Methods: To examine bacterial genetic factors associated with PPE, and investigate whether a propensity to cause PPE is related to shared genetic factors across pneumococcal serotypes, we performed whole-genome sequencing of 214 invasive S. pneumoniae isolates from Utah children collected pre and post PCV licensure (1996-2000 and 2001-2013 respectively). We mapped our sequences against a number of published S. pneumoniae genomes (R6, Spn23F and INV104B). To find variants associated with PPE we used a probabilistic Fst approach to measure genetic differentiation between PPE and non-PPE causing strains.
Results: We identified a total of 5.9-7.8x10^4 single nucleotide polymorphisms and 2.5-2.6x10^5 putative structural variants (minor allele frequency > 5%) across strains. We identified genetic differentiation at a number of regions throughout the S. pneumoniae genome, including previously identified and putative virulence factors such as zmpB, cpbF, and pspA. Other areas of differentiation correspond to novel putative PPE virulence genes such as ABC-MSP. Both point mutations and larger structural variants were associated with PPE. To ensure that differential strain enrichment did not confound our results, we performed genetic analyses between PPE and non-PPE causing strains within single serotypes (1, 3, 7F, and 19A) with similar results.
Conclusion: Our study demonstrates genomic variation in S. pneumoniae associated with PPE, and presents new candidate genes for functional screens in PPE disease models. Identification of genetic variants enriched in pneumococcal isolates causing PPE is a critical step in evaluating potential new targets for treatment and prevention of complicated pneumonia in children.
bioMerieux, Inc: Collaborator , Investigator and Scientific Advisor , Consulting fee and Research support
Merck: Investigator , Research grant
K. Ampofo, None
H. Crandall, None
J. Killpack, None
C. R. Stockmann, None
A. P. Farrell, None
K. F. Fischer, None
A. Pavia, None
K. Eilbeck, None
R. Schlaberg, IDbyDNA: Consultant and Shareholder , Licensing agreement or royalty
M. Yandell, IDbyDNA: Shareholder , Licensing agreement or royalty
C. L. Byington, NIH: Grant Investigator , Grant recipient
BioFire Diagnostics: Intellectual Property for the FilmArray , Intellectual Property