Putative novel cps loci in a large global collection of pneumococci

• Type of Material: Article
• Authors: Andries J. van Tonder, Wellcome Sanger Institute; Rebecca A. Gladstone, Wellcome Sanger Institute; Stephanie W. Lo, Wellcome Sanger Institute; Moon H. Nahm, University of Alabama Birmingham; Mignon du Plessis, National Institute for Communicable Diseases; Jennifer Cornick, Malawi-Liverpool-Wellcome-Trust; Brenda Kwambana-Adams, MRC Unit; Shabir A. Madhi, University of Witwatersrand; Paulina A. Hawkins, Emory University; Rachel Benisty, Ben-Gurion University of the Negev; Ron Dagan, Ben-Gurion University of the Negev; Dean Everett, University of Edinburgh; Keith P Klugman, Emory University; Martin Antonio, MRC Unit; Anne von Gottberg, National Institute for Communicable Diseases; Robert F Breiman, Emory University; Lesley McGee, Centers for Disease Control and Prevention; Stephen D. Bentley, Wellcome Sanger Institute
• Language: English
• Date: 2019-07-01
• Publisher: Microbiology Society: Microbial Genomics
• Publication Version: Final Published Version
• Copyright Statement: © 2019 The Authors.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1099/mgen.0.000274
• Title of Journal or Parent Work: Microbial Genomics
• ISSN: 2057-5858
• Volume: 5
• Issue: 7
• Grant/Funding Information: This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556); the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194); and the US Centers for Disease Control and Prevention.
• Keywords: polysaccharide capsule; PROTEIN; DISEASE; CHILDREN; Microbiology; Streptococcus pneumoniae; SEROTYPES; CONJUGATE VACCINES; serotype; STREPTOCOCCUS-PNEUMONIAE; PNEUMONIAE CAPSULAR POLYSACCHARIDE; pneumococcus; cps locus; Genetics & Heredity; Science & Technology; Life Sciences & Biomedicine
• Research Categories: Biology, Microbiology; Health Sciences, Public Health

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.