The ABRomics platform is addressing the following objectives:
- Build a database of interoperable, standardized and well-annotated multi-omics microbiological data from human, animal and environmental origins to ensure data sharing, sustainable storage and submission procedures to international repositories. FAIR (Findable, Accessible, Interoperable and Reusable) data management procedures will allow retrospective studies.
- Improve an antibiotic resistance genes database via curation and expertise
- Provide an open access to genomic and metagenomic analyses through standardised and controlled pipelines.
- Integrate multi-omics for the analysis of bacterial genomes and samples. Based on the ABRomics six use cases, tailored mathematical and bioinformatic tools will be developed to answer research questions related to ABR
- Enable the surveillance of antibiotic resistance by data sharing
The combination of these objectives is unique to the ABRomics-PF: linking field investigation in multiple sectors to fundamental research will allow us to address the most urgent clinical and environmental issues using an up-to-date arsenal of mathematical and bioinformatic tools.
ABRomics will provide a unique platform to the diverse communities addressing the antibiotic resistance issue :
| Users | Application |
| Microbiology lab in veterinary clinic and medium size hospital | Storage and analysis of WGS for isolate characterization, outbreak investigation and source identification |
| Microbiology lab in University Hospitals | Omics data storage and analysis for clinical research |
| Public health laboratory: NRC (human), ANSES (animal, food, environment) | Global and One Health surveillance of AMR, strains and ARG transmission |
| Environmental research | One health analysis of emergence and dissemination of AMR by combining genomic and metagenomic data |
| Public health agencies | Integrating omics data for global surveillance and retrospective analysis |
| Diagnostic research | Omics resource and link with biobanks for the development of new methods for AST |
| Therapeutic research | Omics resource and link with biobanks for developing efficient therapeutic strategies and anticipating resistance |
| Fundamental research | The platform will offer an environment (tools and multi omics data) to answer research questions through integrative bioinformatics procedures. It should also facilitate interaction with clinicians. |
| Bioinformatician and modelers | Platform to develop and disseminate new methods and access to multi-omics data. |
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