Comparative genomic analyses of seventeen Streptococcus pneumoniae strains:: Insights into the pneumococcal supragenome

被引:209
作者
Hiller, N. Luisa
Janto, Benjamin
Hogg, Justin S.
Boissy, Robert
Yu, Susan
Powell, Evan
Keefe, Randy
Ehrlich, Nathan E.
Shen, Kai
Hayes, Jay
Barbadora, Karen
Klimke, William
Dernovoy, Dmitry
Tatusova, Tatiana
Parkhill, Julian
Bentley, Stephen D.
Post, J. Christopher
Ehrlich, Garth D.
Hu, Fen Z.
机构
[1] Allegheny Gen Hosp, Allegheny Singer Res Inst, Ctr Genom Sci, Pittsburgh, PA 15212 USA
[2] Drexel Univ, Coll Med, Dept Microbiol & Immunol, Pittsburgh, PA 15212 USA
[3] Childrens Hosp Pittsburgh, Pittsburgh, PA 15213 USA
[4] NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA
[5] Sanger Inst, Cambridge CB10 1SA, England
基金
英国惠康基金;
关键词
D O I
10.1128/JB.00690-07
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
The distributed-genome hypothesis (DGH) states that pathogenic bacteria possess a supragenome that is much larger than the genome of any single bacterium and that these pathogens utilize genetic recombination and a large, noncore set of genes as a means of diversity generation. We sequenced the genomes of eight nasopharyngeal strains of Streptococcus pneumoniae isolated from pediatric patients with upper respiratory symptoms and performed quantitative genomic analyses among these and nine publicly available pneumococcal strains. Coding sequences from all strains were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%) were conserved among all 17 strains. The majority of the gene clusters, 1,716 (54%), were not found in all strains. Genic differences per strain pair ranged from 35 to 629 orthologous clusters, with each strain's genome containing between 21 and 32% noncore genes. The distribution of the orthologous clusters per genome for the 17 strains was entered into the finite-supragenome model, which predicted that (i) the S. pneumoniae supragenome contains more than 5,000 orthologous clusters and (ii) 99% of the orthologous clusters (similar to 3,000) that are represented in the S. pneumoniae population at frequencies of >= 0.1 can be identified if 33 representative genomes are sequenced. These extensive genic diversity data support the DGH and provide a basis for understanding the great differences in clinical phenotype associated with various pneumococcal strains. When these findings are taken together with previous studies that demonstrated the presence of a supragenome for Streptococcus agalactiae and Haemophilus influenzae, it appears that the possession of a distributed genome is a common host interaction strategy.
引用
收藏
页码:8186 / 8195
页数:10
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