摘要
      质粒携带具有抗微生物耐药性（AMR）和其他临床重要特征的基因；它们在物种内部和物种之间移动的能力可能为这些基因的快速传播提供了机制。现有的使用完整质粒组装体的研究对可靠推断至关重要，但研究规模较小和/或仅限于携带特别抗微生物耐药性基因（ARGs）的研究。在这项研究中，我们对2009年和2018年英国牛津郡血液感染（BSI）的738个分离株（194个分离株）中的1880个完整质粒进行了测序，并对其间年份的分层选择（176个分离物）进行了测序。我们证明，质粒在很大程度上，但不是完全局限于宿主物种，尽管质粒基因库的物种之间有很大的重叠。大多数ARGs由相对较少的具有可预测生物学特征的质粒组携带。携带ARGs的质粒（包括编码碳青霉烯酶的质粒）与不携带此类基因的质粒共享假定的核心基因“主干”。这些发现表明，除了追踪目前与临床重要基因相关的质粒外，未来的监测还应侧重于识别和监测具有快速获取和传播这些基因潜力的高危质粒群的传播。
Abstract
Plasmids carry genes conferring antimicrobial resistance (AMR), and other clinically important traits; their ability to move within and between species may provide the machinery for rapid dissemination of such genes. Existing studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to those carrying particularly antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections (BSI) in 2009 (194 isolates) and 2018 (368 isolates) in Oxfordshire, UK, plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.

https://www.medrxiv.org/content/10.1101/2022.04.03.22273290v3