Plasmidome derived antibiotic resistome reveals the partitioning of different geographic regions and treatment compartments in the urban water systems

Mobile genetic elements such as plasmids drive the dissemination and evolution of antibiotic resistance in the microbiome. And plasmid-mediated antibiotic resistance has been a growing concern in the wastewaters since urban water systems (UWSs) are known to breed and spread antibiotic resistance to the downstream rivers, which constitutes environmental exposure risks to human health. Here we investigated the plasmid derived antibiotic resistance at different treatment compartments in three comparable UWSs located in Spain, Denmark, and the United Kingdom using direct plasmid DNA metagenome sequencing. We assembled contigs (circular and linear) and removed chromosome ones using bioinformatic tools. Thereby, a plasmidome dataset was generated and analysed. We identified 225 different ARGs belonging to 180 groups of ARG families in the wastewater plasmidome. Genes conferring resistance to aminoglycoside, tetracycline, macrolide and phenicol drug contributed to more than half of the plasmidome resistome abundance across samples. The plasmid resistome richness and relative abundance detected in Spanish UWS samples were significantly ( p  < 0.05) higher than the other studied countries, which mirrors the remarkable domestic antibiotic use in Spain. And we only detected significant ( p  < 0.05) differences in ARG risk scores between the hospital and residential sewers in Spain. Meanwhile, different sewer compartments showed a partitioning role for the resistome richness and abundance distributions. Intriguingly, we perceived a group of shared ARGs among the three countries regardless of treatment stages. Further, ≥ 80% of ARG types in the wastewater treatment plants could be found in the sewer sources, which implies these ARGs were persistent in the UWSs. Overall, this study shed light on the plasmidome derived resistome as an integral part of the total resistome, and this resistome is shaped by geographic-regional and UWS-sectional variations in the UWS environment.