Aquatic environments are important dissemination routes of antibiotic resistance genes (ARGs) from and to pathogenic bacteria. Nevertheless, in these complex matrices, identifying and characterizing the driving microbial actors and ARG dissemination mechanisms they are involved in remain difficult. We here explored the distribution/compartmentalization of a panel of ARGs and mobile genetic elements (MGEs) in bacteria and bacteriophages collected in the water, suspended material and surface sediments from the Orne River ecosystem (France). By using a new bacteriophage DNA extraction method, we showed that, when packaging bacterial DNA, bacteriophages rather encapsidate both ARGs and MGEs than 16S rRNA genes, i.e. chromosomal fragments. We also show that the bacteria and bacteriophage capsid contents in ARGs/MGEs were similarly influenced by seasonality but that the distribution of ARGs/MGEs between the river physical compartments (water vs. suspended mater vs. sediment) is more impacted when these markers were carried by bacteria. These demonstrations will likely modify our understanding of the formation and fate of transducing viral particles in the environment. Consequently, they will also likely modify our estimations of the relative frequencies of the different horizontal gene transfer mechanisms in disseminating antibiotic resistance by reinforcing the roles played by environmental bacteriophages and transduction.

中文翻译：

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噬菌体在奥恩河生态系统中携带大量细菌来源的抗生素耐药性决定因素

水生环境是抗生素抗性基因（ARGs）从病原菌传播到病原菌的重要传播途径。然而，在这些复杂的基质中，识别和表征驱动微生物行为者及其参与的 ARG 传播机制仍然很困难。我们在这里探索了一组 ARG 和移动遗传元件 (MGE) 在奥恩河生态系统（法国）的水、悬浮物质和表面沉积物中收集的细菌和噬菌体中的分布/划分。通过使用一种新的噬菌体 DNA 提取方法，我们发现，在包装细菌 DNA 时，噬菌体将 ARGs 和 MGEs 都包裹在壳内，而不是 16S rRNA 基因，即染色体片段。我们还表明，ARGs/MGEs 中的细菌和噬菌体衣壳含量同样受季节性影响，但是当携带这些标记时，河流物理隔间（水与悬浮物质与沉积物）之间的 ARGs/MGEs 分布受到更大影响由细菌。这些演示可能会改变我们对在环境中转导病毒颗粒的形成和命运的理解。因此，他们也可能通过加强环境噬菌体和转导所发挥的作用来修改我们对不同水平基因转移机制在传播抗生素抗性中的相对频率的估计。当这些标记被细菌携带时，沉积物）受到的影响更大。这些演示可能会改变我们对在环境中转导病毒颗粒的形成和命运的理解。因此，他们也可能通过加强环境噬菌体和转导所发挥的作用来修改我们对不同水平基因转移机制在传播抗生素抗性中的相对频率的估计。当这些标记被细菌携带时，沉积物）受到的影响更大。这些演示可能会改变我们对在环境中转导病毒颗粒的形成和命运的理解。因此，他们也可能通过加强环境噬菌体和转导所发挥的作用来修改我们对不同水平基因转移机制在传播抗生素抗性中的相对频率的估计。