EPIdemiology of Animal and zoonotic diseases

The Joint Research Unit Epidemiology of animal and zoonotic diseases (UMR0346 - EPIA) is a joint research unit of INRAE-VetAgro Sup.

To prevent infectious risks associated with global changes and promote agro-ecological transition, the unit studies the epidemiology of infectious diseases in animal populations, some of which are transmissible to humans.

The originality of our unit lies in its ability to combine epidemiology, biology, ecology, and evolution in an integrated approach, using modeling and artificial intelligence.

The unit is located on two sites, one at the INRAE Center in Theix, and the other at the veterinary campus of VetAgro Sup in Marcy l'Étoile near Lyon.

The research of the UMR focuses on pathogens and diseases of interest in terms of animal health or public health (zoonoses). They cover both directly transmitted diseases (avian influenza, Q fever, leptospirosis, Bovine Viral Diarrhea (BVD)...) and vector-borne diseases (Lyme disease, tick-borne encephalitis (TBE), granulocytic anaplasmosis, bluetongue). The UMR also works on the evolution of bacterial resistance to antibiotics.

Mission and Objectives

The main objectives are:

• The study of the relationship between practices and infectious risk in farming, their monitoring, and their impact on disease distribution. We participate in the surveillance of health hazards through the ESA platform. We model the development of pathogen populations within farms and their transmission between farms. Our goal is to identify levers to reduce transmissions and the use of medicinal inputs in farming.
• The analysis and modeling of the spatial and temporal distribution of ticks, the pathogens carried by these ticks, and the associated health risks. We use data from tick observation and surveillance devices with participatory approaches. We study the transmission of pathogens and the resulting diseases. We model the transmission risk to understand its evolution in the environment and inform public authorities and citizens.

The unit's work mainly involves:

The spatiotemporal construction of animal and zoonotic risk within the framework of global change, broken down into 2 components:

• For sustainable farming systems: support public policies for the surveillance and management of animal diseases, better understand the ecology of microbial systems to reduce the use of medicinal inputs (antibiotics).
• For the prevention of zoonoses related to wild and domestic fauna: understand the link between host community diversity and zoonotic risk, predict the evolution of vectorial risk within the framework of climate change and land use, build participatory prevention of zoonotic risk.

Collaboration and Expertise

The network of scientific collaborations extends regionally (SAARA network, Hub-VPH, Shape-med@Lyon, FR BioEEnViS in the Grand Lyon Metropolis, IRC-SAE, FR SysMyc in Clermont-Ferrand), nationally (ANSES, CIRAD, GDS France, SOERE Tempo...) and internationally (Thailand, Bangladesh, United Kingdom, Canada...). The unit also regularly collaborates with public or private field actors (DDCSPP, ARS, GDS, breeders, RESPE, GTV, TERANA...).

Agents of the UMR EPIA also participate in the National Platform for Animal Health Epidemiological Surveillance (ESA Platform), which provides methodological and operational support to competent state services and other managers of health and biological surveillance systems in the territory for their design, deployment, animation, valorization, and evaluation. The ESA Platform aims to improve the efficiency of surveillance with a view to decision support and the implementation of actions. The UMR EPIA is also directly involved in the CiTIQUE program, a national citizen science program that allows every citizen to contribute to tick research by reporting bites and sending ticks.

Scientific Infrastructures

The UMR EPIA regularly conducts field campaigns to obtain relevant data for the study of various pathogens, vectors, or sensitive animals or disease reservoirs. It has an equipped field laboratory, where various collected samples are prepared.

These samples can then be analyzed by the unit's molecular biology laboratory to detect and characterize the studied pathogens, using direct detection methods for nucleic acids of pathogens (plate PCR and ddPCR). In some matrices, real-time PCR can be used to obtain quantitative results in equivalent numbers of genomes of pathogenic bacteria. With our high-throughput sequencing capabilities of small or long fragments, we characterize the genetic diversity of pathogens. We can use the ELISA serological method to indirectly characterize an organism's exposure to a pathogen.

In support of epidemiological modeling, phylogenetic studies, and artificial intelligence projects, we have computer servers with suitable computing power, developed and maintained by the unit.

Teaching

UMR EPIA agents are involved in various types of training at the veterinary curriculum level as well as university-level training. In Lyon, we are involved in the One-Health Master's program, the University Research School EID@Lyon, and partly affiliated with the ED E2M2. In Clermont-Ferrand, we contribute to the common core of Polytech, the M2 microbio UE "Emergence and Spread of Pathogens," and the ED SVSAE. We also teach in foreign universities such as Mahidol University (Thailand) and the University of Montreal (Canada) for master's and doctoral courses on the modeling of communicable diseases including zoonoses and emerging diseases. The unit hosts around ten interns every year, from discovery internships in the 3rd year to master's degree, as well as doctoral and post-doctoral students.