Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium.
Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium.
复制标题
DOI：
10.1371/journal.pone.0030187
复制
发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Murray BE
中科院分区：
文献类型：
--
作者：
Galloway-Peña J;Roh JH;Latorre M;Qin X;Murray BE
最近的研究指出存在两个屎肠球菌亚群，一个主要包含肠道/社区相关（CA）菌株，另一个包含大多数临床或医院相关（HA）菌株，包括通过多位点序列分型（MLST）归类为CC 17组的菌株。HA亚群更经常地具有IS 16、致病性岛以及与抗生素抗性、定殖和/或毒力相关的质粒或基因。支持两个进化枝概念，我们先前发现来自HA进化枝菌株与CA进化枝菌株的四个基因之间存在3-10%的差异，包括氨苄青霉素抗性HA菌株的pbp 5-R与氨苄青霉素敏感CA菌株的pbp 5-S之间存在5%的差异。为了进一步研究这些亚群的核心基因组，我们研究了来自21个E.屎基因组序列;我们的分析串联序列，单核苷酸多态性和单个基因都确定了两个不同的群体。利用串联序列，HA进化枝菌株彼此相差0-1%，而CA进化枝菌株彼此相差0- 1.1%，两个进化枝之间的差异为3.5-4.2%。虽然许多菌株有少数基因聚在一个分支中，而它们的大多数基因在另一个分支中，但一个菌株有28%的基因在CA分支中，72%的基因在HA分支中，这与重组在E.屎室使用大肠杆菌的估计，使用sSNP分析的分子钟计算表明，这两个分支可能在≥ 100万年前发生了分歧，或者使用炭疽杆菌的较高突变率，大约30万年前。这些数据证实了E.表明HA和CA进化枝之间的差异发生在核心基因组水平，并且早在现代抗生素时代之前。
Recent studies have pointed to the existence of two subpopulations of Enterococcus faecium, one containing primarily commensal/community-associated (CA) strains and one that contains most clinical or hospital-associated (HA) strains, including those classified by multi-locus sequence typing (MLST) as belonging to the CC17 group. The HA subpopulation more frequently has IS16, pathogenicity island(s), and plasmids or genes associated with antibiotic resistance, colonization, and/or virulence. Supporting the two clades concept, we previously found a 3–10% difference between four genes from HA-clade strains vs. CA-clade strains, including 5% difference between pbp5-R of ampicillin-resistant, HA strains and pbp5-S of ampicillin-sensitive, CA strains. To further investigate the core genome of these subpopulations, we studied 100 genes from 21 E. faecium genome sequences; our analyses of concatenated sequences, SNPs, and individual genes all identified two distinct groups. With the concatenated sequence, HA-clade strains differed by 0–1% from one another while CA clade strains differed from each other by 0–1.1%, with 3.5–4.2% difference between the two clades. While many strains had a few genes that grouped in one clade with most of their genes in the other clade, one strain had 28% of its genes in the CA clade and 72% in the HA clade, consistent with the predicted role of recombination in the evolution of E. faecium. Using estimates for Escherichia coli, molecular clock calculations using sSNP analysis indicate that these two clades may have diverged ≥1 million years ago or, using the higher mutation rate for Bacillus anthracis, ∼300,000 years ago. These data confirm the existence of two clades of E. faecium and show that the differences between the HA and CA clades occur at the core genomic level and long preceded the modern antibiotic era.
登录
查看更多内容
影响因子：
5.4
作者：
Klare, I;Konstabel, C;Witte, W
通讯作者：
Witte, W
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
影响因子：
4.9
作者：
Galloway-Pena, Jessica R.;Rice, Louis B.;Murray, Barbara E.
通讯作者：
Murray, Barbara E.
影响因子：
5.4
作者：
Pearson T;Giffard P;Beckstrom-Sternberg S;Auerbach R;Hornstra H;Tuanyok A;Price EP;Glass MB;Leadem B;Beckstrom-Sternberg JS;Allan GJ;Foster JT;Wagner DM;Okinaka RT;Sim SH;Pearson O;Wu Z;Chang J;Kaul R;Hoffmaster AR;Brettin TS;Robison RA;Mayo M;Gee JE;Tan P;Currie BJ;Keim P
通讯作者：
Keim P
影响因子：
6.7
作者：
Leavis HL;Willems RJ;van Wamel WJ;Schuren FH;Caspers MP;Bonten MJ
通讯作者：
Bonten MJ