NGS-Based

EQA NGS SNP bacterial typing external quality assessment next generation sequencing quality control ring trial

Journal

Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977

Informations de publication

Date de publication:
2020
Historique:
received: 03 08 2020
accepted: 19 10 2020
entrez: 11 1 2021
pubmed: 12 1 2021
medline: 12 1 2021
Statut: epublish

Résumé

Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible

Identifiants

DOI: 10.3389/fmicb.2020.591093 PMID: 33424794 PMC: PMC7793906
pubmed: 33424794
doi: 10.3389/fmicb.2020.591093
pmc: PMC7793906
doi:

Types de publication

Journal Article

Langues

eng

Pagination

591093

Informations de copyright

Copyright © 2020 Dylus, Pillonel, Opota, Wüthrich, Seth-Smith, Egli, Leo, Lazarevic, Schrenzel, Laurent, Bertelli, Blanc, Neuenschwander, Ramette, Falquet, Imkamp, Keller, Kahles, Oberhaensli, Barbié, Dessimoz, Greub and Lebrand.

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Auteurs

David Dylus (D)

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Trestan Pillonel (T)

Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Onya Opota (O)

Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Daniel Wüthrich (D)

Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.

Helena M B Seth-Smith (HMB)

Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.

Adrian Egli (A)

Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.

Stefano Leo (S)

Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland.

Vladimir Lazarevic (V)

Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland.

Jacques Schrenzel (J)

Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland.

Sacha Laurent (S)

Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Claire Bertelli (C)

Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Dominique S Blanc (DS)

Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Stefan Neuenschwander (S)

Institute for Infectious Diseases, University of Bern, Bern, Switzerland.

Alban Ramette (A)

Institute for Infectious Diseases, University of Bern, Bern, Switzerland.

Laurent Falquet (L)

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Department of Biology, University of Fribourg, Fribourg, Switzerland.

Frank Imkamp (F)

Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Peter M Keller (PM)

Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Andre Kahles (A)

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland.

Simone Oberhaensli (S)

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland.

Valérie Barbié (V)

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Christophe Dessimoz (C)

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
Department of Computer Science, University College London, London, United Kingdom.

Gilbert Greub (G)

Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.

Aitana Lebrand (A)

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Classifications MeSH