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Antimicrobial Resistance and Bacterial Virulence (AVB) Unit of the Lyon Laboratory

Head of Unit: Jean-Yves Madec

Deputy Head of Unit: Marisa Haenni

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

The unit works to strengthen the different surveillance schemes (RESAPATH network and European Antimicrobial Resistance Surveillance network in veterinary medicine (EARS-Vet)). It is also involved in French strategic actions (Carlet reportEcoantibio plans, interministerial roadmap for controlling antimicrobial resistancepriority research programme on antimicrobial resistance).

Research activities

The unit contributes to furthering knowledge on risks to humans associated with antimicrobial resistance in bacteria isolated from animals and the environment. It implements conventional microbiological, molecular, genomic and functional approaches. Its research topics deal in particular with gene flows between animals, the environment and humans (One Health approach) and the impact of exposure to antibiotics on microbiotas. As part of its research into alternatives limiting the use of antimicrobials, the unit is also engaged in studies on phage therapy. It participates in European (One Health EJP) and international (Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), FAO) programmes. Lastly, it contributes to an interdisciplinary approach to antimicrobial resistance including through the perspective of human and social sciences.

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. Dyaspeo assumes that contact with a pet (one in two households in France) also plays a role; it calls on experts in the fields of human and veterinary medicine, social sciences, genomics, mathematics, and in vitro/in vivo modelling to clarify this issue.

  • Seq2Diag (2021-2026)

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 diagnostic tools for antimicrobial susceptibility. This project combines expertise in human and animal microbiology, genomics, pharmacology and artificial intelligence. It also aims to discover new mechanisms of treatment resistance and 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 members include microbiologists, biochemists, structuralists, veterinarians, clinicians, pharmacologists, ecologists and intestinal microbiome experts working to determine the full spectrum of these compounds’ antimicrobial activity: bactericidal action, synergy/antagonism with other antibiotics, mechanisms of action, resistance and target(s), pharmacokinetic/pharmacodynamic parameters and experimental efficacy, impact on the gut microbiota and human metabolome, stability in the environment, and impact on microbial communities.

  • Full-Force (2020-2022)

Full-length sequencing for an enhanced EFFORT to map and understand drivers and reservoirs of antimicrobial resistance

Funding: One Health European Joint Programme (EJP)

The genomic surveillance of antimicrobial resistance needs to rely on methodological approaches capable of better distinguishing between the transmission of bacterial clones and that of mobile genetic elements (plasmids). Based on selected human and veterinary contexts, the European Full-Force consortium is focusing its efforts on harmonising long-read sequencing technologies and studying how they can contribute to a better understanding of antimicrobial resistance gene flows as part of a One Health approach.

Find out more about the One Health EJP

  • Pre-Empt (2021-2023)

High-throughput identification of antibiotic resistance progenitors across interconnected settings

Funding: French Research Agency, generic call for projects

Clinically important antimicrobial resistance genes originate in environmental bacteria. However, little is known about how these genes are mobilised from the environment. Using latest-generation genomic, metagenomic and functional approaches, Pre-Empt is pooling the forces of ANSES, INRAE, Institut Pasteur and Inserm to identify and quantify the reservoir of these genes that can potentially be transferred to pathogenic bacteria from aquatic environments. Its aim is to contribute to the development of predictive indicators for the transfer of resistance genes from the environment to clinically relevant bacteria.

Find out more about the project