摘要
      地球栖息地广泛存在的抗生素耐药性已成为一个严重的健康问题。然而，对大多数类型生态系统的微生物群中抗生素抗性基因（ARGs）的分布仍缺乏大规模的研究。在这项研究中，我们对覆盖地球各种生态系统的52515个微生物基因组的ARG进行了全面的表征，并在进一步鉴定移动遗传元件（MGE）和毒力因子基因（VFG）的基础上，对携带ARG的物种进行了风险评估。我们总共鉴定了6159个携带ARG的宏基因组组装基因组（ACM），其中大多数是从人类肠道和城市地铁中回收的。我们的研究结果表明，外排泵是细菌在地球微生物群中获得多药耐药性基因的最常见机制。肠杆菌科物种是ARG最大的宿主，占总ACM的14%，占总ARG命中率的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，而所有生态系统类别通常共享33个潜在的背景ARG。然后，我们在所有ACM中检测到36种可能威胁公众健康的高风险ARG。根据携带ARG的物种在不同生态系统类别中的重要性排序，大肠杆菌、粪肠球菌和伪Monas_A stutzeri等几种细菌分类群被认为是监测和控制的优先物种。总的来说，我们的研究对环境中ARG宿主的关联有了广泛的了解。
Abstract
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.

https://www.sciencedirect.com/science/article/abs/pii/S0048969721066894