The Antimicrobial Resistance and Bacterial Virulence (AVB) Unit contributes to national and international policies to control antimicrobial resistance. It has nine permanent employees, including three researchers and six engineers/technicians. It also regularly hosts students at various stages of their university curriculum (Master, thesis, post-doctoral positions).

Surveillance activities 

The unit works to strengthen the different surveillance schemes (RESAPATH network and the European Antimicrobial Resistance Surveillance Network in Veterinary Medicine (EARS-Vet)). It is also involved in several French strategic actions (Carlet report, EcoAntibio plans, interministerial roadmap for controlling antimicrobial resistance, priority research programme on antimicrobial resistance). Lastly, it contributes to the activities of the FAO Reference Centre for antimicrobial resistance, an international mandate held by ANSES since 2020.

Research activities

The unit helps advance knowledge on risks to humans associated with antimicrobial resistance in bacteria carried by animals and found in the environment. It uses conventional microbiological, molecular, genomic and functional approaches. Its research topics mainly deal with gene flows between animals, the environment and humans (One Health approach) and the impact of antibiotic exposure on microbiotas. As part of its research into alternatives limiting the use of antibiotics, the unit is also engaged in studies on phage therapy. It participates in European and international programmes (Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), FAO). 

Main ongoing research projects

DYASPEO (2021–2027)

Dynamics of antimicrobial resistance spread, persistence and evolution between humans, animals and their environment

Funding: Priority research programme on antimicrobial resistance (ANR-PIA3)

Strategies to control the transmission of antimicrobial resistance from animals to humans focus primarily on the food chain. That said, methicillin-resistant Staphylococcus aureus (MRSA) transmitted to humans through contact with pigs – and not through food – sparked the only major political crisis that has occurred in Europe in the past 20 years[JA1] . DYASPEO hypothesises that contact with pets (owned by one in two French households) also plays a role; it calls on expertise in the fields of human and veterinary medicine, social sciences, genomics, mathematics and in vitro/in vivo modelling to clarify this issue.

Seq2Diag (2021–2027)

Whole genome sequencing and artificial intelligence to characterise and diagnose antimicrobial resistance and the potential for treatment failure

Funding: Priority research programme on antimicrobial resistance (ANR-PIA3)

Bacterial genome sequencing techniques have revolutionised our understanding of antimicrobial resistance. The objective of Seq2Diag is to provide proof of concept for their use in human and veterinary medicine as in silico tools for diagnosing antimicrobial susceptibility. This project combines expertise in human and animal microbiology, genomics, pharmacology and artificial intelligence. It also aims to discover new mechanisms of resistance and treatment failure.

NAILR (2021–2026)

Novel Anti-Infectives with Limited Resistance

Funding: Priority research programme on antimicrobial resistance (ANR-PIA3)

Faced with the shortage of novel antimicrobial agents, NAILR is studying four compounds in a new class of peptidomimetics. The consortium brings together microbiologists, biochemists, structuralists, veterinarians, clinicians, pharmacologists, ecologists and gut microbiome experts to determine the full spectrum of these compounds' antimicrobial activity.

FightAMR (2024–2026)

Novel global One Health surveillance approach to fight antimicrobial resistance using artificial intelligence and big data mining

Funding: ERA-NET JPIAMR-ACTION (DISTOMOS)

This project aims to develop new AI-powered surveillance solutions to identify the increased risk of the emergence of antimicrobial resistance (AMR) and the dynamics of its spread via food, based on the "One Health" concept. This will be achieved by a triangular approach aimed at: 

• developing a cloud-solution including auto-adaptive learning to integrate and mine public data from different sources (metagenomics, phenotypes, satellite, etc.), at different scales (region/setting/country, etc.) and with different subjects (human, animal, etc.);
• conducting an AI-guided experimental sample collection campaign;
• identifying monitorable biomarkers indicating an increased risk of infectious diseases.

SHINE-Vet (2025–2027)

Hygiene and nosocomial infections in veterinary establishments

Funding: EcoAntibio3 (2023–2028 National Plan)

In veterinary medicine, the term nosocomial, or hospital-acquired infection (HAI), covers all infections acquired by an animal during its hospitalisation. The aim of this project is to gain a better understanding of the causes and dynamics of HAIs so that they can be avoided as far as possible. It has two strands: a prospective longitudinal study conducted in six veterinary care establishments to map microbiological contamination, and the establishment of a multidisciplinary working group tasked with issuing recommendations for the prevention and management of HAIs. 

COMPASCOPE (2025–2027)

Study of the healthy carriage of multi-drug resistant bacteria (MRB) in dogs and cats

Funding: EcoAntibio3 (2023–2028 National Plan)

In France, monitoring of pets is currently limited to pathogenic bacteria (RESAPATH), as there is no programmed surveillance system for resistant bacteria found in healthy carriage in animals not intended for consumption. The aim of this project is therefore to provide an initial overview of the healthy carriage of MRB in dogs and cats in the Nouvelle-Aquitaine region. According to the prevalence observed for each of the pathogens, the results will be used to determine whether or not it is appropriate to establish a regular surveillance system for AMR in healthy carriage in pets, and define actions to prevent its spread.

SentiRub (2026–2028)

Study of the role of peridomestic rodents as sentinels for antibiotic resistance in urban environments as part of a One Health approach

Funding: EcoAntibio3 (2023–2028 National Plan)

The SentiRub project will document the presence of multi-drug-resistant bacteria in rodent populations in Lyon, according to the sources of contamination of their habitats (near hospitals, dog parks or wastewater treatment plants). This coordinated One Health approach will help determine whether rodents could serve as indicators of contamination sources, and therefore play a role in AMR monitoring and the implementation of public health strategies.

ResaFaune (2026–2028)

Surveillance of antimicrobial resistance in wildlife

Funding: EcoAntibio3 (2023–2028 National Plan)

There is currently no scheme in place in France for monitoring antimicrobial resistance in wildlife. The RESAPATH network only monitors domestic animal species. This project therefore aims to lay the foundations and demonstrate proof of concept for national surveillance of antimicrobial resistance in wildlife, developed around professional bodies recognised for their expertise in this animal sector and integrated into a coordinated scheme able to provide reliable, regular data on the current state of antimicrobial resistance contamination.

INOCULA project (2026–2027)

Airborne fungal inocula and fungicide resistance markers in sugar beet cultivation

Funding: ANSES

Partners: ANSES (Mycology Unit of the Plant Health Laboratory, National Genomics Platform – Ploufragan-Plouzané-Niort Laboratory) and the Technical Institute for Beet.

In studies of fungicide resistance, field samples generally consist of fungal lesions on leaves or fruit. These samples can only be taken once a disease has been diagnosed and the symptoms are clearly visible, despite the application of fungicide treatments. This monitoring provides information on the phenotypes and genotypes that have been selected following the treatments, but cannot be used to characterise the composition of the airborne inoculum populations. A better understanding of the allelic composition of fungicide resistance in this primary inoculum, along with monitoring of its temporal dynamics, could provide crucial information for adapting treatments and developing resistance management strategies. The deployment of spore traps combined with high-throughput sequencing technologies offers new opportunities for monitoring and characterising airborne spore populations of plant pathogens. This project aims to assess the value of low-cost passive spore traps for studying airborne inocula using high-throughput sequencing. More specifically, it will monitor populations of Cercospora beticola and the fungicide-resistance alleles they carry, in beet crops. This type of approach could ultimately enable better monitoring of the development of fungicide resistance in time and space, as well as the study of its link to field practices.