Author/Authors :
Miller, Ruth R School of Population and Public Health - University of British Columbia, Canada , Langille, Morgan G. I Department of Pharmacology - Dalhousie University, Canada , Montoya, Vincent British Columbia Centre for Disease Control, Vancouver, Canada , Crisan, Anamaria British Columbia Centre for Disease Control, Vancouver, Canada , Stefanovic, Aleksandra Department of Pathology and Laboratory Medicine - University of British Columbia, Vancouver, Canada , Martin, Irene National Microbiology Laboratory - Public Health Agency of Canada, Canada , Hoang, Linda Department of Pathology and Laboratory Medicine - University of British Columbia, Vancouver, Canada , Patrick, David M School of Population and Public Health - University of British Columbia, Canada , Romney, Marc Department of Pathology and Laboratory Medicine - University of British Columbia, Vancouver, Canada , Tyrrell, Gregory Department of Laboratory Medicine and Pathology - University of Alberta, Canada , Jones, Steven J. M Department of Molecular Biology and Biochemistry - Simon Fraser University, Canada , Brinkman, Fiona S. L Department of Molecular Biology and Biochemistry - Simon Fraser University, Canada , Tang, Patrick School of Population and Public Health - University of British Columbia, Canada
Abstract :
Background. Streptococcus pneumoniae can cause a wide spectrum of disease, including invasive pneumococcal disease (IPD). From 2005 to 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 investigate the incidence of IPD due to this S. pneumoniae strain and to characterize the outbreak in British Columbia 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. The sequences were analyzed for single nucleotide variants (SNVs) and putative genomic islands. Results. The peak of the outbreak in British Columbia was in 2006, when 57% of invasive S. pneumoniae isolates were serotype 5. Comparison of two whole-genome sequenced strains showed only 10 SNVs between them. A 15.5 kb genomic island was identified in outbreak strains, allowing the design of a PCR assay to track the spread of the outbreak strain. Discussion. We show that the serotype 5 MLST 289 strain contains a distinguishing genomic island, which remained genetically consistent over time. Whole-genome sequencing holds great promise for real-time characterization of outbreaks in the future and may allow responses tailored to characteristics identified in the genome.
Keywords :
Genomic Analysis , Serotype 5 , Streptococcus pneumoniae Outbreak , British Columbia
