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

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 in...

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Bibliographic Details
Published inbioRxiv
Main Authors Matamoros, Sébastien, Hendriksen, Rene, Pataki, Balint, Pakseresht, Nima, Rossello, Marc, Silvester, Nicole, Amid, Clara, Compare Ml-Amr Group, Cochrane, Guy, Csabai, Istvan, Lund, Ole, Schultsz, Constance
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 28.01.2019
Subjects
Antimicrobial agents
Antimicrobial resistance
Collaboration
Consortia
Drug resistance
Genomes
Internet
Surveillance
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Summary: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.
DOI:10.1101/532267