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The European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) is a key component of the genomic surveillance of multidrug-resistant bacteria and, as such, plays a vital role in public health. It is coordinated by the European Centre for Disease Prevention and Control (ECDC).

This European surveillance programme, based on epidemiology and whole-genome sequencing, aims, in particular, to determine the geographic distribution and population dynamics of multidrug-resistant clones and transmissible resistance elements to inform risk assessment, prevention and control policies and to support countries in developing technical capability and proficiency for genomic-based surveillance of multidrug-resistant bacteria with epidemic potential.

A pasteurian leading biobank

To address these public health challenges, EURGen-Net currently relies on the participation of national reference laboratories (CNR) or equivalent laboratories from 34 European countries. 
 
For the past two years, the ECDC, as part of EURGen-Net, has been contracting the expertise of the Biological Resource Centre of the Institut Pasteur (CRBIP), headed by Fay Betsou. Recognized and commissioned as a specialist central biobank, the CRBIP centralises, purifies and analyses bacterial isolates from 34 European countries for two groups of pathogens: Acinetobacter baumannii and Klebsiella pneumoniae, bacteria that have become resistant to the carbapenem class of antibiotics and/or colistin (for more information, see the box dedicated to these bacterial strains).  A third group, Pseudomonas aeruginosa, will follow in 2027.

The handling of bacterial samples is carried out by the team of the Collection of the Institut Pasteur (CIP), a unit part of the CRBIP and led by Meriem Paris. The scientists of this unique unit within the institute thus carry out a series of essential steps using standardized methods and innovative bioinformatics technologies, which include:

• receipt of isolates,  

• their analysis and identification by mass spectrometry,  

• the characterisation of their resistance profiles against a target panel of antibiotics,  

• their provision to a sequencing partner, commissioned by the ECDC, for whole-genome analysis,

• the storage and preservation of all isolates on behalf of the ECDC.

This process ensures that samples are thoroughly characterized and purified, in compliance with health and safety and environmental standards, as well as with applicable laws and regulations. These methodologies and their implementation now place the CRBIP, and all its entities, in a unique position at national, European and international levels as a leading transdisciplinary biobank. These activities are characterized by a substantial volume of laboratory work and bioinformatic analyses, and generate a wealth of data.  

Figures that reflect ongoing and sustained efforts to make strains of interest available

Related to the EURGen-Net network alone, the CRBIP, via the CIP, has accumulated several thousand isolates and an equivalent number of analyses to be carried out on more than 2,000 genomes ready for sequencing. The sequences are then sent to the ECDC for analysis, with the aim of making them publicly available, in line with the principle of Open Science. 

Find some key figures here

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As part of this project, the CRBIP’s GIPhy bioinformatics group has developed an original and innovative in silico analysis method for detecting contamination. Tested across a wide range of scenarios, this computational pipeline can detect the presence of a contaminating strain down to relatively low levels, e.g. < 5% contamination by a very closely related genome (ANI > 98%).

Thanks to its expertise, research and innovative methods, the CRBIP effectively meets the needs and requirements of the EURGen-Net network, thereby demonstrating a genuine ability to respond swiftly and contribute to the fight against bacterial antibiotic resistance and multidrug resistance. This involves addressing health, epidemiological and public health challenges as well as scientific ones.

At the same time, and covering a wider range of bioresources, the CRBIP continues its mission to preserve and make available, for research, training and quality control purposes, microbial (bacteria, fungi, viruses) and human bioresources, whether historical or newly collected. This substantial volume of fully characterized samples constitutes extremely valuable biological material for the scientific community as a whole and for the Pasteurian community in particular. The CRBIP teams are at your disposal to make the bioresources in their catalogues available to you for your fundamental and clinical research projects.

Verbatim
 
 

“We are thrilled to have delivered on the first survey of this flagship and high impact project. We have proven our capabilities and expertise and the robustness of our processes in high throughput mode.”

Fay Betsou, CRBIP Director

“This project has truly highlighted the amazing mobilization and dedication of the CIP team throughout. Every member stepped up with a strong commitment, ensuring that each phase of this key public health study was carried out with rigor and precision. This achievement reflects more than just technical expertise, quality and reliability of results, it demonstrated our ability of working together toward a shared Public Health objective. The CIP is proud to ensure the safe preservation of such a high number of key AMR strains.” 

Meriem Paris, head of the CIP

“The ECDC project requires navigation through high-throughput operations and multi-site complexities while maintaining strict international standards. From secure reception and standardized characterization  to preservation and sequencing readiness, we ensure full traceability and sample integrity. By providing fit-for-purpose biological resources to the ECDC network, CRBIP reinforces global antimicrobial resistance surveillance. The planned extension to P. aeruginosa underscores the ECDC’s continued trust and CRBIP’s established role as a transdisciplinary reference biobank serving open science and international health security.”

Camille Alizadeh, CRBIP Project Manager

 

“Carbapenem-resistant Acinetobacter baumannii is a critical pathogen for public health in Europe. The services provided by CRBIP, in the ongoing contract with ECDC directly enable the participation of 36 countries in the ‘ECDC CRAb survey 2024–2025’, by supporting their submission of strains, with MALDI-ToF speciation, and performing antimicrobial susceptibility testing (AST) on a subset. These CRBIP activities enable ECDC to provide national representatives with information to support their activities for CRAb preparedness, and infection prevention and control, in acute care hospitals.
Additionally, I greatly appreciated that CRBIP has also worked closely with the EUCAST Development Laboratory (EDL) to calibrate its AST results for the survey, and is collaborating with EDL and EUCAST to enhance its AST methodologies. As a result, EUCAST has uploaded a large subset of the AST results from this survey to its public database, thereby benefiting the broader scientific community. The competence, service-mindedness and efficiency of the team are something I truly appreciate – together with their friendly, collaborative, and collegial outlook."
 

Pete Kinross, interlocuteur ECD