Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Animal and Plant Health Agency, Weybridge, Addlestone, UK.
ISME J. 2021 Aug;15(8):2322-2335. doi: 10.1038/s41396-021-00926-w. Epub 2021 Mar 1.
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
F 型质粒具有多样性，且具有重要的临床意义，通常携带赋予抗生素耐药性（AMR）的基因，如广谱β-内酰胺酶，尤其是在肠杆菌目中。组织这种质粒多样性具有挑战性，目前的知识主要基于临床环境中的质粒。在这里，我们对来自环境（进水、出水和废水处理厂周围的上游/下游水道）和牲畜环境的大量 F 型质粒的大型调查进行了网络社区分析。我们使用一种易于处理和扩展的方法来检查质粒元数据和网络社区之间的关系。这揭示了生态位（采样室和宿主属）如何划分和塑造质粒多样性。我们还对网络社区进行了泛基因组分析。我们表明，这些社区定义了独特的核心基因组合，重叠有限。基于这些核心基因的比对构建质粒系统发育树，我们证明了质粒辅助功能与核心基因含量密切相关。总之，我们的结果表明，稳定的 F 型质粒骨架结构可以在环境中存在，同时允许辅助基因含量发生巨大变化，这可能与生态位适应有关。F 型质粒与 AMR 的关联可能反映了它们在快速适应生态位方面的适用性。
