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Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000274. Epub 2019 Jun 11.

Putative novel cps loci in a large global collection of pneumococci.

Author information

1
1​Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
2
2​Division of Pulmonary Medicine, Departments of Medicine and Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA.
3
3​Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.
4
4​School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
5
5​Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi.
6
6​Vaccines and Immunity Theme, MRC Unit, Banjul, The Gambia.
7
7​Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
8
8​Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
9
9​Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheeba, Beer-Sheva, Israel.
10
10​Queens Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK.
11
11​Centers for Disease Control and Prevention, Atlanta, GA, USA.
12
12​Emory Global Health Institute, Emory University, Atlanta, GA, USA.
13
13​https://www.pneumogen.net/gps/.

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.

KEYWORDS:

Streptococcus pneumoniae; cps locus; pneumococcus; polysaccharide capsule; serotype

PMID:
31184299
PMCID:
PMC6700660
DOI:
10.1099/mgen.0.000274
[Indexed for MEDLINE]
Free PMC Article

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