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Comparative genomics of carriage and disease isolates of Streptococcus pneumoniae serotype 22F reveals lineage specific divergence and niche adaptation

Comparative genomics of carriage and disease isolates of Streptococcus pneumoniae serotype 22F reveals lineage specific divergence and niche adaptation
Comparative genomics of carriage and disease isolates of Streptococcus pneumoniae serotype 22F reveals lineage specific divergence and niche adaptation
Streptococcus pneumoniaeis a major cause of meningitis, sepsis and pneumonia worldwide. Pneumococcal conjugate vaccines (PCV) have been part of the UK's childhood immunisation programme since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types (MLST) 433 and 698) and conducted comparative genomic analysis on four isolates, paired by ST with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of non-synonymous mutations inpgdA, encoding peptidoglycanN-acetylglucosamine deacetylase A, which were found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Whilst no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonisation, including: bacteriocins, lantibiotics, and toxin-antitoxin systems, were also observed.
1759-6653
1243-1251
Cleary, D.W.
f4079c6d-d54b-4108-b346-b0069035bec0
Devine, V.T.
ce4845c0-7013-4e4f-9f57-e1616cc96e98
Jefferies, J.M.C.
9468e292-0b41-412d-9470-944e257c7bcf
Webb, J.S.
ec0a5c4e-86cc-4ae9-b390-7298f5d65f8d
Bentley, S.D.
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Gladstone, R.A.
c75d747c-0663-49e3-8d81-4e797eb79d0a
Faust, S.N.
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, S.C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Cleary, D.W.
f4079c6d-d54b-4108-b346-b0069035bec0
Devine, V.T.
ce4845c0-7013-4e4f-9f57-e1616cc96e98
Jefferies, J.M.C.
9468e292-0b41-412d-9470-944e257c7bcf
Webb, J.S.
ec0a5c4e-86cc-4ae9-b390-7298f5d65f8d
Bentley, S.D.
633dc14f-9cef-4fba-b267-83d87a4f45a6
Gladstone, R.A.
c75d747c-0663-49e3-8d81-4e797eb79d0a
Faust, S.N.
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, S.C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17

Cleary, D.W., Devine, V.T., Jefferies, J.M.C., Webb, J.S., Bentley, S.D., Gladstone, R.A., Faust, S.N. and Clarke, S.C. (2016) Comparative genomics of carriage and disease isolates of Streptococcus pneumoniae serotype 22F reveals lineage specific divergence and niche adaptation. Genome Biology and Evolution, 8 (4), 1243-1251. (doi:10.1093/gbe/evw066). (PMID:27016484)

Record type: Article

Abstract

Streptococcus pneumoniaeis a major cause of meningitis, sepsis and pneumonia worldwide. Pneumococcal conjugate vaccines (PCV) have been part of the UK's childhood immunisation programme since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types (MLST) 433 and 698) and conducted comparative genomic analysis on four isolates, paired by ST with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of non-synonymous mutations inpgdA, encoding peptidoglycanN-acetylglucosamine deacetylase A, which were found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Whilst no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonisation, including: bacteriocins, lantibiotics, and toxin-antitoxin systems, were also observed.

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Accepted/In Press date: 11 March 2016
e-pub ahead of print date: 24 March 2016
Organisations: Clinical & Experimental Sciences

Identifiers

Local EPrints ID: 391261
URI: https://eprints.soton.ac.uk/id/eprint/391261
ISSN: 1759-6653
PURE UUID: 71342a17-92c8-48f8-b298-3cbf3e986e8b
ORCID for D.W. Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for J.S. Webb: ORCID iD orcid.org/0000-0003-2068-8589
ORCID for S.N. Faust: ORCID iD orcid.org/0000-0003-3410-7642
ORCID for S.C. Clarke: ORCID iD orcid.org/0000-0002-7009-1548

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Date deposited: 11 Apr 2016 09:39
Last modified: 03 Dec 2019 01:46

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