Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2017

A novel serogroup 11 genetic variant of Streptococcus pneumoniae discovered in nasopharyngeal swabs from Fijian children (#56)

Sam Manna 1 , Belinda Ortika 1 , Eileen M Dunne 1 , Kathryn E Holt 2 3 , Mike Kama 4 , Fiona M Russell 5 6 , Jason Hinds 7 8 , Catherine Satzke 1 5 9
  1. Murdoch Childrens Research Institute, Parkville, VIC, Australia
  2. Centre for Systems Genomics, University of Melbourne,, Parkville, VIC, Australia
  3. Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
  4. Ministry of Health and Medical Services, Suva, Fiji
  5. Department of Paediatrics,, The University of Melbourne, Parkville, VIC, Australia
  6. Centre for International Child Health, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
  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

Streptococcus pneumoniae (the pneumococcus) is a leading cause of morbidity and mortality in children under the age of five causing otitis media, pneumonia, sepsis and meningitis. Over 90 antigenically-distinct serotypes of pneumococcus exist, determined by variation in capsule structure, encoded by the capsular polysaccharide (cps) locus. Currently licensed vaccines only target a subset of serotypes, resulting in increased nasopharyngeal carriage and disease caused by non-vaccine serotypes. Accurate serotyping of carriage and invasive disease isolates is therefore essential to monitor changes in serotype prevalence following vaccine introduction. As part of a pneumococcal vaccine impact study in Fiji, we used DNA microarray to conduct pneumococcal serotyping on nasopharyngeal swabs from children and their adult caregivers. From 2,045 swabs, 78 (3.8%) contained pneumococci that serotyped as ‘11F-like’, suggesting they were genetic variants of serotype 11F. To identify the genetic basis underlying the divergence in the 11F-like cps locus, the genomes of two randomly selected 11F-like isolates were sequenced. Most 11F-like cps genes were closely related to the canonical 11F sequences except wcwC and wcrL, which were phylogenetically distinct from all serogroup 11 serotypes. Although the 11F gct gene is non-functional, we identified a single nucleotide insertion in a homopolymeric region of the 11F-like gct gene, which restores the open reading frame. In contrast to the 11F capsule, phenotypic serotyping (Quellung reaction) of 11F-like isolates confirmed the 11F-like capsule contains glycerol phosphate and lacks N-acetyl-glucosamine. This is due to changes in the 11F-like gct and wcrL genes, which mediate these modifications, respectively. As a result, phenotypic typing methods identify 11F-like isolates as serotype 11A. Our study provides evidence that the presence of previously undiscovered genetic variants in clinical samples can yield discrepant serotyping results depending on whether a genotypic or phenotypic approach is used. This work has implications for vaccine impact studies that monitor changes in pneumococcal serotype prevalence in both carriage and invasive disease.