Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences.

Anti-Bacterial Agents / pharmacology Bacteria / drug effects Databases, Genetic Drug Resistance, Bacterial High-Throughput Nucleotide Sequencing Internet Phenotype Whole Genome Sequencing / methods
antimicrobial resistance data sharing database surveillance whole-genome sequencing

Journal

Microbial genomics
ISSN: 2057-5858
Titre abrégé: Microb Genom
Pays: England
ID NLM: 101671820

Informations de publication

Date de publication:
05 2020
Historique:
pubmed: 8 4 2020
medline: 3 6 2021
entrez: 8 4 2020
Statut: ppublish

Résumé

Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collaboration between international partners. Here, we present the 'AMR Data Hub', an online infrastructure for storage and sharing of structured phenotypic AMR data linked to bacterial whole-genome sequences. Leveraging infrastructure built by the European COMPARE Consortium and structured around the European Nucleotide Archive (ENA), the AMR Data Hub already provides an extensive data collection of more than 2500 isolates with linked genome and AMR data. Representing these data in standardized formats, we provide tools for the validation and submission of new data and services supporting search, browse and retrieval. The current collection was created through a collaboration by several partners from the European COMPARE Consortium, demonstrating the capacities and utility of the AMR Data Hub and its associated tools. We anticipate growth of content and offer the hub as a basis for future research into methods to explore and predict AMR.

Identifiants

DOI: 10.1099/mgen.0.000342 PMID: 32255760 PMC: PMC7371118
pubmed: 32255760
doi: 10.1099/mgen.0.000342
pmc: PMC7371118
doi:

Substances chimiques

Anti-Bacterial Agents 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Références

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Auteurs

Sébastien Matamoros (S)

Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands.

Rene S Hendriksen (RS)

National Food Institute, Technical University of Denmark, Lyngby, Denmark.

Bálint Ármin Pataki (BÁ)

Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary.
Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.

Nima Pakseresht (N)

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

Marc Rossello (M)

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

Nicole Silvester (N)

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

Clara Amid (C)

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

Frank M Aarestrup (FM)

National Food Institute, Technical University of Denmark, Lyngby, Denmark.

Marion Koopmans (M)

Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.

Guy Cochrane (G)

European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

Istvan Csabai (I)

Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.
Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary.

Ole Lund (O)

National Food Institute, Technical University of Denmark, Lyngby, Denmark.

Constance Schultsz (C)

Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands.
Amsterdam UMC, University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.
See the full list of the COMPARE ML-AMR group members, in acknowledgements.

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Classifications MeSH

questionsmedicales.fr › Actions chimiques et utilisations › Actions pharmacologiques › Utilisations thérapeutiques › Anti-infectieux › Antibactériens › Accelerating surveillance and research of...
questionsmedicales.fr › Bactéries › Accelerating surveillance and research of...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Accelerating surveillance and research of...
questionsmedicales.fr › Phénomènes physiologiques › Phénomènes pharmacologiques et toxicologiques › Phénomènes pharmacologiques › Résistance aux substances › Résistance microbienne aux médicaments › Résistance bactérienne aux médicaments › Accelerating surveillance and research of...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Accelerating surveillance and research of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Réseaux de communication entre ordinateurs › Internet › Accelerating surveillance and research of...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › Accelerating surveillance and research of...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Accelerating surveillance and research of...