Evidence map›Paper›PMID 27366170›Full record

ArticleThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale2016

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

Ruth R Miller, Morgan G I Langille, Vincent Montoya, Anamaria Crisan, Aleksandra Stefanovic, Irene Martin, Linda Hoang, David M Patrick, Marc Romney, Gregory Tyrrell and 3 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Ruth R MillerSchool of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Morgan G I LangilleDepartment of Pharmacology, Dalhousie University, Halifax, NS, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Vincent MontoyaBritish Columbia Centre for Disease Control, Vancouver, BC, Canada.
Anamaria CrisanBritish Columbia Centre for Disease Control, Vancouver, BC, Canada.
Aleksandra StefanovicDepartment of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
Irene MartinNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Linda HoangDepartment of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; British Columbia Public Health Laboratory, Vancouver, BC, Canada.ORCID 0000-0001-7769-6120
David M PatrickSchool of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
Marc RomneyDepartment 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.
Gregory TyrrellDepartment of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada; The Provincial Laboratory for Public Health (Microbiology), Edmonton, AB, Canada.
Steven J M JonesDepartment 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.
Fiona S L BrinkmanDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Patrick TangDepartment of Pathology, Sidra Medical and Research Center, Doha, Qatar.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Identifiers

PMID27366170
PMCPMC4904568

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.