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. 2019 Jul;5(7):e000274.
doi: 10.1099/mgen.0.000274. Epub 2019 Jun 11.

Putative novel cps loci in a large global collection of pneumococci

Andries J van Tonder  1 , Rebecca A Gladstone  1 , Stephanie W Lo  1 , Moon H Nahm  2 , Mignon du Plessis  3   4 , Jennifer Cornick  5 , Brenda Kwambana-Adams  6 , Shabir A Madhi  7 , Paulina A Hawkins  8 , Rachel Benisty  9 , Ron Dagan  9 , Dean Everett  10 , Martin Antonio  6 , Keith P Klugman  8 , Anne von Gottberg  3   4 , Robert F Breiman  8   10 , Lesley McGee  11 , Stephen D Bentley  1   12 ; The Global Pneumococcal Sequencing Consortium  13
Collaborators, Affiliations

Putative novel cps loci in a large global collection of pneumococci

Andries J van Tonder et al. Microb Genom. 2019 Jul.

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.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
(a) World map showing the global distribution of the samples in the study dataset. (b) Bubble plot showing the 66 serotypes included in the dataset (the area of each circle is proportional to the number of samples).
Fig. 2.
Fig. 2.
Identification of putative novel cps loci; plots of total SNPs against the percentage of the serotype reference covered by sequence reads are shown for nine serotypes with putative novel cps loci (highlighted in red).
Fig. 3.
Fig. 3.
(a) Phylogeny and SNP map of serotype 9L. (b) Comparison of the putative serotype 9X sequence and the serotype 9L and 9N reference sequences.
Fig. 4.
Fig. 4.
(a) Phylogeny and SNP map of serotype 11A. (b) Comparison of the putative serotype 11X sequence and the serotype 11A and 11F reference sequences. (c) Phylogeny containing the serogroup 11 references, serotype 11X and PMP1343.
Fig. 5.
Fig. 5.
(a) Phylogeny and SNP map of serotype 16F. (b) Comparison of the putative serotype 16X sequence and the serotype 16F reference sequence.
Fig. 6.
Fig. 6.
(a) Phylogeny and SNP map of serotype 18A. (b) Phylogeny and SNP map of serotype 18C. (c) Comparison of the putative serotype 18X sequences and the serotype 18A and 18C reference sequences.
Fig. 7.
Fig. 7.
(a) Phylogeny and SNP map of serotype 18F. (b) Comparison of the putative serotype 18Xii sequence and the serotype 18F reference sequence.
Fig. 8.
Fig. 8.
(a) Phylogeny and SNP map of serotype 29. (b) Comparison of the putative serotype 29X sequence and the serotype 29 reference sequence.
Fig. 9.
Fig. 9.
(a) Phylogeny and SNP map of serotype 33F. (b) Comparison of the putative serotype 33X sequence and the serotype 33F reference sequence.
Fig. 10.
Fig. 10.
(a) Phylogeny and SNP map of serotype 36. (b) Comparison of the putative serotype 36X sequence and the serotype 36 reference sequence.
See this image and copyright information in PMC

References

    1. Wahl B, O'Brien KL, Greenbaum A, Majumder A, Liu L, et al. Burden of Streptococcus pneumoniae and Haemophilus influenzae type B disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15. Lancet Glob Health. 2018;6:e744–e757. doi: 10.1016/S2214-109X(18)30247-X. - DOI - PMC - PubMed
    1. Briles DE, Crain MJ, Gray BM, Forman C, Yother J. Strong association between capsular type and virulence for mice among human isolates of Streptococcus pneumoniae . Infect Immun. 1992;60:111–116. - PMC - PubMed
    1. Hyams C, Camberlein E, Cohen JM, Bax K, Brown JS. The Streptococcus pneumoniae capsule inhibits complement activity and neutrophil phagocytosis by multiple mechanisms. Infect Immun. 2010;78:704–715. doi: 10.1128/IAI.00881-09. - DOI - PMC - PubMed
    1. Larson TR, Yother J. Streptococcus pneumoniae capsular polysaccharide is linked to peptidoglycan via a direct glycosidic bond to beta-D-N-acetylglucosamine. Proc Natl Acad Sci U S A. 2017;114:5695–5700. doi: 10.1073/pnas.1620431114. - DOI - PMC - PubMed
    1. Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, et al. Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet. 2006;2:e31. doi: 10.1371/journal.pgen.0020031. - DOI - PMC - PubMed

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