ABRomics: the national multiomics platform for Antibiotic Resistance research and surveillance

Funded by the French Priority Plan on antibioresistance, the ABRomics project aims at developing an online community-driven platform to scale up and improve surveillance and research on antibiotic resistance from a One Health perspective.

The platform is made of:

  • A repository of structured, interoperable, standardized and well-annotated multi-omics microbiological data from human, animal and environmental origins,
  • An up-to-date arsenal of mathematical and bioinformatic tools to answer generic and specific research questions related to AMR.

The developments of the ABRomics platform are organized around several technical work packages for the computing architecture, the integrated multi-omics microbiological database, the standard analysis workflows and some original mathematical and bioinformatics tools for data integration and modelisation of ABR emergence, and the ABRomics Web portal. These developments are driven by the biological questions raised in six transversal use cases.

In collaboration with MetaGenoPolis, The LABGeM team is coordinated the use case 3 about the application of meta-pangenomic concept for tracking antibioresistance in metagenomic samples. We are contributing in the following deliverable:

  • the development of a Meta-PanGenome graph method to estimate strain abundance and their variable genomic regions from metagenomic samples These developments will be based on the PPanGGOLiN software.
  • an up-to-date comprehensive pangenome resource of the most relevant species to study ABR in microbiota including functional annotations.
  • a web interface for the visualization of the ARG location on the pangenome graph
  • the integration of the Meta-PanGenomic approach in the ABRomics platform as a ready-to-use tool for investigating antimicrobial resistance dissemination in complex microbial ecosystems

ABRomics: the national multiomics platform for Antibiotic Resistance research and surveillance