摘要

       河流通常被认为是环境中抗生素耐药基因（ARGs）的天然库。为了预防和控制ARGs的风险，对河流系统中的抗药性及其相关性进行全面的研究是非常重要的。在这项研究中，我们提出了一个从多个类别（包括ARG电位、ARG宿主、致病性电位、共选择电位和基因转移电位）鉴定河流沉积物中抗生素抗性的宏基因组框架，并将其应用于了解沉积物中抗生素抗性的存在、宿主和基因转移电位，北京某城市河流沉积物中ARGs的共生现象。结果表明，在河流沉积物中共检测到203个ARG亚型，隶属于21个ARG亚型，其丰度范围为107.7-1004.1×Gb，以多药、大环内酯类林可酰胺链球菌素、杆菌肽、喹诺酮类和磺胺类耐药基因为主。寄主追踪分析表明，十二氯单胞菌、假黄单胞菌、芳烃、溶菌酶和假单胞菌是ARGs的主要寄主。一些携带ARG的contigs（ACCs）被注释为病原菌的片段，并携带多种多药ARGs。此外，在河流沉积物中还检测到了多种杀菌剂/金属抗性基因（B/MRGs）和可移动遗传元素（MGEs），包括前噬菌体、质粒、整合子和转座子。更重要的是，通过ACCs进行的共生分析表明，ARGs与B/MRGs和MGEs之间存在着很强的关联，表明ARGs在河流环境中具有很高的协同选择和水平主动传播的潜力，这可能是该地区人类活动频繁影响的驱动力。

        River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7-1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas, Pseudoxanthomonas, Arenimonas, Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area.

        https://www.sciencedirect.com/science/article/pii/S0269749118341083?via%3Dihub