Antimicrobial resistance is a global phenomenon with no geographical or species boundaries, which poses an important threat to human, animal and environmental health. It is a complex and growing problem that compromises our ability to treat bacterial infections.

The French Priority Research Programme (Programme Prioritaire de Recherche, PPR) on Antimicrobial resistance

In response to this urgent global challenge and in agreement with the Word Health Organisation (WHO) recommendations, France has joined other European countries and the USA, in launching a national Priority Research Programme (PPR) focused on antibiotic resistance, and financed with a €40 million budget by the Government. The plan is developed around four inter-disciplinary and interconnected pillars within the “One Health” context: 

– Creation of a professional network (PROMISE)

This network aims to federate all research and surveillance actors in the field of antibiotic resistance, to foster collaborations and generate new clinical, epidemiological, veterinary and environmental data. This will accelerate research and improve estimations of the true impact and cost of antibiotic resistance.

– Creation of a national observatory group dedicated to social sciences (DOSA)

This observational network, which focuses on the analysis of dialogue, behaviors and social practices linked to prescription, is a key element in understanding the socio-cultural and contextual roots of antibiotic resistance and prescription.

– Creation of an integrated microbial and multi-omics data platform dedicated to antibioresistance (ABRomics-PF).

The platform will take into account the interoperability of biobanks and databases, and include the development of mathematical and bioinformatic tools. ABRomics-PF will facilitate modeling of the evolution and spread of resistance: it will both enhance surveillance in France and boost research in a holistic, cross-sectoral approach.  

The ABRomics platform: an answer to the need of a national portal allowing interoperability of data and analysis tools related to antimicrobial resistance

Genome sequence data contain all the genetic information of an organism: it can be used for molecular typing purposes with the highest resolution, the identification of Antibiotic Resistance Genes (ARGs) and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility.  Antibiotic resistance is not specific to bacteria responsible for infectious diseases: the microbiome – a collection of non-pathogenic bacteria, viruses, parasites, fungi and their genetic material – represents a reservoir and potential source of resistant bacteria that can enhance dissemination.  Combination of  bacterial Whole Genome Sequencing (WGS) and Metagenome Sequencing with epidemiological information can enable tracking transmissions of outbreaks and identifying a source of contamination. A One Health approach is thus needed to identify and quantify transmissions of strains, plasmids and genes between the three sectors (human, animal, environment).

Analysis tools are essential to produce secondary research data and new knowledge for clinical and public health microbiologists. These tools provide information on the submitted isolates (or the community for metagenomics data) such as taxonomy, plasmid and ARGs content, virulome, and information on the relations with other isolates, for example to infer hypothetical transmissions. Moreover, the research community needs to perform more sophisticated analyses on stored information, which goes beyond automated surveillance (i.e., complex transmission models), ideally by integrating other types of omics data (proteomics, metabolomics, etc). Indeed, the exploitation of the different data types requires reliable software tools, effective and reproducible workflows, standardized software environments, and powerful computing resources. 

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. 

Compare to different countries that have already set up specific web platforms dedicated to pathogenic bacteria and resistance genes analysis (see “Related links” section), France is catching up with the funding of the ABRomics project with aims at developing a secure One Health cross-sectorial online platform to make accessible bacterial infectious disease (meta)genomics data and their associated clinical and epidemiological metadata to a meta-network of researchers including epidemiologists, clinical microbiologists, and the broader research community.

For more information see: Goals of ABRomics 

Related links:

National ANTIBIOTIC RESISTANCE portal : https://ppr-antibioresistance.inserm.fr/fr/

Road map of the French Ministery :
https://sante.gouv.fr/IMG/pdf/strategie_nationale_2022-2025_prevention_des_infections_et_de_l_antibioresistance.pdf
https://i3m.aviesan.fr/Local/ihp/files/389/AntibioticResistanceV3_2020.04.27_VFinale.pdf

Selected projects of the ANR  call for research projects “Antibiotic resistance: understand, innovate, act” : 
https://anr.fr/en/call-for-proposals-details/call/8d247b7a1dd49c697f3a18b20d4bf59e/

World Health Organisation (WHO): Global genomic surveillance strategy :
https://www.who.int/initiatives/genomic-surveillance-strategy

Platforms set up in different countries :
NCBI Pathogen Detection: https://www.ncbi.nlm.nih.gov/pathogens 
Swiss Pathogen Surveillance Platform, SPSP: https://www.spsp.ch
The Integrated Rapid Infectious Disease Analysis, IRIDA: https://www.irida.ca
Center for Genomic Epidemiology, CGE: http://www.genomicepidemiology.org
Pathogenwatch: https://pathogen.watch
Enterobase: https://enterobase.warwick.ac.uk
Pathosystems Resource Integration Center, PATRIC: https://www.patricbrc.org