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ABRomics - a numerical platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data


Based on the software environment and the data management system developed in the context of MUDIS4LS, the ABRomics-PF project aims at developing a secure One Health cross-sectorial online platform to make accessible bacterial infectious disease (meta)genomics data and their associated clinical and epidemiological metadata to a meta-network of researchers including epidemiologists, clinical microbiologists, and the broader research community.


 The platform will address two main objectives:

  • Establish a repository of structured, interoperable, standardized and well-annotated multi-omics microbiological data, with tailored mathematical and bioinformatic tools, that can be used to answer specific research questions related to ABR.
  • Establish a shared platform to assist ABR surveillance across human and veterinary medicine, also including environmental and food isolates, to allow transmission and outbreak surveillance of pathogens in near real-time, with actionable results for public health authorities. FAIR (Findable, Accessible, Interoperable and Reusable) data management procedures will allow retrospective studies.


The development of the three main technical components of the platform (IT infrastructure, integrated multi-omics microbiological databases, and mathematical and bioinformatics tools) will be driven by dedicated use-cases.

The ABRomics-PF project is led by IFB and Institut Pasteur and is formed by a consortium of 45 teams belonging to the main French research organizations. These teams bring together all the expertise required to build this platform (diversity of ABR research in clinical and fundamental fields, mathematical modeling methods and the whole range of expertise in computer science, bioinformatics, database and computer architecture).  ABRomics-PF is funded at 2 M€ for 4 years and will start in september 2021.

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