总结
      水生环境是抗生素抗性基因（ARGs）从致病菌传播到致病菌的重要途径。然而，在这些复杂的基质中，识别和表征它们所涉及的驱动微生物因子和ARG传播机制仍然很困难。我们在这里探索了一组ARGs和可移动遗传元素（MGE）在奥恩河生态系统（法国）的水中、悬浮物质和表面沉积物中收集的细菌和噬菌体中的分布/区隔。通过使用一种新的噬菌体DNA提取方法，我们发现，当包装细菌DNA时，噬菌体更包裹ARG和MGE，而不是16S rRNA基因，即染色体片段。我们还表明，ARGs/MGE中的细菌和噬菌体衣壳含量同样受到季节性的影响，但当细菌携带这些标志物时，ARGs/MGE在河流物理分区（水与悬浮物质与沉积物）之间的分布受到更大的影响。这些演示可能会改变我们对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起的作用，改变我们对不同水平基因转移机制在传播抗生素耐药性中的相对频率的估计。
Summary
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.

https://ami-journals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.16083