly shared by all ecosystem categories. We then detect 36 high-risk ARGs that likely threat public health in all ACMs. Based on ranking the importance of ARG-carrying species in the different ecosystem categories, several bacterial taxa such as Escherichia coli, Enterococcus faecalis, and Pseudomonas_A stutzeri are recognized as priority species for surveillance and control. Overall, our study gives a broad view of ARG-host associations in the environments.
抗生素在地球各个生境中的广泛耐药性已成为一个严重的健康问题。然而，对于大多数生态系统的微生物组中抗生素耐药基因（ARGs）的分布情况，仍缺乏大规模的调查。在本研究中，我们对涵盖各种地球生态系统的 52515 个微生物基因组中的 ARGs 进行了全面的特征描述，并基于移动遗传元件（MGEs）和毒力因子基因（VFGs）的进一步鉴定，对携带 ARG 的物种进行了风险评估。我们共鉴定出 6159 个携带 ARG 的宏基因组组装基因组（ACMs），其中大部分是从人类肠道和城市地铁中获得的。结果表明，外排泵是地球微生物组中细菌获得多药耐药基因的最常见机制。肠杆菌科是 ARGs 的最大宿主，占 ACMs 的 14%，占总 ARG 命中数的 64%。大多数携带 ARG 的物种在不同的生态系统类别中是独特的，而 33 个潜在的背景 ARG 在所有生态系统类别中是共同存在的。然后，我们在所有 ACMs 中检测到 36 种可能对公众健康构成威胁的高风险 ARG。基于对不同生态系统类别中携带 ARG 的物种重要性的排序，一些细菌类群，如大肠杆菌、粪肠球菌和施氏假单胞菌，被认为是监测和控制的优先物种。总的来说，本研究提供了环境中 ARG-宿主关联的广泛视角。
