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PLoS One. 2018 Nov 5;13(11):e0206622. doi: 10.1371/journal.pone.0206622. eCollection 2018.

Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene.

Author information

1
Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
2
Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
3
Ministry of Health and Medical Services, Suva, Fiji.
4
Centre for International Child Health, Royal Children's Hospital, Melbourne, Australia.
5
National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia.
6
Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom.
7
Institute for Infection and Immunity, St. George's, University of London, London, United Kingdom.
8
BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom.
9
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia.

Abstract

As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated '33F-1'). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

Conflict of interest statement

We have the following interests. Sam Manna, Eileen Dunne and Catherine Satzke have each received a Robert Austrian Research Award in Pneumococcal Vaccinology funded by Pfizer. There are no patents, products in development or marketed products to declare. Jason Hinds is affiliated with BUGS Bioscience, London Bioscience Innovation Centre. BUGS Bioscience is a not-for-profit spin-out of St George’s, University of London (SGUL) founded to support molecular serotyping services and develop associated software. Jason Hinds is employed by SGUL and not BUGS Bioscience. Jason Hinds is co-founder, board member and shareholder of BUGS Bioscience but receives no personal income. Jason Hinds is an investigator on studies conducted on behalf of SGUL or BUGS Bioscience that are sponsored and/or funded by vaccine manufacturers including Pfizer, GlaxoSmithkline, Sanofi Pasteur and PATH. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

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