Gordon David M, Geyik Sarah, Clermont Olivier, O'Brien Claire L, Huang Shiwei, Abayasekara Charmalie, Rajesh Ashwin, Kennedy Karina, Collignon Peter, Pavli Paul, Rodriguez Christophe, Johnston Brian D, Johnson James R, Decousser Jean-Winoc, Denamur Erick
Ecology and Evolution, Research School of Biology, the Australian National University, Acton, Australian Capital Territory, Australia.
UMR 1137 INSERM and Université Paris Diderot, IAME, Sorbonne Paris Cité, Paris, France.
mSphere. 2017 May 31;2(3). doi: 10.1128/mSphere.00168-17. eCollection 2017 May-Jun.
The lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.
被称为克隆复合体95（CC95）的谱系是一种与人类相关的全球分布谱系，在人类肠道外感染中占相当大的比例。来自不同来源的200株CC95菌株的全基因组序列数据使得能够确定CC95泛基因组。泛基因组分析表明，该复合体的菌株可分为五个亚组之一，这些亚组在血清型、肠道外毒力、毒力基因含量和抗生素抗性基因谱方面存在差异。使用基于PCR的方法对从法国、澳大利亚和美国的人类中分离出的总共511株CC95菌株进行了亚组成员筛选。CC95亚组在地理起源方面呈非随机分布。亚组的相对频率显示随时间变化，尽管变化的性质因大陆而异。亚组的菌株在分离源（血液、尿液或粪便）和宿主性别方面也呈非随机分布。总体而言，证据表明，尽管属于CC95的菌株可能是全球性的，但人类流动模式不足以使CC95亚组的分布均匀化。相反，CC95菌株的进化方式似乎在空间和时间上都有所不同。尽管CC95菌株作为大流行菌株出现在全球，但精细结构分析显示了CC95亚组的流行模式。此外，单个地点CC95亚组的相对频率随时间变化的观察结果表明，亚组的相对适应性发生了变化。克隆复合体95代表了一个全球分布、遗传多样的谱系，在该谱系中观察到的广泛亚结构在流行病学和临床上具有相关性。在过去15年中，CC95菌株导致肠道外感染的频率似乎一直稳定。然而，在这个谱系中鉴定出的不同亚组具有取决于宿主、样本、大陆和时间的流行结构。因此，属于CC95的菌株的进化和传播与另一个全球分布的与人类相关的克隆复合体CC131非常不同，由于两个非常密切相关、几乎单态的谱系的进化和传播，CC131作为肠道外感染原因的频率在过去15年中显著增加。
