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Putative novel cps loci in a large global collection of pneumococci

Putative novel cps loci in a large global collection of pneumococci
Putative novel cps loci in a large global collection of pneumococci
The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18  000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6  % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis.
serotype, polysaccharide capsule, cps locus, Streptococcus pneumoniae, pneumococcus
2057-5858
Van Tonder, Andries J.
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Gladstone, Rebecca
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Lo, Stephanie W.
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Nahm, Moon H
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Du Plessis, Mignon
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Cornick, Jennifer E.
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Kwambana-Adams, Brenda
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Madhi, Shabir A.
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Hawkins, Paulina A.
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Benisty, Rachel
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Dagan, Ron
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Everett, Dean B.
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Antonio, Martin
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Klugman, Keith P.
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Von Gottberg, Anne
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Breiman, Robert F.
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McGee, Lesley
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Bentley, Stephen D
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Clarke, Stuart
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The Global Pneumococcal Sequencing Consortium
Van Tonder, Andries J.
a600d507-76aa-48e8-b1d5-e75d90bb8e6e
Gladstone, Rebecca
6a2011bf-2561-4956-9928-46e6b927ba6d
Lo, Stephanie W.
607ccad6-93b1-484c-ba8d-9821432fce90
Nahm, Moon H
972db96a-ab8c-449c-8d25-3a9b4163329c
Du Plessis, Mignon
22fdbb8a-0bcd-4e0d-8a32-520cb5e59e7f
Cornick, Jennifer E.
6d915388-bfcd-458a-a9f5-3593b41019bc
Kwambana-Adams, Brenda
ad0a85c9-1ee1-406e-818c-bb9fda608bdb
Madhi, Shabir A.
dbe03afd-0de6-49c6-b31c-f952193ebc62
Hawkins, Paulina A.
8c2fdf53-ab4d-4484-b08b-6728fccc8bb7
Benisty, Rachel
47176607-7fda-4131-af64-c74e1f6ac770
Dagan, Ron
f384a61e-90a0-491d-8d51-3abea05890a4
Everett, Dean B.
6518700c-7cda-4221-b0ff-e27bb84a4bf5
Antonio, Martin
ac8a8442-881c-4d64-af8e-6ecf34f07c83
Klugman, Keith P.
52451fd0-e5f1-4904-ab95-66552a786a66
Von Gottberg, Anne
2e435fdc-f9f3-4c37-b96a-f4d5184661f0
Breiman, Robert F.
38ff5868-bb32-43c3-97c4-d52ceba325d0
McGee, Lesley
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Bentley, Stephen D
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Clarke, Stuart
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17

Van Tonder, Andries J., Gladstone, Rebecca, Lo, Stephanie W., Nahm, Moon H, Du Plessis, Mignon, Cornick, Jennifer E., Kwambana-Adams, Brenda, Madhi, Shabir A., Hawkins, Paulina A., Benisty, Rachel, Dagan, Ron, Everett, Dean B., Antonio, Martin, Klugman, Keith P., Von Gottberg, Anne, Breiman, Robert F., McGee, Lesley and Bentley, Stephen D , The Global Pneumococcal Sequencing Consortium (2019) Putative novel cps loci in a large global collection of pneumococci. Microbial Genomics. (doi:10.1099/mgen.0.000274).

Record type: Article

Abstract

The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18  000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6  % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis.

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Accepted/In Press date: 14 May 2019
Published date: 11 June 2019
Keywords: serotype, polysaccharide capsule, cps locus, Streptococcus pneumoniae, pneumococcus

Identifiers

Local EPrints ID: 431905
URI: http://eprints.soton.ac.uk/id/eprint/431905
ISSN: 2057-5858
PURE UUID: c7dd1be4-9e42-4501-a26c-74770b0e8c8e
ORCID for Stuart Clarke: ORCID iD orcid.org/0000-0002-7009-1548

Catalogue record

Date deposited: 21 Jun 2019 16:30
Last modified: 10 Jan 2022 02:51

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Contributors

Author: Andries J. Van Tonder
Author: Rebecca Gladstone
Author: Stephanie W. Lo
Author: Moon H Nahm
Author: Mignon Du Plessis
Author: Jennifer E. Cornick
Author: Brenda Kwambana-Adams
Author: Shabir A. Madhi
Author: Paulina A. Hawkins
Author: Rachel Benisty
Author: Ron Dagan
Author: Dean B. Everett
Author: Martin Antonio
Author: Keith P. Klugman
Author: Anne Von Gottberg
Author: Robert F. Breiman
Author: Lesley McGee
Author: Stephen D Bentley
Author: Stuart Clarke ORCID iD
Corporate Author: The Global Pneumococcal Sequencing Consortium

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