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

Sébastien Matamoros, Rene. S. Hendriksen, Balint Pataki, Nima Pakseresht, Marc Rossello, Nicole Silvester, Clara Amid, COMPARE ML- AMR group, Guy Cochrane, Istvan Csabai, Ole Lund, Constance Schultsz
doi: https://doi.org/10.1101/532267
Sébastien Matamoros
1Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands.
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  • For correspondence: sebastien.matamoros@gmail.com
Rene. S. Hendriksen
2National Food Institute, Technical University of Denmark, Lyngby, Denmark.
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Balint Pataki
3Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.
4Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary.
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Nima Pakseresht
5European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Marc Rossello
5European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Nicole Silvester
5European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Clara Amid
5European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Guy Cochrane
5European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Istvan Csabai
3Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.
4Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest, Hungary.
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Ole Lund
2National Food Institute, Technical University of Denmark, Lyngby, Denmark.
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Constance Schultsz
1Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam, The Netherlands.
6Amsterdam UMC, University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.
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Abstract

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 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 for some 500 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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 28, 2019.
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Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole genome sequences
Sébastien Matamoros, Rene. S. Hendriksen, Balint Pataki, Nima Pakseresht, Marc Rossello, Nicole Silvester, Clara Amid, COMPARE ML- AMR group, Guy Cochrane, Istvan Csabai, Ole Lund, Constance Schultsz
bioRxiv 532267; doi: https://doi.org/10.1101/532267
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Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole genome sequences
Sébastien Matamoros, Rene. S. Hendriksen, Balint Pataki, Nima Pakseresht, Marc Rossello, Nicole Silvester, Clara Amid, COMPARE ML- AMR group, Guy Cochrane, Istvan Csabai, Ole Lund, Constance Schultsz
bioRxiv 532267; doi: https://doi.org/10.1101/532267

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