Evidence map›Paper›PMID 27307455›Full record

ArticleJournal of clinical microbiology2016

Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli Isolates.

Keding Cheng, Huixia Chui, Larissa Domish, Angela Sloan, Drexler Hernandez, Stuart McCorrister, Alyssia Robinson, Matthew Walker, Lorea A M Peterson, Miles Majcher and 11 more

Open access · hybridAbstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of clinical microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
1.2field-weighted citation impact, top 21% of its field
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

1 citing paper in PubMed, 5 citations in OpenAlex.

  1. A null model for microbial diversification.Proceedings of the National Academy of Sciences of the United States of America · 2017
    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

21 authors at 6 institutions in 2 countries.

Keding ChengNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Human Anatomy and Cell Sciences, College of Medicine, University of Manitoba, Winnipeg, MB, Canada Keding.Cheng@phac-aspc.gc.ca Gehua.Wang@phac-aspc.gc.ca.
Huixia ChuiHenan Center of Disease Control and Prevention, Zhengzhou, Henan Province, China.
Larissa DomishNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Angela SloanNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Drexler HernandezNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Stuart McCorristerNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Alyssia RobinsonNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Matthew WalkerNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Lorea A M PetersonNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Miles MajcherNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Sam RatnamNewfoundland and Labrador Public Health Laboratory, St. John's, NL, Canada.
David J M HaldaneNova Scotia Provincial Public Health Laboratory Network, Halifax, NS, Canada.
Sadjia BekalLaboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.
John WylieCadham Provincial Laboratory, Winnipeg, MB, Canada.
Linda ChuiProvincial Laboratory for Public Health and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
Shaun TylerNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Bianli XuHenan Center of Disease Control and Prevention, Zhengzhou, Henan Province, China.
Aleisha ReimerNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Celine NadonNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada.
J David KnoxNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada.
Gehua WangNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Keding.Cheng@phac-aspc.gc.ca Gehua.Wang@phac-aspc.gc.ca.
Public Health Agency of Canada · CAHenan Provincial Center for Disease Control and Prevention · CNNova Scotia Health Authority · CAProvincial Laboratory of Public Health · CASte. Anne's Hospital · CAUniversity of Manitoba · CA

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Mass spectrometry-based phenotypic H-antigen typing (MS-H) combined with whole-genome-sequencing-based genetic identification of H antigens, O antigens, and toxins (WGS-HOT) was used to type 60 clinical Escherichia coli isolates, 43 of which were previously identified as nonmotile, H type undetermined, or O rough by serotyping or having shown discordant MS-H and serotyping results. Whole-genome sequencing confirmed that MS-H was able to provide more accurate data regarding H antigen expression than serotyping. Further, enhanced and more confident O antigen identification resulted from gene cluster based typing in combination with conventional typing based on the gene pair comprising wzx and wzy and that comprising wzm and wzt The O antigen was identified in 94.6% of the isolates when the two genetic O typing approaches (gene pair and gene cluster) were used in conjunction, in comparison to 78.6% when the gene pair database was used alone. In addition, 98.2% of the isolates showed the existence of genes for various toxins and/or virulence factors, among which verotoxins (Shiga toxin 1 and/or Shiga toxin 2) were 100% concordant with conventional PCR based testing results. With more applications of mass spectrometry and whole-genome sequencing in clinical microbiology laboratories, this combined phenotypic and genetic typing platform (MS-H plus WGS-HOT) should be ideal for pathogenic E. coli typing.

Indexed as

Antigens, BacterialBacterial ToxinsBacterial Typing TechniquesEscherichia coliEscherichia coli InfectionsGenotyping TechniquesHumansMass SpectrometryO AntigensAntigens, BacterialBacterial ToxinsH antigenO Antigens

Identifiers

PMID27307455
PMCPMC4963523
OpenAlexW2507047328

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.