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Poster Communications Year : 2024

The ABRomics platform — a One Health Antimicrobial resistance analysis service

Kenzo-Hugo Hillion
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Nadia Goué
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Abstract

Antibiotic resistance (ABR) is a major global public health issue designated for urgent action by international institutions, especially regarding the emergence and the global dissemination of multidrug resistant bacteria (MDRB) and antibiotic resistance genes (ARGs) carried by mobile genetic elements. They are widely transmitted between humans, animals, and the environmental domains (One Health context), without borders. Tracking transmissions of outbreaks and identifying sources of contamination is achievable with Whole Genome Sequencing (WGS) data combined with epidemiological information. Ensuring the sharing of high-quality sequence data alongside interoperable curated metadata are key requirements for understanding the spatiotemporal patterns of dissemination of MDRB and ARGs. The ABRomics platform is developed to address such major issues by facilitating systematic bioinformatics analyses for experts working on ABR and the wider research community. Users on the platform can deposit biological sequences, manage projects, and launch various types of analyses to answer generic and specific questions related to AMR. Associated with all deposited sequences, minimal metadata compatible with ENA submission (e.g. ENA prokaryotic pathogen minimal sample checklist: ERC000028) are requested to ensure traceability, and backward and forward compatibility in our data repository. Currently, the platform provides one standardized workflow for the detection of ARGs genes in bacterial genomes. It takes as input genomics WGS sequencing data and does the following analyses: quality checks, genome assembly, taxonomic assignation (species identification), MLST typing (strain identification), plasmid typing and finally detection of ARGs genes and virulence factors. The platform relies on the usegalaxy.fr Galaxy server to perform the bioinformatics analyses allowing complex scientific computation on the IFB Core Cluster. All workflows of the ABRomics project are published on the Intergalactic Workflow Commission and all tools are available on the Galaxy ToolShed to ensure reproducibility and accessibility to the scientific community. The interface enables the users to search and cross-reference results of previous analyses stored in our database. Among the different features provided, we focused on highlighting search results based on the presence of genes conferring resistance or a particular predicted phenotype. Furthermore, fine-tuned permissions management and data encryption ensure the protection and confidentiality of user data. An Application Programming Interface (API) is also available for integration with other systems, enabling the platform to achieve interoperability. The ABRomics platform is accessible at this url: https://analysis.abromics.fr
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Dates and versions

hal-04618645 , version 1 (20-06-2024)

Identifiers

  • HAL Id : hal-04618645 , version 1

Cite

Julie Lao, Raphael Tackx, Pierre Marin, Amanda Dieuaide, Thomas Mignon, et al.. The ABRomics platform — a One Health Antimicrobial resistance analysis service. Journées Ouvertes en Biologie, Informatique, et Mathématiques - 2024, Jun 2024, Toulouse, France. ⟨hal-04618645⟩
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