Characterization and source-tracking of antibiotic resistomes in the sediments of a peri-urban river

Abstract

The peri-urban rivers are one of the critical interfaces between urban-rural symbiotic ecosystems and appear to be a reservoir of antibiotic resistance genes (ARGs) in the environment. To prevent the transmission risks of ARGs between peri-urban river and human, it is essential to explore the prevalence and source of ARGs in the environment for designing potential mitigation strategies. In this study, we focused on the characterization and source-tracking of ARGs in the sediments of a typical peri-urban river in Beijing, Chaobai River. Twenty-seven ARGs frequently reported in the environment, and two integrons (intI1 and intI2) were detected using high-throughput quantitative PCR. The profile of bacterial community was determined by performing 16S rRNA gene sequencing. Meanwhile, crAssphage, a novel recently-discovered DNA bacteriophage, was employed for tracking the contribution of human fecal pollution to the prevalence of ARGs. Results showed that the targeted ARGs were detected widely in the sediments of Chaobai River. Relatively, the abundances of ARGs in downstream were higher than those in the upstream, likely suggesting a gradient impact of anthropogenic activities along the river. Remarkably, the int1 gene was correlated significantly with most of the ARGs and might be the key factor influencing the shaping of ARGs in the river sediments. However, no significant correlations were observed between the ARGs and selective pressure factors, including antibiotics and metals. Of the identified 1039 genera, Escherichia-Shigella, Bacteroides, Arcobacter, Dechloromonas and Pseudomonas were the top most abundant organisms. Microbial source tracking based on the crAssphage annotation suggested that human sewage might be one of the potential sources of resistance bacteria in the river sediments. The study can advance our knowledge about ARGs in the peri-urban river and provides a management reference for ARG pollution control.

Keywords: Antibiotic resistance gene; Bacterial community; Chaobai River; CrAssphage; High-throughput sequencing; Microbial source tracking.