Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.
复制标题
DOI：
10.1186/1471-2180-12-135
复制
发表时间：
2012-07-07
期刊：
影响因子：
4.2
通讯作者：
Murray BE
中科院分区：
文献类型：
--
作者：
Qin X;Galloway-Peña JR;Sillanpaa J;Roh JH;Nallapareddy SR;Chowdhury S;Bourgogne A;Choudhury T;Muzny DM;Buhay CJ;Ding Y;Dugan-Rocha S;Liu W;Kovar C;Sodergren E;Highlander S;Petrosino JF;Worley KC;Gibbs RA;Weinstock GM;Murray BE
在美国和欧洲，肠球菌是医院获得性感染的主要原因之一，粪肠球菌和屎肠球菌是从肠球菌感染中分离出来的两种最常见的物种。在过去十年中，粪肠球菌引起的肠球菌感染比例与其他肠球菌相比稳步上升。虽然在医院环境中粪肠杆菌逐渐被粪肠杆菌取代的潜在机制尚不清楚，但许多使用基因分型和系统发育分析的研究表明，在临床环境中出现了全球分散的粪肠杆菌多克隆亚群。由于缺乏封闭完整的粪肠杆菌基因组作为参考，阻碍了对粪肠杆菌分子流行病学和发病机制的系统研究。在这项研究中，我们报道了粪肠杆菌TX16（也称为DO）的全基因组序列，它属于多位点序列型（ST） 18，是迄今为止第一个被测序的粪肠杆菌菌株。TX16基因组与21个粪肠杆菌草图基因组的全基因组比较证实，除了非医院来源的菌株外，大多数临床、疫情和医院相关（HA）菌株（包括st16、17、18和78）通过系统发育和基因含量相似性分析，它们在进化上的亲缘关系比在群落相关（CA）进化枝中的分离物要密切得多，在核心基因组水平上，两个进化枝之间的平均核苷酸序列差异约为3-4%。我们的研究还揭示了TX16基因组中的许多基因组位点是HA进化支所特有的。TX16中的380个orf是ha枝特异性的，并且在ha枝菌株中富含抗生素抗性基因。如先前报道的那样，在HA菌株中几乎只发现了IS16和转座子等可移动元件。我们的研究结果以及其他研究表明，HA克隆谱系具有特定的遗传元素以及核心基因组序列差异，这可能赋予比异质CA E. faecium分离株更大的选择优势。这些差异中的哪一种对于特定粪肠杆菌谱系在医院环境中的成功繁殖是重要的仍有待确定。
Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references. In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3–4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported. Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.
登录
查看更多内容
影响因子：
3.7
作者：
de Regt MJ;van Schaik W;van Luit-Asbroek M;Dekker HA;van Duijkeren E;Koning CJ;Bonten MJ;Willems RJ
通讯作者：
Willems RJ
影响因子：
12.3
作者：
Bourgogne, Agathe;Garsin, Danielle A.;Qin, Xiang;Singh, Kavindra V.;Sillanpaa, Jouko;Yerrapragada, Shailaja;Ding, Yan;Dugan-Rocha, Shannon;Buhay, Christian;Shen, Hua;Chen, Guan;Williams, Gabrielle;Muzny, Donna;Maadani, Arash;Fox, Kristina A.;Gioia, Jason;Chen, Lei;Shang, Yue;Arias, Cesar A.;Nallapareddy, Sreedhar R.;Zhao, Meng;Prakash, Vittal P.;Chowdhury, Shahreen;Jiang, Huaiyang;Gibbs, Richard A.;Murray, Barbara E.;Highlander, Sarah K.;Weinstock, George M.
通讯作者：
Weinstock, George M.
影响因子：
3.2
作者：
Carias, LL;Rudin, SD;Rice, LB
通讯作者：
Rice, LB
影响因子：
3.2
作者：
ARTHUR, M;MOLINAS, C;COURVALIN, P
通讯作者：
COURVALIN, P
影响因子：
14.9
作者：
Besemer, J;Borodovsky, M
通讯作者：
Borodovsky, M