Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA.
Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, USA; Department of Occupational and Environmental Health, George Washington University, Washington, DC, USA.
mSphere. 2016 Jun 29;1(4). doi: 10.1128/mSphere.00121-16. eCollection 2016 Jul-Aug.
The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B- plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B- plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131's evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage's success.
肠外致病性大肠杆菌（ExPEC）H30 亚克隆属于序列型 131（ST131-H30），它突然成为导致人类疾病的 ExPEC 的主要谱系。ST131-H30 谱系在系统发育上已经得到了很好的描述，但它的质粒组成并不完全清楚。在这里，单分子实时测序被用来生成 ST131-H30 分离株和其他 ST131 分支的完整质粒序列。比较分析显示，不同的 F 型质粒塑造了主要氟喹诺酮耐药 ST131-H30 分支的进化。具体来说，一种 F1:A2:B20 质粒与 H30R/C1 分支强烈相关，而一种 F2:A1:B-质粒与 H30Rx/C2 分支相关。一系列涉及 IS26 的质粒基因丢失、获得和重排可能导致每个 ST131-H30 亚谱系内目前的质粒组成，其中包含几个具有毒力和适应性功能的重叠基因簇，表明质粒介导的趋同进化。有证据表明，与 H30Rx/C2 相关的 F2:A1:B-质粒类型存在于获得氟喹诺酮耐药之前以及携带 bla CTX-M-15 的多药耐药基因盒之前的菌株祖先中。体外实验表明，在宿主菌株之间存在低频率的质粒转移，即使在密切相关的 ST131-H30 菌株之间，质粒稳定性也存在差异，并且这些质粒在 H30R/Rx 谱系中的携带可能存在上位性。
一种被称为 ST131 的大肠杆菌克隆谱系已经成为导致人类肠外感染的主要菌株类型。ST131 大肠杆菌的进化历史现在已经得到很好的理解。然而，质粒在 ST131 的进化历史中的作用还没有被很好地定义。本研究利用实时单分子测序技术比较了来自 ST131 的各种当前和历史谱系的质粒。从这项工作中可以确定，一系列质粒的获得、丢失和重组事件导致了目前 ST131 菌株的流行质粒。这些质粒似乎已经进化到在多次获得相似的基因簇，表明可能存在质粒介导的趋同进化，从而导致进化成功。这些质粒似乎也更适合存在于 ST131 的特定菌株中，因为存在共适应突变。总的来说，一系列事件使 ST131 质粒得以进化，这可能有助于该谱系的成功。
