Miller Ruth R, Langille Morgan G I, Montoya Vincent, Crisan Anamaria, Stefanovic Aleksandra, Martin Irene, Hoang Linda, Patrick David M, Romney Marc, Tyrrell Gregory, Jones Steven J M, Brinkman Fiona S L, Tang Patrick
School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Department of Pharmacology, Dalhousie University, Halifax, NS, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr 14.
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.
背景。肺炎链球菌可引发多种疾病，包括侵袭性肺炎球菌病（IPD）。2005年至2009年，加拿大西部发生了由多位点序列类型（MLST）为289且血清型为5的肺炎链球菌菌株引起的IPD疫情。我们试图调查该肺炎链球菌菌株所致IPD的发病率，并利用全基因组测序对不列颠哥伦比亚省的此次疫情进行特征分析。方法。IPD根据加拿大公共卫生署的指南进行定义。对代表疫情开始和结束的两个分离株进行全基因组测序。对序列分析单核苷酸变异（SNV）和推定的基因组岛。结果。不列颠哥伦比亚省疫情的高峰出现在2006年，当时57%的侵袭性肺炎链球菌分离株为血清型5。两个全基因组测序菌株的比较显示它们之间仅有10个SNV。在疫情菌株中鉴定出一个15.5 kb的基因组岛，据此设计了一种PCR检测方法来追踪疫情菌株的传播。讨论。我们发现血清型5 MLST 289菌株含有一个独特的基因组岛，该岛随时间推移在基因上保持一致。全基因组测序对未来疫情的实时特征分析具有很大潜力，可能使应对措施能够根据基因组中确定的特征进行调整。
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