Thèse Détection Précoce de Pathogènes Zoonotiques dans les Élevages Avicoles Familiaux Backyard Poultry Évaluation Comparée d'Approches de Surveillance One Health en France et aux États-Unis H/F Doctorat.Gouv.Fr

Établissement : Université de Toulouse École doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Laboratoire de recherche : IHAP - Laboratoire Interactions Hôtes-Agents Pathogènes Direction de la thèse : Sébastien SOUBIES ORCID 0000000330653558 Début de la thèse : 2027-09-01 Date limite de candidature : 2026-11-23T23:59:59 Les élevages avicoles familiaux (« backyard poultry ») connaissent un essor marqué en zones urbaines et péri-urbaines, en France comme aux États-Unis. Ils contribuent au bien-être des ménages en fournissant des protéines animales de qualité, en favorisant la circularité par le recyclage des biodéchets, et en jouant le rôle d'animaux de compagnie, notamment pour des personnes isolées. Ce potentiel est toutefois conditionné par la maîtrise du risque sanitaire : ces élevages sont exposés à des pathogènes zoonotiques (Salmonella, Campylobacter, influenza aviaire, virus de Newcastle) dont la surveillance reste largement lacunaire dans les structures de petite taille. Ce projet doctoral, adossé à une collaboration établie entre l'INRAE et l'University of Florida, vise à évaluer et comparer des approches innovantes de surveillance One Health (surveillance environnementale, xénosurveillance, diagnostic moléculaire, analyse spatiale) pour la détection précoce de pathogènes zoonotiques dans les élevages avicoles familiaux, dans deux systèmes agricoles et paysages de risque contrastés. Le travail combinera échantillonnage de terrain, diagnostic moléculaire, analyse de données écologiques et spatiales, et comparaison structurée entre sites français et américains. Il doit permettre de proposer un cadre de surveillance One Health transférable, utile à la préparation des épidémies et au renforcement de la sécurité sanitaire des filières avicoles familiales, tout en formant la doctorante ou le doctorant à une recherche interdisciplinaire (biologie moléculaire, bio-informatique, épidémiologie de terrain, sciences des données) et à la mobilité scientifique internationale. Emerging and re-emerging zoonotic diseases continue to affect animal health, public health, food systems and global economies. Effective surveillance is critical for early detection of pathogen transmission at the human-animal-environment interface, yet traditional systems still rely largely on passive reporting or targeted sampling after disease emergence. Recent advances in environmental surveillance, xenosurveillance, molecular diagnostics and spatial analytics offer new opportunities to detect pathogen circulation before clinical disease is recognised, but their performance has rarely been evaluated across contrasting agricultural, ecological and sociocultural settings.
Backyard poultry flocks provide a particularly relevant and timely model system for this evaluation. On the one hand, they make a genuine contribution to household well-being: they supply eggs, a direct, low-cost source of high-quality animal protein, support circularity in urban and peri-urban settings by converting household biowaste into eggs and fertiliser, and are increasingly recognised as companion animals that provide routine, purpose and social connection, with documented psychosocial benefits particularly relevant to isolated individuals and to healthy-ageing objectives. Backyard poultry keeping has expanded markedly in recent years in both France and the United States, broadening the population directly concerned by this issue.
On the other hand, this same proximity between humans, domestic and wild animals, arthropod vectors and the environment makes backyard flocks a recognised interface for zoonotic pathogen transmission. Backyard poultry are an established source of Salmonella and Campylobacter infection, with recurrent multistate outbreaks, and are also a documented, non-negligible exposure category for avian influenza: in the United States, backyard-flock exposure has been identified as a distinct, recognised risk group for human H5N1 infection, with severe outcomes reported. Children under five, adults over 65 and pregnant women are disproportionately at risk from these zoonotic exposures, directly connecting this issue to the pillar's healthy-ageing and health-equity priorities. Because some of these infections are subclinical for birds, this risk often remains undetected until human illness occurs.
Surveillance is precisely the mechanism needed to capture the well-being benefits of backyard flocks while containing their zoonotic risk - yet small-scale poultry settings are structurally under-surveilled: farmers often have limited veterinary access, and formal monitoring systems rarely reach this segment of the poultry sector. This is compounded by the sentinel value of backyard flocks, which sit at the interface between wild bird reservoirs, commercial poultry and human populations, so that improving their surveillance also strengthens early warning for broader epizootic and pandemic risk.
Building upon an ongoing collaboration between INRAE and the University of Florida, this project will address this gap by evaluating and comparing innovative One Health surveillance approaches for backyard poultry systems in France and the United States - two contrasting agricultural systems and disease-risk landscapes - combining molecular diagnostics, environmental and vector-based sampling, spatial analytics and comparative epidemiology, in line with the interdisciplinary ambition (life sciences, AI/data science, social sciences) called for under the Health and Well-Being pillar.
1. Assess environmental surveillance approaches (water, dust, litter and other matrices) for pathogen detection in backyard poultry settings.
2. Evaluate xenosurveillance and related vector-based approaches as complementary monitoring tools.
3. Compare surveillance performance, operational feasibility and implementation challenges across French and U.S. study sites.
4. Integrate environmental, ecological and spatial data to identify factors associated with pathogen detection and transmission risk.
5. Develop a comparative One Health surveillance framework to inform future monitoring programmes and outbreak-preparedness efforts. The doctoral student will conduct collaborative field and laboratory research in partnership with INRAE and the University of Florida. Study activities will include: environmental sampling (water, dust, litter and other matrices) at backyard poultry sites; xenosurveillance and vector-based sampling as a complementary detection route; pathogen detection using molecular diagnostic methods (PCR/dPCR, sequencing) targeting Salmonella, Campylobacter, avian influenza virus and other relevant pathogens; analysis of ecological and epidemiological data describing flock and site characteristics; and application of classical and artificial intelligence-driven geospatial tools to characterise surveillance outcomes and transmission-risk factors. Comparative analyses will be performed across French and U.S. study sites to evaluate the strengths, limitations and operational feasibility of each surveillance approach under differing environmental, regulatory and management conditions. A social-science component (owner practices, biosecurity behaviour, risk communication) will complement the molecular and spatial work.