ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

Julie Lao (1, 2) , Pierre Marin (1, 3) , Romain Dallet (1, 4) , Fabien Mareuil (5) , Alix De Toisy (1, 5) , Kenzo-Hugo Hillion (6) , Aurélien Birer (7) , Nadia Goué (3) , Richard Bonnet (7) , Etienne Ruppé (2) , Gildas Le Corguillé (1, 4) , Philippe Glaser (8) , Claudine Médigue (1, 9)

1 IFB-CORE - Institut Français de Bioinformatique
2 IAME (UMR_S_1137 / U1137) - Infection, Anti-microbiens, Modélisation, Evolution
3 AuBi - Plateforme Auvergne Bioinformatique
4 ABIMS - ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science
5 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
6 Nantes Univ - Nantes Université
7 CHU Clermont-Ferrand
8 EERA - Écologie et Évolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance
9 UMR 8030 - Génomique métabolique

Antibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors. Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance. We are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with tailored mathematical and bioinformatics tools to answer generic and specific research questions related to ABR. The ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains supported with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results will be achieved through easy-to-use web interfaces. ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be available in summer 2023. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available.

Mots clés: antibioresistance; genomic surveillance; epidemiology; FAIR data; database; Galaxy Workflow

Domaines: Bio-informatique [q-bio.QM]; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Bactériologie

Julie Lao, Pierre Marin, Romain Dallet, Fabien Mareuil, Alix De Toisy, et al.. ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data. FEMS 2023 European Congress of Microbiology, Jul 2023, Congress Center Hamburg Hamburg, Germany, Germany. ⟨hal-04369134⟩