Metagenomic profiling of microbial community, antibiotic resistance genes and co-occurrence pattern in megacity rail transit system

Megacity rail transit systems harbor a pivotal microbial ecosystem that serves as a reservoir for antibiotic resistance genes (ARGs), which is intricately linked to the urban dissemination of infectious diseases. Here, we conducted metagenomic sequencing to elucidate the composition of microbial communities, ARGs, and examine the co-occurrence patterns between microbes and ARGs across various surfaces in the Shanghai rail transit system. Our findings revealed that bacterial genera such as Rhodococcus, Cutibacterium, and Brevundimonas dominated, originating either from human skin or environmental sources. Notably, the bacterial diversity varied according to the type of surface and specific stations. The principal co-ordinates analysis revealed substantial beta-diversity disparities among the examined surfaces. We identified a total of 1930 ARGs conferring resistance to 20 distinct antibiotic classes, including clinically significant ones such as Aminoglycoside, Streptogramin, Multidrug, and Tetracycline, which are associated with either single or multidrug resistance. Network analysis further revealed the co-occurrence relationships between microbial genera and ARGs. This study highlights that the microbial communities and ARGs in the rail transit system are sustained by a metapopulation of human and environmental generalists. These findings provide novel insights into the mechanisms underlying the risks associated with microbial exposure and suggest strategies to mitigate the spread of pathogenic microorganisms in megacity rail transit systems, thereby enhancing public health.