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ABRomics - a digital platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

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  • Title:
    ABRomics - a digital platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data
  • Author: Marin, Pierre ; Lao, Julie ; Hillion, Kenzo-Hugo ; Birer, Aurélien ; Goué, Nadia ; Bonnet, Richard ; Mareuil, Fabien ; Le Gorguille, Gildas ; Ruppe, Etienne ; Abromics, Consortium ; Glaser, Philippe ; Médigue, Claudine
  • Subjects: Bacteriology ; Biochemistry, Molecular Biology ; Bioinformatics ; Computer Science ; Genomics ; Life Sciences ; Microbiology and Parasitology
  • Description: Antibiotic resistance (ABR) is a major public health issue prioritized for mitigation by major international institutions, especially regarding the emergence and the global dissemination of multidrug resistant (MDR) isolates and of antibiotic resistance genes (ARGs) carried by mobile genetic elements. They are also transmitted between humans, animals and the environment, without borders. The evolution of ABR is a complex process with multiple selective forces in different environments.Genome sequences, which contain all the genetic information of an organism, can be used for molecular typing purposes with the highest resolution, the identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Combined with epidemiological information, bacterial Whole Genome Sequencing (WGS) can enable tracking transmissions of outbreaks and identifying a source of contamination. Reinforcing the sharing of high-quality sequence data for diagnostic and epidemiological applications, together with interoperable and curated metadata, which can be integrated with other omics data, is a key requirement for understanding the complexity of spatiotemporal patterns of pathogen and ARGs transmission between compartments.Today, if more systematic genome sequencing and bioinformatics analysis can partially address such major issues, data sharing and comparison across centers, together with standardization of analytical workflows remain major bottlenecks. The ABRomics project aims to develop a secure One Health, online platform to make bacterial infectious disease (meta)genomics data and their associated clinical and epidemiological metadata accessible to a meta-network of researchers including epidemiologists, clinical microbiologists and the wider research community. It should provide the diverse communities with a user-friendly platform to store, share and analyze genomic information together with their metadata. It will also serve as a data brokering hub to ease the submission of data sequences into international repositories.The platform will meet two main objectives:1. Establish a repository of structured, interoperable, standardized, and well-annotated multi-omics microbiology data with tailored mathematical and bioinformatics tools that can be used to answer specific research questions related to ABR.2. Establish a shared platform to facilitate retrospective and prospective surveillance of ABRs in human and veterinary medicine, including environmental and food isolates, to enable near-real-time surveillance of pathogen transmission and outbreaks with actionable results for public health authorities. FAIR (Findable, Accessible, Interoperable and Reusable) data management procedures will enable retrospective studies.We will present here the ongoing development of the three main modules of the ABRomics platform architecture: (i) ABRomics-BIOINFO: an IT infrastructure with high capacity of data storage and data analysis, accessible to users under defined rules and offering a general software environment, both HPC and Cloud environments, (ii) ABRomics-DB: an integrated multi-omics microbiological databases for the Human-Animal-Environment sectors, and (iii) ABRomics-WF: standard tools and pipelines for (semi) automatic analysis of NGS data from pathogenic strains.The ABRomics project is led by the Institut Français de Bioinformatique (IFB), the Institut Pasteur and is made up of a consortium of 45 specialized teams belonging to the main French research organizations.
  • Language: English
  • Source: Hyper Article en Ligne (HAL) (Open Access)
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