Ranking the risk of antibiotic resistance genes by metagenomic and multifactorial analysis in hospital wastewater systems

Antimicrobial resistance poses a serious threat to human health. Hospital wastewater system (HWS) is an important source of antibiotic resistance genes (ARGs). The risk of ARGs in HWS is still an under-researched area. In this study, we collected publicly metagenomic datasets of 71 hospital wastewater samples from 18 hospitals in 13 cities. A total of 9838 contigs were identified to carry 383 unique ARGs across all samples, of which 2946 contigs were plasmid-like sequences. Concurrently, the primary hosts of ARGs within HWS were found to be Escherichia coli and Klebsiella pneumoniae. To further evaluate the risk of each ARG subtype, we proposed a risk assessment framework based on the importance of corresponding antibiotics as defined by the WHO and three other indicators - ARG abundance (A), mobility (M), and host pathogenicity (P). Ninety ARGs were identified as R1 ARGs having high-risk scores, which meant having a high abundance, high mobility, and carried by pathogens in HWS. Furthermore, 25% to 49% of genomes from critically important pathogens accessed from NCBI carried R1 ARGs. A significantly higher number of R1 ARGs was carried by pathogens in the effluents of municipal wastewater treatment plants from NCBI, highlighting the role of R1 ARGS in accelerating health and environmental risks.