Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae Using a modification of the finite supragenome model

BMC Genomics

Research Article

Susan Yu¹  Benjamin Janto¹  Evan Powell¹  Luisa N Hiller¹  Josh Earl¹  Jay Hayes¹  Azad Ahmed¹  Barry G Hall²  Robert Boissy³  Paul Stoodley⁴  J Christopher Post⁵  Fen Z Hu⁵  Garth D Ehrlich⁵  Sandeep Kathju⁵  Gordon D Pusch⁶  Justin S Hogg⁷ 

[1] Center for Genomic Sciences, Allegheny-Singer Research Institute, 320 East North Ave, 15212, Pittsburgh, PA, USA;Center for Genomic Sciences, Allegheny-Singer Research Institute, 320 East North Ave, 15212, Pittsburgh, PA, USA;Bellingham Research Institute, 218 Chuckanut Point Rd, 98229, Bellingham, WA, USA;Center for Genomic Sciences, Allegheny-Singer Research Institute, 320 East North Ave, 15212, Pittsburgh, PA, USA;Department of Internal Medicine, University of Nebraska Medical Center, 68198, Omaha, NE, USA;Center for Genomic Sciences, Allegheny-Singer Research Institute, 320 East North Ave, 15212, Pittsburgh, PA, USA;Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny General Hospital, Allegheny Campus, 15212, Pittsburgh, PA, USA;Center for Genomic Sciences, Allegheny-Singer Research Institute, 320 East North Ave, 15212, Pittsburgh, PA, USA;Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny General Hospital, Allegheny Campus, 15212, Pittsburgh, PA, USA;Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Allegheny General Hospital, Allegheny Campus, 15212, Pittsburgh, PA, USA;Fellowship for Interpretation of Genomes, 60527, Burr Ridge, IL, USA;Computation Institute, University of Chicago, 60637, Chicago, IL, USA;Joint Carnegie Mellon University - University of Pittsburgh Doctoral Program in Computational Biology, University of Pittsburgh, 15260, Pittsburgh, PA, USA;

关键词: Horizontal Gene Transfer;    Haemophilus Influenzae;    Core Gene;    Necrotizing Fasciitis;    mecA Gene;   

DOI  :  10.1186/1471-2164-12-187

 received in 2011-02-02, accepted in 2011-04-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundStaphylococcus 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.ResultsWe 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.ConclusionsUsing 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.

【 授权许可】

Unknown   
© Boissy et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.