Lyon Laboratory

• The Lyon Laboratory is a multi-purpose facility involved in all six of the strategic cross-cutting fields addressed by ANSES. It is active in the following areas:
  • Neurodegenerative diseases in animals and humans, with particular emphasis on transmissible subacute spongiform encephalopathies in animals, and the link between neurodegenerative diseases in humans and pesticides,
  • Antimicrobial resistance and bacterial virulence,
  • Animal mycoplasmas,
  • Characterisation and monitoring of pesticide resistance development phenomena,
  • Epidemiology: surveillance, investigation, research into surveillance methods and antimicrobial resistance.

• The Lyon Laboratory is the national reference laboratory (NRL) for transmissible spongiform encephalopathies in animals (bovine spongiform encephalopathy [BSE] and scrapie).

• The Lyon Laboratory coordinates two major national surveillance networks:
  • RESAPATH, the surveillance network for antimicrobial resistance in pathogenic bacteria of animal origin,
  • Vigimyc, the epidemiological surveillance network for ruminant mycoplasmas.

• The Lyon Laboratory coordinates and contributes to epidemiological surveillance platforms for animal health, plant health and food chain safety.

• The Lyon Laboratory coordinates the writing and publishing of the Bulletin Epidémiologique (BE) on Animal Health - Food Safety. Produced by ANSES and the Directorate General for Food (DGAL) of the Ministry of Agriculture, this French open-access scientific journal allows ANSES and the DGAL to exchange information with local, regional and national players working in the field of animal health and food safety.

• The Lyon Laboratory contributes to the thematic research network for animal health in the Auvergne Rhone-Alps region (SAARA), set up jointly with INRAE and VetAgro Sup in 2018. The objective is to initiate and support a network of regional players in animal health and to balance the network’s positioning to reflect the role of ANSES with respect to INRAE and VetAgro Sup.

• The Laboratory includes:

• An antimicrobial resistance and bacterial virulence (AVB) unit,
• An epidemiology and surveillance support (EAS) unit,
• A neurodegenerative diseases (MND) unit,
• A joint-research unit (UMR) formed by ANSES and VetAgro Sup for ruminant mycoplasmas,
• A contracted unit (USC) for the characterisation and monitoring of pesticide resistance development (CASPER) phenomena in relation with INRAE.

• The antimicrobial resistance and bacterial virulence unit

The scientific positioning of this unit aims to enable a better understanding of the risk posed to humans by antimicrobial resistance of non-human origin, through an approach based on conventional, molecular, genomic and functional microbiology, closely linked with the epidemiological approach implemented by the EAS unit. The scientific projects undertaken mainly concern the flow of genes between animals, the environment and humans as part of a “One Health” approach, the impact of antimicrobial exposure on intestinal microbiota, and an understanding of the formation of bacterial biofilms acting as an ecological barrier against antimicrobial efficiency. As part of its research into alternatives limiting the impact of antimicrobials, the unit is also engaged in studies on phage therapy.

• The epidemiology and surveillance support unit

Research into epidemiology and surveillance concerns:

• the determinants of population health (risk factors, resistance factors),
• improvements to surveillance methods (syndromic, risk-based),
• assessments of the efficiency of surveillance, prevention and control methods in the fields of animal health, plant health and food safety (cost-benefit analyses, decision trees, qualitative assessments),
• the epidemiology of antimicrobial resistance (temporal dynamics, links between use and resistance, determinants of resistance).

• The neurodegenerative diseases unit

This unit studies the diseases associated with protein folding anomalies, represented primarily by prion diseases and other neurodegenerative diseases such as Parkinson’s in humans. The projects underway primarily concern disorders associated with the alpha-synuclein protein, the best known of which is Parkinson’s disease. One of the remarkable characteristics of this disease is the early and significant involvement of the digestive tract, based on the hypothesis of an as-yet undetermined pathogen initiating the pathological process, which is then thought to progress to the central nervous system through prion-like mechanisms. In the same way as for studies on prion diseases, research is based on transgenic or conventional experimental models. The objective is to establish the extent to which exposure to pesticides, particularly via food, is likely to initiate the associated protein aggregation phenomena and/or chronic neuroinflammatory processes.

• The joint-research unit on ruminant mycoplasmas

Given the exotic nature of mycoplasmas, their resistance to antimicrobial therapy, and the lack of effective vaccines, the emergence or re-emergence of these animal diseases can have serious consequences from both an economic and health standpoint. In the case of ruminants, three mycoplasma pathogens are listed by the OIE. The Vigimyc network provides a detailed picture of the circulation of mycoplasmas in ruminants across France, and has made it possible to build up a large collection of strains for use in scientific studies on the biodiversity and virulence of Mycoplasma genus bacteria, and on the clinical expression of the associated diseases in ruminants. The scientific orientations of the joint-research unit concern two main fields: 1) the virulence and emergence of mycoplasmas and 2) the diversity and antimicrobial resistance of mycoplasmas.

• The contracted unit on the characterisation and monitoring of phenomena of pesticide resistance development

The contracted unit is studying the emergence and development of phenomena of pesticide resistance development in the main plant pests (fungi and oomycota, insects, bacteria and weeds). It is working in a context where the requirement is to reduce the quantity and diversity of the active substances authorised. With this in mind, the Unit develops methods and tools for detecting resistance through both biological and molecular approaches. Its research activities are focused on two model biological systems: adaptation dynamics and resistance mechanisms of the green peach aphid (Myzus persicae), and spatial and temporal changes in resistance to respiration-inhibiting fungicides in grapevine downy mildew (Plasmopara viticola).

The unit is a member of the Pesticide Resistance Forum and Research network (R4P), alongside INRAE and the Ministry of Agriculture. The aim of the R4P network is to develop greater dialogue between scientists and to widely disseminate resistance detection methods between research communities, primarily in order to predict, delay and/or manage resistance selection more effectively.

• Visit the network website: https://www.r4p-inra.fr

In the reference field (first-line or confirmatory analyses, development of analytical methods, coordination of accredited laboratory networks through the organisation of inter-laboratory tests, reagent verification, scientific and technical support, expert appraisals, etc.), the Lyon Laboratory holds several mandates:

• National reference laboratory for transmissible spongiform encephalopathies (TSEs) in animals (bovine spongiform encephalopathy [BSE] and scrapie). In this capacity, the Lyon Laboratory:
  • Develops, optimises, approves and implements reference techniques for confirming first-line diagnoses and for the molecular typing of the prions involved in these diseases,
  • Conducts research into this topic,
  • Coordinates the network of TSE accredited laboratories,
  • Organises inter-laboratory proficiency testing on screening methods for accredited laboratories,
  • Stores TSE reference materials and makes them available to accredited laboratories,
  • Carries out batch control for one of the screening tests on behalf of the European Union reference laboratory for TSEs,
  • Responds to requests for scientific and technical support from the authorities, primarily with respect to the reallocation of TSE facilities in accredited laboratories.

• Reference laboratory without a mandate for contagious bovine pleuropneumonia (CBPP) and contagious caprine pleuropneumonia (CCPP),

• Reference laboratory without a mandate for resistance to pesticides, involved in the annual “Resistance” surveillance plans put in place by the Ministry of Agriculture to study the resistance of plant pests to plant protection products.

• Laboratory contributing to the mandate of the FAO Reference Centre for Antimicrobial Resistance.

In the surveillance field, the Lyon Laboratory:

• Jointly leads RESAPATH, the surveillance network for antimicrobial resistance in pathogenic bacteria of animal origin, with the Ploufragan-Plouzané-Niort Laboratory,
  • Visit the network website
• Coordinates Vigimyc, the epidemiological surveillance network for ruminant mycoplasmas,
  • Visit the website
• Analyses the quality of data from food safety monitoring and control plans,
• Centralises, analyses, prepares and submits annual data on zoonoses (TSSEs, tuberculosis, brucellosis, salmonellosis, rabies, West Nile fever, echinococcosis) and antimicrobial resistance (on E. coli, Salmonella, Campylobacter) to EFSA as part of European surveillance plans.

The Lyon Laboratory is also a contributor to the three national epidemiological surveillance platforms:

• Platform for the epidemiological surveillance of animal health (ESA): coordination, cross-cutting support in epidemiology, IT and biostatistics, involvement in working and monitoring groups,
  • Visit the platform website
• Platform for the surveillance of the food chain (SCA): cross-cutting support in epidemiology, IT and biostatistics, involvement in working and monitoring groups,
• Platform for the epidemiological surveillance of plant health (ESV): coordination, cross-cutting support in epidemiology, IT and biostatistics, involvement in working and monitoring groups,
  • Visit the platform website

Regional partners

VetAgro Sup, University of Lyon 1, University of Lyon 3, University of Auvergne, University of Lyon (ENS), Lyon Neuroscience Research Centre, Bioaster, Rhone-Alps Regional Federation for Controlling Harmful Organisms (FREDON), LVD69 Departmental Veterinary Laboratory, National Centre of Reference for Staphylococci.

National partners

INRAE (French National Research Institute for Agriculture, Food and the Environment), CIRAD (French Agricultural Research Centre for International Development), INSERM (French National Institute of Health and Medical Research), CNRS (French National Centre for Scientific Research), Institut Pasteur, ENVT (National Veterinary School of Toulouse), ONIRIS (National Veterinary School of Nantes), ENVA (National Veterinary School of Alfort), EFS-Montpellier Blood Bank, Paris Brain and Spinal Cord Institute, University of Paris VII, University of Limoges, Santé Publique France, CEA (French Alternative Energies and Atomic Energy Commission), ONERBA (French National Observatory of the Epidemiology of Bacterial Resistance to Antimicrobials), ADILVA (French Association of Managers of Public Veterinary Testing Laboratories), SNGTV (French National Society of Veterinary Technical Groups), AFVAC (French Association of Vets for Pets), AVEF (French Equine Veterinary Association), IFCE (French Institute of Horses and Riding), INTERBEV (French Interprofessional Association for Livestock and Meat), IDELE (French National Livestock Institute), CTIFL (Technical Interprofessional Centre for Fruit and Vegetables), ACTA (French Agricultural Technical Institute), GDS France Health Protection Group, APCA Chambers of Agriculture, INRIA (French National Institute for Research in Digital Science and Technology).

International partners

Federal Institute for Risk Assessment (BfR, Germany), Federal Office of Consumer Protection and Food Safety (BVL, Germany), Freie University Berlin (Germany), Friedrich Loeffler Institut (FLI, Germany), Max Planck Institute (MPIWG, Germany), Robert Koch Institute (RKI, Germany), Austrian Agency for Health and Food Safety (AGES, Austria), Medical University of Vienna (Austria), VIB-VUB Center for Structural Biology (Belgium), University of Calgary (Canada), University of Guelph (Canada), Statens Serum Institut (SSI, Denmark), Technical University of Denmark (DTU, Denmark), Complutense University of Madrid (UCM, Spain), Fundación Pública para la Gestión de la Investigación de Salud en Sevilla (FISEVI, Spain), Ramón y Cajal Institute for Health Research (IRYCIS, Spain), Veterinary Medical Research Institute of the Hungarian Academy of Sciences (VMRI, Hungary), National University of Ireland Galway (NUIG, Ireland), University College Dublin (UCD, Ireland), European Food Safety Authority (EFSA, Italy), Istituto Superiore di Sanità (ISS, Italy), Istituto Zooprofilattico Sperimentale del Piemonte (IZS, Italy), University of Tripoli (Lebanon), Norwegian Veterinary Institute (NVI, Norway), National Institute for Public Health and the Environment (RIVM, Netherlands), Nederlands Center for One Health (NCOH, Pays-Bas), Wageningen Bioveterinary Research (CVI, Netherlands), National Veterinary Research Institute (PIWET, Poland), University of Veterinary and Pharmaceutical Science (VFU Brno, Czech Republic), National Veterinary Institute (SVA, Sweden), Office Fédéral de la Sécurité Alimentaire et des Affaires Vétérinaires (OSAV, Switzerland), University of Fribourg (Switzerland), Animal and Plant Health Agency, (APHA, UK), Cambridge University (UK), Exeter University (UK), Liverpool University (UK), Public Health England (PHE, UK), Iowa State University (USA), Finnish Food Authority (Finland).