摘要

       河流通常被认为是环境中抗生素抗性基因 (ARG) 的天然储存库。为了预防和控制 ARG 风险，全面表征河流系统中的抗生素抗性组及其关联至关重要。在这项研究中，我们提出了一个宏基因组框架，用于从多个类别中识别河流沉积物中的抗生素抗性组，包括 ARG 潜力、ARG 宿主、致病性潜力、共选择潜力和基因转移潜力，并将其应用于了解存在、宿主和北京某城市河流沉积物中ARGs的共存[J].结果表明，在河流沉积物中共检测到203个ARG亚型，属于21个ARG类型，丰度范围为107.7-1004.1×/Gb，以多药、大环内酯-林可酰胺-链球菌素、杆菌肽、喹诺酮和磺胺类抗性基因为主。宿主追踪分析确定脱氯单胞菌、假单胞菌属、沙单胞菌属、溶杆菌属和假单胞菌属是 ARG 的主要宿主。许多携带 ARG 的重叠群 (ACCs) 被注释为病原菌的片段，并携带多个多药 ARG。此外，在河流沉积物中检测到各种杀生物剂/金属抗性基因（B/MRGs）和移动遗传元件（MGEs），包括原噬菌体、质粒、整合子和转座子。更重要的是，通过 ACCs 的共现分析显示 ARGs 与 B/MRGs 和 MGEs 有很强的关联，表明河流环境中 ARGs 的共同选择和主动水平传播的潜力很大，可能是由人为活动的频繁影响驱动的在那个区域。

       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/abs/pii/S0269749118341083