ABRomics consortium meeting and technical workshop: two days focused on innovation

On November 17, the ABRomics project consortium met at the Pasteur Institute in Paris for its annual meeting. This was a key opportunity to present the major advances of the ABRomics project to the various members of the consortium and to discuss actions to optimize the use of the platform for a larger number of users.

Presentations by the development team provided an update on the features of the ABRomics platform currently in production (https://analysis.abromics.fr/) and those that will enable a complete “genomic” version to be offered from the beginning of 2026 (i.e., also containing point mutation prediction and cgMLST typing calculation) .

Developments for metagenomic data analysis are currently being integrated into the ABRomics PF (H. Lefeuvre), and the scaling up of these analyses to “real” metagenomic samples was discussed following this presentation.

Finally, progress in WP3 developments, in particular (i) the use of ontologies and a knowledge graph to query all data in the ABRomics database (B. Quemeneur), (ii) the development of a public bacterial species pangenome database (J. Mainguy), and (iii) software enabling metagenomic data to be projected onto a pangenome database (T. Lemane), were then presented.

The connection between these original developments and the ABRomics platform will be discussed through the project use cases proposed in WP4, which will enable us to start from specific biological questions addressed.

The discussions during the day highlighted the importance of several strategic issues :
– The implementation of interoperability mechanisms between ABRomics and other domain resources in Europe and internationally;
– Establishing links between data managed in ABRomics and PROMISE through a use case proposed by one of the CNRs partnering with the two structuring projects of the PPR antibacterial resistance program;
– The integration of reference pathogen species and their metadata into ABRomics and the ABRomics-specific pangenome database, and the definition of use cases enabling ABRomics users to query pangenomes;
– Implementation of communication initiatives on the platform’s features and the benefits of using ABRomics for antibiotic resistance surveillance and research.

The platform development team, most of the steering committee members, and several consortium members who use the ABRomics platform also met for a technical workshop on the morning of November 18. This was an opportunity for these users to try out the features of the current version of ABromics and to give their feedback and suggestions for future versions.

Beyond technical advances, these two days of discussions, workshops, and meetings provided an opportunity to take stock of the project and its prospects, and illustrated the strength and richness of the exchanges between the teams.
The interactions and commitment of everyone involved have enabled progress towards an ever more efficient platform that is open to innovation.