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Canadian Journal of Infectious Diseases and Medical Microbiology
Volume 2016, Article ID 5381871, 7 pages
Research Article

Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009

1School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
2Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
3Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
4British Columbia Centre for Disease Control, Vancouver, BC, Canada
5Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
6National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
7British Columbia Public Health Laboratory, Vancouver, BC, Canada
8Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Providence Health Care, Vancouver, BC, Canada
9Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
10The Provincial Laboratory for Public Health (Microbiology), Edmonton, AB, Canada
11Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
12Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
13Department of Pathology, Sidra Medical and Research Center, Doha, Qatar

Received 2 April 2015; Accepted 4 October 2015

Copyright © 2016 Ruth R. Miller et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.