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A Galaxy-based One Health

Antimicrobial Resistance Platform

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Bérénice Batut on behalf of the ABRomics consortium

Galaxy Community Conference 2024

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AntiMicrobial Resistance (AMR)

Bacteria, viruses, fungi and parasites no longer respond to antimicrobial medicines

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Copyright: AdobeStock

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One of the Top Global Public Health and Development Threats

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Figure 2 - Antimicrobial Resistance Collaborators et al, The Lancet, 2022.

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Rationale for ABRomics

  1. Increasing access to sequencing for clinical laboratories, including outside university-teaching hospitals
  2. Improvement thanks to genomics and metagenomics of our knowledge about the (complex) circulation of antibiotic-resistant bacteria, mobile genetic elements (MGE) and antibiotic resistance genes (ARG)
  3. Mostly siloed investigations, while a global picture is needed

To address this gap in the French ecosystem:

ABRomics (2 M€ for 4 years): a multi-omics One Health platform for collaboration and data sharing between researchers and clinicians for AMR surveillance

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ABRomics Consortium

National team effort

  • 43 partners
  • Multidisciplinary consortium
  • National reference centers for antibiotic resistance

Coordination

  • Claudine Médigue (French Institute of Bioinformatics)
  • Philippe Glaser (Institut Pasteur)

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ABRomics Objectives

  • Provide an open access to genomic and metagenomic analyses through standardised and controlled pipelines and an up-to-date set of mathematical and bioinformatic tools
  • Build a repository of structured, interoperable, standardized and well-annotated multi-omics microbiological data from human, animal and environmental origins
  • Be easily usable by non bio-informaticians and experts in AMR analysis
  • Provide a shared platform to improve the surveillance and research on antibiotic resistance across human, animal and environment sectors

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Online One Health community-driven platform �to scale up and improve surveillance of antibiotic resistance

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Work Packages of ABRomics

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ABRomics Platform

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ABRomics Platform

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ABRomics Platform

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ABRomics Platform

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ABRomics Platform

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ABRomics Platform

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Genomics Workflows

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Genomics Workflows

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Genomics Workflows

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Genomics Workflows

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Genomics Workflows

Subworkflows

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  • Available on WorkflowHub and Dockstore via IWC

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  • Documented as Learning Pathways on the GTN - https://gxy.io/GTN:P00018

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Next Steps

Workflows beyond genomics

  • cgMLST
  • Metagenomics
  • Pangenomics
  • Multi-OMICs

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Thank You!

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https://www.abromics.fr/

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