Sequencing reads from two isolates from a S. pneumoniae serotype 5 outbreak in Western Canada from 2005-2009

Background: Streptococcus pneumoniae can cause a wide spectrum of disease, including invasive pneumococcal disease (IPD). From 2005-2009 an outbreak of IPD occurred in Western Canada, caused by a S. pneumoniae strain with multilocus sequence type (MLST)289 and serotype 5. We sought to update understanding of the outbreak to date, including characterising two circulating strains using whole-genome sequencing. Methods: IPD was defined according to Public Health Agency of Canada guidelines. Two isolates representing the beginning and end of the outbreak were whole-genome sequenced using the Illumina platform. IslandPick/IslandViewer were used to identify putative genomic islands in the outbreak strain, for which PCR assays were developed. Results: The peak of the outbreak in British Columbia was in 2006, when 57% of invasive S. pneumoniae isolates were serotype 5. Comparison of the two whole-genome sequenced strains showed only 10 single nucleotide variants between them. A 15.5 kb genomic island was identified in outbreak strains, which has not been found in any other S. pneumoniae MLST or serotypes. The island includes genes involved in carbohydrate metabolism, which may potentially confer a selective advantage through increased growth or virulence. Discussion: We show that the serotype 5 MLST289 outbreak was due to a unique strain, which remained genetically consistent, and contained a distinguishing genomic island. Whole-genome sequencing holds great promise for real-time characterisation of outbreaks in the future, and may allow responses tailored to characteristics identified in the genome.