Persistence of Antibiotic Resistance from Agricultural Effluents to Surface Water Revealed in Metagenome Assembled Genomes

BackgroundDespite the increasing concerns about antibiotic resistance genes (ARGs) in wastewaters released from livestock or fish farms into the natural environment, studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we assessed the impact of the microbial antibiotic resistome and mobilome in wastewaters released in Korean rivers by reconstructing metagenome-assembled genomes (MAGs) using a novel refining method.ResultsWe reconstructed 1,100 MAGs using Korean river and wastewater metagenome samples and presented Additional Clustering Refiner (ACR), a method that significantly reduced contamination of genome quality. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into the downstream environment of rivers. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria harbored ARGs co-localized with mobile genetic elements. The most abundantly detected ARGs associated with mobile genetic elements in the wastewater effluents and downstream regions of the rivers were found to originate from Patescibacteria; the detected genes represented the potential for horizontal gene transfer of beta-lactam A-, sulfonamide-, and carbapenem-resistance genes. ConclusionsOur study tracked microorganisms that were transmitted from agricultural wastewater to receiving rivers through genome-resolved metagenomics. Based on the genomic analysis of MAGs, it was found that ARGs are more commonly co-localized with MGEs in agricultural wastewater than in river water. Furthermore, this suggests that members of Patescibacteria, which are relatively unknown, are carriers that disseminate ARGs into the environment, and a potential vector for disseminating ARGs in the environmental bacterial community. Overall, this study suggests that dissemination of ARGs by uncultured bacteria should be investigated further in multiple environments.