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Antimicrobial resistance has been a global public health concern. The river-lake systems are one of the tightly connected terrestrial ecosystems and, appear to be reservoirs of antibiotic resistant genes (ARGs) and dispersal routes of resistant pathogens because they are easily impacted by human activities. Currently, systematic knowledge on the prevalence, transfer risk and source of ARGs in river-lake systems is largely lacking. In this study, we focused on the high-throughput profiling and source-sink relationship disentangling of ARGs in the sediments of an interconnected river-lake system (Fuhe River and its receiving Lake Baiyang in northern China). To this end, 40 surface sediments were collected for metagenomic shotgun sequencing. The profile and co-occurrence of ARGs in the sediments of the river-lake system were comprehensively characterized, as well as the mobile genetic elements (MGEs) carrying ARGs and their potential resistome dissemination risk. CrAssphage, a recently-discovered bacteriophage, was used to track human fecal pollution on the prevalence of ARGs. Meanwhile, a novel fast expectation-maximization microbial source tracking (FEAST) method was combined with linear discriminant analysis effect size method (LEfSe) for quantitatively apportioning the contribution of river sediment to the presence of ARGs in the receiving lake. Results showed abundant and diverse ARGs (24 types consisting of 510 subtypes) were detected in the sediments of the river-lake system, including some emerging ARGs such as mcr-1, tetX and carbapenemases types. Network analysis suggested non-random co-occurrence patterns of ARGs within the same type and among different types. Importantly, a number of MGE-carrying contigs were identified with jointly containing one or more ARGs, resulting in higher resistome risk potential in Lake Baiyang than many worldwide lakes. Source tracking indicated the prevalence of ARGs in the sediments of the river-lake system might be largely explained by the extent of human fecal contamination, and apportionment estimates the load transport from Fuhe River contributed more than 80% of ARGs to the receiving Lake Baiyang., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., (Copyright © 2019. Published by Elsevier B.V.)