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Characterization of antibiotic resistance genes in the sediments of an urban river revealed by comparative metagenomics analysis

Chen, Haiyang, Bai, Xiaomei, Jing, Lijun, Chen, Ruihui, Teng, Yanguo
The Science of the total environment 2019 v.653 pp. 1513-1521
anthropogenic activities, antibiotic resistance, antibiotic resistance genes, antibiotics, human health, marine sediments, metagenomics, niches, risk, rivers, sediment contamination, soil, statistical analysis, urban areas, Antarctic region, China
The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments). In total, 442 ARG subtypes belonging to 22 ARG types were detected in the human-impacted river sediments with an abundance range of 1.1 × 10−1–8.1 × 10−1 copy of ARG per copy of 16S-rRNA gene. The most abundant and diverse ARGs were commonly associated with antibiotics that have been extensively used in that area, likely indicating the spread of ARGs in river environments because of the selective pressure resulting from antibiotic use. As a whole, anthropogenic activities were the dominant contributor of major ARG types, for example, occupying 100% for sulfonamide-ARGs, 97% for beta-lactam-ARGs, 94% for aminoglycoside-ARGs and 64% for tetracycline-ARGs. This study provides insights into the role of human activities in accelerating the dissemination and proliferation of ARGs in urban river environment and draws attention to controlling the use and discharge of antibiotics for protection of public health.