ABRomics: a platform for antibiotic resistance research and public health using an integrated "One Health" approach
Year: 2026
Type: conference-paper
Abstract: Antibiotic resistance is a major public health concern. Whole Genome Sequencing (WGS) is essential for characterizing the diffusion and the monitoring of Multidrug resistant bacteria (MDRB) within and between the human, animal and environmental sectors. In this context, the French Priority Plan on Antimicrobial Resistance has funded the development of an online platform dedicated to the surveillance and research of antibiotic resistance within a One Health framework (www.abromics.fr). The ABRomics platform is hosted at the French Institute of Bioinformatics (www.ifb-elixir.fr), which has extensive data analysis and storage capacity.The web service ABRomics-analysis (analysis.abromics.fr) offers a user-friendly interface for uploading and managing genomic samples as well as for running, through usegalaxy.fr, a standardized workflow comprising: quality control, species identification, MLST (MultiLocus Sequence Typing), genome assembly and annotation, cgMLST (core genome MLST) using standardized nomenclatures, plasmid typing, and the detection of antibiotic resistance and virulence genes. The ABRomics database aims to facilitate data exploration and foster collaboration across sectors and communities. To this end, it provides tools for exploring freely accessible data on all submitted isolates and for connecting scientists who share related strains.Ongoing developments of the ABRomics platform include data brokering of genomic samples to the European Nucleic Archive (ENA), standardized workflows for metagenomics analysis, and tools for analyzing (meta)pangenomes. Importantly, data management procedures comply with the FAIR principle (Findable, Accessible, Interoperable and Reusable) thus enabling retrospective epidemiological studies to be conducted.
Source: HAL
Authors: Lao, Julie, Tackx, Raphaël, Dieuaide, Amanda, Mignon, Thomas, Siguret, Cléa, Lefeuvre, Hugo, Quemeneur, Brieuc, Marin, Pierre, Batut, Bérénice, Goué, Nadia, Ruppe, Etienne, Le Corguillé, Gildas, Consortium, Abromics, Bihouée, Audrey, Chaffron, Samuel, Gaignard, Alban, Glaser, Philippe, Medigue, Claudine, Mareuil, Fabien
Institutions: Centre National de la Recherche Scientifique, Institut Français de Bioinformatique, Station Biologique de Roscoff, Université Clermont Auvergne, Laboratoire des Sciences du Numérique de Nantes, Université de Nantes, Nantes Université, Institut du Thorax, Université Paris Diderot, Infection, Anti-microbiens, Modélisation, Evolution, Institut Pasteur
Language: English
Subfield: Microbiology (medical)
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7204673126