Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France.
Environ Microbiol. 2022 Sep;24(9):4317-4328. doi: 10.1111/1462-2920.16083. Epub 2022 Jun 7.
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.
水生环境是抗生素耐药基因（ARGs）从病原体细菌传播到其他细菌的重要途径。然而，在这些复杂的基质中，识别和描述驱动微生物因子及其参与的 ARG 传播机制仍然具有挑战性。我们在这里探索了一组 ARGs 和可移动遗传元件（MGEs）在法国奥恩河生态系统中采集的水中、悬浮物质和底泥中的细菌和噬菌体中的分布/区室化。通过使用一种新的噬菌体 DNA 提取方法，我们表明，在包装细菌 DNA 时，噬菌体比 16S rRNA 基因更能同时封装 ARGs 和 MGEs，即染色体片段。我们还表明，细菌和噬菌体衣壳内容物中的 ARGs/MGEs 受季节性的影响相似，但当这些标记物由细菌携带时，ARGs/MGEs 在河流物理隔室（水与悬浮物质与沉积物）之间的分布受到的影响更大。这些证明可能会改变我们对环境中转导病毒颗粒形成和命运的理解。因此，它们还可能通过加强环境噬菌体和转导在传播抗生素耐药性方面的作用，改变我们对不同水平基因转移机制传播抗生素耐药性的相对频率的估计。
