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Comparative supragenomic analyses among the pathogens staphylococcus aureus, streptococcus pneumoniae, and haemophilus influenzae using a modification of the finite supragenome model

Boissy, Robert, Ahmed, Azad, Janto, Benjamin, Earl, Josh, Hall, Barry G, Hogg, Justin S, Pusch, Gordon D, Hiller, N Luisa, Powell, Evan, Hayes, Jay D, Yu, Susan, Kathju, Sandeep, Stoodley, Paul, Post, J Christopher, Ehrlich, Garth D and Hu, Fen Z (2011) Comparative supragenomic analyses among the pathogens staphylococcus aureus, streptococcus pneumoniae, and haemophilus influenzae using a modification of the finite supragenome model BMC Genomics, 12, (1), 187-[15pp]. (doi:10.1186/1471-2164-12-187). (PMID:21489287).

Record type: Article

Abstract

Background: 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.

Results: 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.

Conclusions: 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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Published date: 13 April 2011
Organisations: Engineering Mats & Surface Engineerg Gp

Identifiers

Local EPrints ID: 185789
URI: http://eprints.soton.ac.uk/id/eprint/185789
ISSN: 1471-2164
PURE UUID: 1cf78f61-892b-47cf-8b60-331f269b7f21

Catalogue record

Date deposited: 11 May 2011 08:34
Last modified: 18 Apr 2017 02:15

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Contributors

Author: Robert Boissy
Author: Azad Ahmed
Author: Benjamin Janto
Author: Josh Earl
Author: Barry G Hall
Author: Justin S Hogg
Author: Gordon D Pusch
Author: N Luisa Hiller
Author: Evan Powell
Author: Jay D Hayes
Author: Susan Yu
Author: Sandeep Kathju
Author: Paul Stoodley
Author: J Christopher Post
Author: Garth D Ehrlich
Author: Fen Z Hu

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