title: Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009.
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.
authors.affiliation: School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Ruth R
authors.initials: RR
authors.lastname: Miller
authors.affiliation: Department of Pharmacology, Dalhousie University, Halifax, NS, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Morgan G I
authors.initials: MG
authors.lastname: Langille
authors.affiliation: British Columbia Centre for Disease Control, Vancouver, BC, Canada.
authors.forename: Vincent
authors.initials: V
authors.lastname: Montoya
authors.affiliation: British Columbia Centre for Disease Control, Vancouver, BC, Canada.
authors.forename: Anamaria
authors.initials: A
authors.lastname: Crisan
authors.affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Stefanovic
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
authors.forename: Irene
authors.initials: I
authors.lastname: Martin
authors.affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; British Columbia Public Health Laboratory, Vancouver, BC, Canada.
authors.forename: Linda
authors.identifier: 0000-0001-7769-6120
authors.initials: L
authors.lastname: Hoang
authors.affiliation: School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
authors.forename: David M
authors.initials: DM
authors.lastname: Patrick
authors.affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, St. Paul's Hospital, Providence Health Care, Vancouver, BC, Canada.
authors.forename: Marc
authors.initials: M
authors.lastname: Romney
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada; The Provincial Laboratory for Public Health (Microbiology), Edmonton, AB, Canada.
authors.forename: Gregory
authors.initials: G
authors.lastname: Tyrrell
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Fiona S L
authors.initials: FS
authors.lastname: Brinkman
authors.affiliation: Department of Pathology, Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tang