Infections caused by antibiotic-resistant pathogenic bacteria pose a growing global threat to human, animal, and environmental health. Antimicrobial resistance (AMR) manifests as the failure of treatment for an infection caused by a microorganism (bacteria, virus, fungus, or parasite). It can lead to a therapeutic dead end and result in excess mortality.
AMR is driven by the widespread and uncontrolled use of antibiotics. It arises from changes in the bacterial genome caused by mutations or by the exchange of antibiotic resistance genes between bacteria. The spread of AMR is particularly rapid among bacteria that possess two types of DNA: the main chromosome and smaller mobile DNA molecules (mobile genetic elements). When a bacterial population becomes resistant to an antibiotic and the responsible gene is located on a mobile genetic element, this gene can be transferred from one bacterium to another, whether of the same or a different species. Bacteria that are multi-resistant to antibiotics are found everywhere: in humans, animals, food, and associated with plants and the environment (water, soil, and air). Their spread knows almost no bounds!
The multidisciplinary “One Health” approach takes into account these three sectors: human, animal, and environmental. It is essential for gaining a real-time overview of the emergence, evolution, and spread of (multi-)drug-resistant bacteria among human populations and ecosystems.
Bioinformatics as a Tool for Research and Surveillance of Antibiotic Resistance
A bacterium’s genome is an extremely rich source of information for identifying mechanisms of antibiotic resistance and for reconstructing its evolutionary history and spread. On average, bacterial genomes consist of 3,000 genes, corresponding to 3 million DNA base pairs. Bioinformatics is the application of computer science to the life sciences to extract relevant information from biological data. It is an essential tool for rapidly analyzing the vast amounts of data represented by the genomic sequences of thousands of bacterial strains, as well as for querying and visualizing data on nucleic acid sequences, bacteria (i.e., location and date of isolation), and analysis results. Computing is also necessary to store and organize data in database structures, and finally to share this data.
Pathogen bioinformatics (viruses, bacteria, fungi, and parasites) integrates various fields of bioinformatics to understand the genetic and molecular mechanisms of pathogens and antimicrobial resistance, with the aim of improving diagnosis, treatment, prevention, and surveillance of epidemics.
Pathogen bioinformatics therefore plays a crucial role in modern infectious disease research, providing essential information for public authorities to develop preventive and emergency measures.
ABRomics: A Solution for Managing, Processing, and Sharing Data on Antibiotic Resistance
To support research in the field of antibiotic resistance, the Priority Research Program has been funding the ABRomics structuring project since 2022. This national digital platform enables the hosting, management, processing, and sharing of genomic and metagenomic data for the surveillance and research of antibiotic resistance, using a One Health approach.
ABRomics brings together a multidisciplinary consortium of 43 teams from leading French research organizations. These teams cover the full spectrum of antibiotic resistance research in both clinical and basic science fields across the human, animal, and environmental sectors, as well as a range of expertise in bioinformatics, computer science, databases, IT architecture, and mathematical modeling. The ABRomics project is coordinated by the French Institute of Bioinformatics and the Pasteur Institute.
The main objectives of the ABRomics project are:
Establish a centralized, multi-omic, structured, interoperable, and standardized repository of microbiological data from human, animal, and environmental sources by
- covering a wide range of sample types collected from patients, in food, from animals, and in the environment.
- developing and expanding a database of resistance genes
- applying FAIR principles (Findable, Accessible, Interoperable, Reusable) to facilitate data sharing in the context of surveillance and research on antibiotic resistance
Provide open access to a suite of genomic and metagenomic data processing pipelines, along with quality control measures and standard and specialized (meta)genomic analysis methods, to facilitate reproducible data analysis in accordance with the principles of open science.
The ABRomics project therefore aims to establish an infrastructure for storing and sharing data on pathogenic bacteria and antibiotic resistance in order to optimize surveillance and research, first at the national level and then at the international level.
The services currently offered by the ABRomics platform in its genomic version
The ABRomics platform is available to users with a personal account, which allows them to upload and analyze their data. Creating an ABRomics account is quick and easy. It is open to anyone with an institutional email address in France; others may be eligible if they are collaborating with an institution and have been approved by the ABRomics steering committee.
The platform offers user-friendly interfaces that allow you to:
Create and manage (collaborative) projects: Users set the privacy level for their projects and invite collaborators with different access rights
Upload sequence files and metadata from a pre-filled Excel file (metadata repository) for the strains to be analyzed, or from the dedicated web interface, which guides the user through the expected values using controlled vocabulary
Follow the steps of the genomic analyses that are performed automatically once the data has been uploaded to ABRomics:
- Data quality control and assembly of short DNA reads from genome sequencing into longer fragments when uploading files in fastQ format; or quality control of an assembly when uploading files in fastA format.
- species identification and bacterial typing using Multi-Locus Sequence Typing (MLST and cgMLST) methods (core genome)
- characterization of plasmid genes and prediction of Mobile Genetic Elements (MGEs)
- Prediction of antibiotic resistance genes and virulence genes
View the full analysis report and download the results (Excel or PDF format)
Explore data (metadata, analysis results) using filters that can be easily combined. Queries can be performed within a single project or across projects among ABRomics users, with different data sets accessible depending on whether samples are private or public.
Visually display certain results in an interactive manner: maps showing the spatial distribution of resistance genes, clustering of the studied strains based on the distance between their cgMLST profiles in terms of the number of different genes, etc.
Create alerts that notify you when new data added to the community database matches specific search criteria you have defined.
A fundamental principle of the ABRomics platform is to make data available that enables connections to be made between strains and fosters collaboration among partners within the One Health framework.
In conclusion: Why choose the ABRomics platform?
At the laboratory level, ABRomics provides bioinformatics support for the automation of sequence analysis using standardized, regularly updated pipelines that draw on reference databases on antibiotic resistance, which are also updated. The platform allows users to manage and query all of their laboratory’s genomic data—and soon metagenomic data—which is organized in a database. This enables them to identify an older strain belonging to the same clone as a recent strain using cgMLST analyses. All of these analyses can be performed without any prior knowledge of bioinformatics.
ABRomics enables consortium-based projects through its project-based organization, which features different levels of access rights. The sharing of certain data across all ABRomics bacterial genomes facilitates collaboration and helps break down barriers between the environmental, animal, and human sectors; between academic and clinical research; and with surveillance networks, particularly national reference centers.
On a national scale, ABRomics aims to build, in real time, genomic and metagenomic repositories on antibiotic resistance and to contribute to health surveillance in this field. “FAIRification” and data integration enable reproducible analyses, optimize data reuse while protecting data providers and privacy, and facilitate the sharing of information with public authorities and citizens.
Finally, bacteria know no borders, and the ABRomics project aims to foster international collaboration with similar organizations in other countries or at the European level.
Short video introducing the ABRomics platform
Authors
Claudine Médigue
ABRomics Project Coordinator
CNRS UAR3601 French Institute of Bioinformatics & UMR8030 Genoscope/LABGeM, Evry, France
Philippe Glaser
ABRomics Project Coordinator
Institut Pasteur, Ecology and Evolution of Antibiotic Resistance, Paris, France
