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


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

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. A15.5 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 5MLST 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.
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  • Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009

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Authors

Ruth R. Miller
School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
Morgan G. I. Langille
Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
Vincent Montoya
British Columbia Centre for Disease Control, Vancouver, BC, Canada
Anamaria Crisan
British Columbia Centre for Disease Control, Vancouver, BC, Canada
Aleksandra Stefanovic
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
Irene Martin
National Microbiology Laboratory, Public Health Agency of Canada,Winnipeg, MB, Canada
Linda Hoang
British Columbia Public Health Laboratory, Vancouver, BC, Canada
David M. Patrick
School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
Marc Romney
Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Providence Health Care, Vancouver, BC, Canada
Gregory Tyrrell
Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
Steven J. M. Jones
Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
Fiona S. L. Brinkman
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
Patrick Tang
Department of Pathology, Sidra Medical and Research Center, Doha, Qatar

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. A15.5 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 5MLST 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.