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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

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
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.
1471-2164
187-[15pp]
Boissy, Robert
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Ahmed, Azad
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Janto, Benjamin
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Earl, Josh
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Hall, Barry G
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Hogg, Justin S
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Pusch, Gordon D
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Hiller, N Luisa
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Powell, Evan
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Hayes, Jay D
a436a383-9cdc-4fb6-8dda-89f6b0a2ec1a
Yu, Susan
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Kathju, Sandeep
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Stoodley, Paul
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Post, J Christopher
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Ehrlich, Garth D
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Hu, Fen Z
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Boissy, Robert
305ae798-afc8-4123-9a07-889aa1d41dd4
Ahmed, Azad
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Janto, Benjamin
60d7d2fe-8118-4973-9c7a-1f26410a2073
Earl, Josh
3abcd42d-6bba-42d0-84bf-7d48d93d4174
Hall, Barry G
47fe9faa-98dd-42c1-aff4-a490fcd3ecc2
Hogg, Justin S
c9605752-5d1a-4f23-874c-f658c783f1f7
Pusch, Gordon D
520bcf39-d830-4c9d-a2e1-aa6d485098b7
Hiller, N Luisa
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Powell, Evan
ecaa4d3a-a58e-4d5c-b00a-b097ace26a7f
Hayes, Jay D
a436a383-9cdc-4fb6-8dda-89f6b0a2ec1a
Yu, Susan
e265601b-0b8a-4948-a18d-7eb946813f15
Kathju, Sandeep
80cdb7ee-2e0d-4e70-98c9-93682ce05a09
Stoodley, Paul
08614665-92a9-4466-806e-20c6daeb483f
Post, J Christopher
d6d584b1-78bd-44cf-a8f4-255b88ffa904
Ehrlich, Garth D
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Hu, Fen Z
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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: https://eprints.soton.ac.uk/id/eprint/185789
ISSN: 1471-2164
PURE UUID: 1cf78f61-892b-47cf-8b60-331f269b7f21
ORCID for Paul Stoodley: ORCID iD orcid.org/0000-0001-6069-273X

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Date deposited: 11 May 2011 08:34
Last modified: 12 Nov 2019 01:42

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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 ORCID iD
Author: J Christopher Post
Author: Garth D Ehrlich
Author: Fen Z Hu

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