Epidemiology and Surveillance Support Unit of the Lyon Laboratory



Head of Unit: Jean-Philippe Amat

Deputy Head of Unit: Viviane Hénaux

This unit carries out research and surveillance support activities in the areas of animal health, plant health and food-chain safety. It is made up of epidemiologists, biostatisticians, computer scientists, database administrators and a technical secretary, in addition to PhD students and interns.

Surveillance activities

The unit runs and provides scientific and technical support for several surveillance schemes coordinated by the Agency:

  • Resapath: French surveillance network for antimicrobial resistance in pathogenic bacteria of animal origin;
  • Vigimyc: epidemiological surveillance network for ruminant mycoplasmas;
  • Salmonella network: national epidemiological surveillance network for Salmonella of non-human origin throughout the food chain;
  • Resumeq: equine mortality surveillance network.

The unit also provides occasional support for the epidemiological and surveillance activities of the National Reference Laboratories (transmissible spongiform encephalopathies, Xylella, antimicrobial resistance, etc.). Moreover, it leads a consortium working to design a European surveillance network for antimicrobial resistance in veterinary medicine (EARS-Vet).

The unit coordinates the national epidemiological surveillance platforms for animal health (ESA) and plant health (ESV), in collaboration with the Directorate General for Food (DGAL) and the French National Research Institute for Agriculture, Food and the Environment (INRAE). It leads and contributes to several working groups within these platforms and within the surveillance platform for food-chain safety (SCA), and provides expertise in the areas of epidemiology, biostatistics and information technology (websites, applications) to benefit their surveillance schemes:

  • epidemiological surveillance platform for animal health: Observatory for Livestock Mortality (bovine/equine OMAR) and Surveillance programme for tuberculosis in wildlife (Sylvatub);
  • surveillance platform for food-chain safety: National optimisation of the epidemiological surveillance schemes for Salmonella (ONDES) and Data quality for surveillance and control plans, coordination of the network of stakeholders (Qualiplan);
  • epidemiological surveillance platform for plant health: monitoring of Xylella fastidiosa (including through the Shiny application) and contribution to the publication of health assessments and identification sheets for emerging and regulated pests.

The unit is involved in the national and international monitoring of major health hazards in the three areas and publishes dedicated bulletins (ESA, ESV, SCA). It also contributes to the inter-platform monitoring group on the quality of surveillance data and helps develop and improve methodologies for the evaluation of surveillance systems (Oasis method and other types of evaluations).

As part of the support provided to the French Ministry of Agriculture and the international authorities, the unit coordinates the writing and publishing by the DGAL and ANSES of the Bulletin Epidémiologique on Animal Health - Food Safety. It processes and analyses national surveillance data on zoonoses and antimicrobial resistance and submits them to the European Food Safety Authority (Efsa). Lastly, it supports the activities of the Food and Agriculture Organization of the United Nations (FAO) and its Member Nations as part of ANSES's mandate of FAO Reference Centre for antimicrobial resistance.

Research activities

The unit’s research activities are aimed at improving epidemiological surveillance methods and better understanding the determinants of population health in the fields of animal health, antimicrobial resistance, food safety and plant health. These activities are carried out as part of national or European funding programmes and deal with five themes: epidemiology of antimicrobial resistance, descriptive epidemiology, syndromic surveillance, evaluation and improvement of surveillance schemes, and risk assessment. The unit also initiates work to assess the role of high-throughput whole genome sequencing (WGS) methods in improving surveillance.

Main ongoing or recent research projects

NOWCASTING (2023-2024)

Nowcasting to estimate animal disease incidence based on reported outbreaks

Funding: CoVetLab

Having accurate data on the occurrence of a disease in infected areas is essential for assessing the risk of disease introduction. However, while multiple sources are available, the data are often incomplete, late or even absent. This project aims to explore the use of analytical techniques such as nowcasting to better predict the actual incidence of diseases in affected regions using available databases, and to recommend a methodology for real-time prediction of animal disease incidence.

ENVIRE (2021-2024)

Evaluation of the effectiveness of individual and group interventions to further control the spread of antimicrobial resistance from poultry via the environment

Funding: European Joint Programming Initiative on Antimicrobial Resistance-HARISSA (French Research Agency)

The purpose of the Envire project is to reduce the spread of antimicrobial resistance on poultry farms and in the environment, in order to reduce the risks to humans. The impact of various types of on-farm interventions will be evaluated: farming without antibiotics, E. coli vaccination, use of bacteriophages and phytotherapy as alternatives to antibiotics, and treatment of farm effluents. Five European countries and Tunisia are participating in the project, which will involve experimental and field studies. The unit will develop a model for the quantitative analysis of risks of human contamination via food and occupational activity.

See the project’s web page

REACTOSURV (2021-2024)

Reagent vigilance in animal health in France: current situation and avenues for development

Funding: ANSES-GDS France

This thesis includes an evaluation of the surveillance system for laboratory reagents (to detect problems such as lack of sensitivity, specificity, etc.) in the ruminant sector in France and is studying the feasibility of a supplementary real-time monitoring scheme, via the development and implementation of methods for modelling and analysing time series in order to detect anomalies.

COVRIN (2021-2023)

One Health research integration on SARS-CoV-2 emergence, risk assessment and preparedness

Funding: One Health EJP

The aims of this project are to identify drivers for the emergence and spread of SARS-CoV2 and to develop risk assessment models for this virus. The unit is involved in the part of the project dedicated to surveillance and risk assessment (animal-human interface), with a focus on the integration of surveillance activities and the mapping of surveillance data: comparison of surveillance activities between countries, identification of key partners with a view to integrative surveillance.

See the project’s web page

Surv1Health (2020-2023)

The monitoring of antimicrobial resistance in France: a One Health system?

Funding: EcoAntibio plan (DGAL)

The aims are to map the surveillance schemes for antimicrobial resistance implemented in various areas (human health, animal health and the environment), assess collaborative efforts across these schemes and obstacles and incentives for their implementation, and identify avenues for improvement with a view to integrated surveillance. The ECoSur tool is being used to assess the collaborations.

MOOD and DELSSA (2020-2023)

Monitoring Outbreak Events for Disease Surveillance in a Data Science Context

Deep Learning for Animal Health Surveillance

Funding: Horizon 2020 programme

The objective of the European MOOD project is to harness recent data analysis and visualisation techniques, including big data, to improve the surveillance of (re)emerging diseases as well as risk analysis and management. Tools are being developed for various types of users (general public, risk managers and assessors, etc.), for monitoring trends and anomalies, mapping risks, and accessing the results of models of disease spread. The unit is contributing to one of the project's components (DELSSA) by assessing the role of artificial intelligence methods (deep learning) in identifying emerging health phenomena and quantifying the impact of potential threats on human and animal health; it will propose a method for the spatial-temporal detection of anomalies.

See the project’s website 

MATRIX (2020-2022)

Connecting dimensions in One-Health surveillance

Funding: One Health EJP

The European MATRIX project is seeking to characterise and evaluate integrative surveillance covering the fields of human health, animal health and the environment (One Health approach). The unit helped develop the OH-EpiCap tool for describing and assessing the organisation and functioning of operational activities and the impact of integrative surveillance, in order to define good practices for One Health surveillance.

See the project’s web page

NOVA (2018-2021)

Novel approaches for design and evaluation of cost-effective surveillance across the food chain

Funding: One Health EJP

The benefits of multivariate approaches to syndromic hazard surveillance in the area of food safety are being evaluated through the European NOVA project, using Salmonella in particular as a practical example.

See the project’s web page

BRUSELE (2017-2020)

Evaluation of the cost effectiveness of the surveillance-control system for bovine brucellosis: avenues for improvement and socio-economic impact

Funding: French Ministry of Agriculture, ANSES

As part of the “Brusele” thesis, the production and circulation of information for outbreak surveillance in animal health were characterised according to the local organisation of stakeholders, using organisational sociology tools. This work followed an assessment of the cost effectiveness of the bovine brucellosis surveillance system.

SURICATE (2016-2019)

Antimicrobial resistance in animal health in France: characterisation for evaluation and control purposes and examination in a One Health context

Funding: French Ministry of Agriculture, National School of Veterinary Services, ANSES, INRAE

This thesis studied the comparative epidemiology of antimicrobial resistance in Escherichia coli in farm animals and humans, the representativeness and coverage of the Resapath network, the resistance of E. coli to multiple antibiotics in animals, and changing trends in antimicrobial resistance in sick farm animals, equines and domestic animals.

RESAVEL (2016-2019)

Antimicrobial resistance in calves from dairy farms

Funding: EcoAntibio plan (DGAL)

The influence of exposure to antibiotics on antimicrobial resistance was assessed in E. coli in the digestive flora of calves from dairy farms, as follow-up to work on the qualitative and quantitative assessment of links between antibiotic use and antimicrobial resistance in veal calves.

SEDUIRE (2016-2019)

Evaluation by simulation of the effectiveness of the French bluetongue surveillance and control plan

Funding: ANSES-CIRAD (French Agricultural Research Centre for International Development)

This thesis assessed the cost effectiveness of the bluetongue surveillance system and modelled the dynamics of the Culicoides population (insect vectors of the disease) and its impact on surveillance in France.

ValDonEqui & EVADE (since 2016)

Combined use of demographic and health data on horses

Estimation of the distribution of the equine population in France: spatial statistical methods applied to various data sources

Funding: French Horse and Riding Institute – Eperon Fund – ANSES

As part of the ValDonEqui project, and in particular one of its components based on a university thesis (EVADE, 2017-2021), the quality of demographic data on the equine population and their possible use for research and surveillance purposes were evaluated.

OMAR (since 2013)

Observatory for Livestock Mortality (cattle, horses)

Funding: Directorate General for Food, GDS France, ANSES

The Omar project illustrates the unit’s research work on syndromic surveillance (ongoing monitoring of one or more or indicators not specific to the hazard being monitored, to ensure its early detection and assess the related health risks), which was conducted through to its move to an operational stage (proof of concept). Several university theses have focused on syndromic surveillance, one of which specifically dealt with the Omar project.  It modelled data on bovine mortality and developed models for the detection of spatial and/or temporal anomalies, based on rendering plant data and traceability data on cattle movements. Two other theses studied the feasibility of syndromic surveillance models based on slaughterhouse and cattle reproduction data. These studies also defined a cattle herd typology and prompted a thesis evaluating the impact of spatial and temporal data aggregation on syndromic surveillance models (Ustenssyle, 2019-2022). More recently, this work was extended to the equine sector.

Temperature and bovine mortality (since 2014)

The unit carries out work to assess the relationship between temperature and bovine mortality, in particular to evaluate the impact of episodes of extreme temperatures (heat waves, cold spells) using various regression models including distributed lag non-linear models.