Characterization of antibiotic resistance across Earth's microbial genomes

Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, largescale 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 ARGcarrying 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. (c) 2021 Elsevier B.V. All rights reserved.

Automated summary

Antibiotic resistance is a critical health concern across Earth's habitats. This study provides a comprehensive understanding of antibiotic resistance genes (ARGs) in various ecosystems by analyzing microbial genomes. The findings reveal that species from the Enterobacteriaceae family are the major hosts of ARGs and identify several priority species for surveillance and control.