Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model.
Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model.
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DOI：
10.1186/1471-2164-12-187
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发表时间：
2011-04-13
期刊：
影响因子：
4.4
通讯作者：
Hu FZ
中科院分区：
文献类型：
--
作者：
Boissy R;Ahmed A;Janto B;Earl J;Hall BG;Hogg JS;Pusch GD;Hiller LN;Powell E;Hayes J;Yu S;Kathju S;Stoodley P;Post JC;Ehrlich GD;Hu FZ
金黄色葡萄球菌与其人类宿主从携带到败血症的一系列共生关系相关，并且经常与医院和社区获得性感染相关，因此菌株之间的差异基因含量是令人感兴趣的。我们对三种临床菌株进行了测序，并将这些数据与13种临床可用的人分离株和一种牛菌株进行了比较基因组分析。使用RAST对所有基因组进行注释，然后描绘它们的基因相似性和差异。基因聚类得到3，155个直向同源基因簇，其中2，266个是核心基因簇，755个是分布基因簇，134个是独特基因簇。单个基因组包含2，524至2，648个基因。所有可能的S.金黄色葡萄球菌菌株对（n = 136）显示296个基因的平均差异和476个基因的最大差异。我们开发了一个有限超基因组模型的修订版本来估计S。金黄色葡萄球菌超基因组（3，221个基因，2，245个核心基因），并与流感嗜血杆菌和肺炎链球菌的超基因组进行比较。RAST的注释和我们的CDS聚类程序之间有很好的一致性，提供了高保真的代谢组学子系统分析，以扩展我们对这些菌株的比较基因组学表征。使用多物种的比较超基因组分析，使我们的有限超基因组模型的改进版本，我们提供的数据和解释解释相对较大的核心基因组的S。金黄色葡萄球菌与其他鼻咽机会性病原体相比。此外，我们提供独立验证我们的正交基因聚类算法的效率和有效性。
Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the differential gene content among strains is of interest. We sequenced three clinical strains and combined these data with 13 publically available human isolates and one bovine strain for comparative genomic analyses. All genomes were annotated using RAST, and then their gene similarities and differences were delineated. Gene clustering yielded 3,155 orthologous gene clusters, of which 2,266 were core, 755 were distributed, and 134 were unique. Individual genomes contained between 2,524 and 2,648 genes. Gene-content comparisons among all possible S. aureus strain pairs (n = 136) revealed a mean difference of 296 genes and a maximum difference of 476 genes. We developed a revised version of our finite supragenome model to estimate the size of the S. aureus supragenome (3,221 genes, with 2,245 core genes), and compared it with those of Haemophilus influenzae and Streptococcus pneumoniae. There was excellent agreement between RAST's annotations and our CDS clustering procedure providing for high fidelity metabolomic subsystem analyses to extend our comparative genomic characterization of these strains. Using a multi-species comparative supragenomic analysis enabled by an improved version of our finite supragenome model we provide data and an interpretation explaining the relatively larger core genome of S. aureus compared to other opportunistic nasopharyngeal pathogens. In addition, we provide independent validation for the efficiency and effectiveness of our orthologous gene clustering algorithm.
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影响因子：
12.3
作者：
Hogg JS;Hu FZ;Janto B;Boissy R;Hayes J;Keefe R;Post JC;Ehrlich GD
通讯作者：
Ehrlich GD
影响因子：
4.5
作者：
Halpern, David;Chiapello, Helene;El Karoui, Meriem
通讯作者：
El Karoui, Meriem
影响因子：
2.8
作者：
Hall, Barry G.;Ehrlich, Garth D.;Hu, Fen Z.
通讯作者：
Hu, Fen Z.
影响因子：
120.7
作者：
Klevens, R. Monina;Morrison, Melissa A.;Fridkin, Scott K.
通讯作者：
Fridkin, Scott K.
影响因子：
5.8
作者：
Grasso, C;Lee, C
通讯作者：
Lee, C