Research Article Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009 Ruth R. Miller, 1 Morgan G. I. Langille, 2,3 Vincent Montoya, 4 Anamaria Crisan, 4 Aleksandra Stefanovic, 5 Irene Martin, 6 Linda Hoang, 5,7 David M. Patrick, 1 Marc Romney, 5,8 Gregory Tyrrell, 9,10 Steven J. M. Jones, 3,11,12 Fiona S. L. Brinkman, 3 and Patrick Tang 13 1 School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada 2 Department of Pharmacology, Dalhousie University, Halifax, NS, Canada 3 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada 4 British Columbia Centre for Disease Control, Vancouver, BC, Canada 5 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada 6 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada 7 British Columbia Public Health Laboratory, Vancouver, BC, Canada 8 Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Providence Health Care, Vancouver, BC, Canada 9 Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada 10 Te Provincial Laboratory for Public Health (Microbiology), Edmonton, AB, Canada 11 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada 12 Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada 13 Department of Pathology, Sidra Medical and Research Center, Doha, Qatar Correspondence should be addressed to Patrick Tang; ptang@sidra.org Received 2 April 2015; Accepted 4 October 2015 Copyright © 2016 Ruth R. Miller et al. Tis 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 defned according to Public Health Agency of Canada guidelines. Two isolates representing the beginning and end of the outbreak were whole-genome sequenced. Te sequences were analyzed for single nucleotide variants (SNVs) and putative genomic islands. Results. Te 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 identifed 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 identifed in the genome. 1. Introduction Streptococcus pneumoniae is a ubiquitous bacterium that can cause a wide spectrum of disease, as well as being found in the normal fora of the respiratory tract in healthy individ- uals. Streptococcal disease ranges from ear and respiratory tract infections to invasive pneumococcal disease (IPD), which includes bacteremia and its complications, such as meningitis, arthritis, and endocarditis. In many countries, including Canada, IPD is a reportable disease to public health authorities. Prior to the introduction of pneumococ- cal conjugate vaccines, the incidence of IPD was highest amongst infants. However, since then, IPD rates from vaccine serotypes in children and adults have dropped signifcantly, Hindawi Publishing Corporation Canadian Journal of Infectious Diseases and Medical Microbiology Volume 2016, Article ID 5381871, 7 pages http://dx.doi.org/10.1155/2016/5381871