Our work focuses primarily on wild rodents, insectivores, and bats, as well as the zoonotic agents for which these species serve as reservoirs. We develop integrative approaches that consider the full range of organisms associated with small mammals — including vector-borne ectoparasites, microbiota — that may influence host health and infectious disease transmission processes.
We also investigate the environmental and anthropogenic factors that shape zoonotic risks and, more broadly, socio-ecosystem health. Our main study sites are located in France, West Africa, and Madagascar, in both urban and non-urban contexts undergoing rapid environmental change.
|
Embedded within an EcoHealth-One Health continuum, our research explores the ecological mechanisms shaping zoonotic risks. |
Our research aims to characterize small mammal communities, the parasites and pathogens they host, their microbiomes, and the environments in which they live, in order to identify the factors influencing zoonotic disease transmission. More broadly, we seek to better understand the relationships between biodiversity, environmental change, and health.
Our work is based on medium- and long-term monitoring of natural populations conducted in both urban and non-urban sites, in France and in the Global South (see the “Base Petits Mammifères” – BPM), several of which are part of the ObsMiCE observatory. These study sites provide opportunities to investigate temporal community dynamics in response to various disturbances, such as population control operations, habitat management practices, pathogen emergence, or the introduction of exotic species.
We also develop non-invasive approaches, notably based on environmental DNA (eDNA), to characterize biodiversity while limiting our impact on wildlife and improving the detection of rare or difficult-to-capture species.
Finally, we use a wide range of molecular and serological tools, some of which have been developed within our research group, to detect and characterize parasites and pathogens associated with small mammals. Collaborations with geographers and researchers in the social sciences and humanities also enable us to provide a detailed characterization of the socio-environmental contexts under study.
Ecological and evolutionary processes play a central role in the health of small mammals, their ability to host and transmit pathogens, and consequently their role as sentinels of ecosystem health. Our research aims to understand how environmental changes influence immunity, the microbiome, and population dynamics in small mammals, as well as the consequences of these changes for the circulation of infectious agents.
At the interface between ecophysiology and health ecology, eco-immunology approaches are used to investigate the eco-evolutionary mechanisms underlying small mammals’ susceptibility, resistance, and reservoir competence toward pathogens. In this context, we study the variability of immune responses and their evolution in response to environmental disturbances such as biological invasions and pollution.
Our work also focuses on variations in the gut microbiome along environmental gradients, particularly urbanization gradients, in order to better understand the links between microbiome composition, host health, and infectious disease transmission.
Using landscape genetics and epidemiological approaches, we analyze how environmental changes affect the dispersal and connectivity of reservoir populations, thereby influencing the circulation of infectious agents among wildlife, domestic animals, and human populations.
Finally, we investigate the role of small mammals as “biotic hubs” from which new pathogens may emerge.
Our operational research focuses on the health and socio-economic impacts of anthropogenic changes, whether linked to globalization, urbanization, habitat artificialization, or ecosystem restoration initiatives. We are particularly interested in how these changes affect interactions between small mammals, pathogens, and human societies.
Special attention is given to local perceptions of health risks, management practices, and health governance systems, both in the Global North and the Global South. This research is fully embedded within a One Health framework, at the interface between ecology, public health, and sustainable territorial planning. In collaboration with partners from multiple disciplines, we develop approaches aimed at predicting zoonotic risks in specific socio-ecological contexts.
This operational perspective is reflected in the development and long-term monitoring of zoonotic risk surveillance and control systems co-designed with local stakeholders. The Environmental Surveillance Port Platform of the Port of Cotonou (PPSE) is a representative example of this approach.
Research conducted within the “Health Ecology and Small Mammals” thematic area is therefore intended to support public policies and local authorities in integrating ecological and health-related challenges, through strong partnerships with non-academic stakeholders in France and in countries of the Global South.
Project manager: Nathalie Charbonnel
Funding : European union (HORIZON RIA, call HORIZON-CL6-2021-BIODIV-01-11)
The BEPREP project aims to identify ecological restoration strategies with mutual benefits for biodiversity and health, with a view to ultimately promoting ‘nature-based solutions’ as major tools for preventing zoonotic epidemics.
https://www.beprep-project.eu/
Project managers: Gauthier Dobigny & Florent Sebbane (Institut Pasteur, Lille)
Funding PEPR Emerging infectious diseases
DEBS-Plague aims at gathering historians, archaelogists, biologists, soil scientists and mathematicians in order to investigate the respective roles of animal reservoir and flea vector diversity.bacterial genome evolution and soil physcio-chemical characteristics in the risk of of plague (re)location, circulation and (re)emergence in French territories, with Madagascar used as reference current endemic region.
Project manager: Christophe Diagne
Funding: Agence Nationale de la Recherche (ANR)
ECOZOON aims to understand the mechanisms of human exposure to rodent borne infectious diseases and to develop science-based solutions for a sustainable urban transition resilient to rodent-borne zoonoses in North Senegal. At the interface of health anthropology, urban geography, integrative health ecology and participatory modelling, ECOZOON adopts an integrative, comparative EcoHealth approach across 10 localities carefully selected to reflect the spectrum of rural-to-urban landscapes in North Senegal. The specific objectives are to (i) enhance our understanding of the links between socio-environmental factors, rodent ecology, and zoonotic risks during urban transitions; (ii) investigate, for the first time in natural populations, the relationships between multiple co-infections, immune responses, and exposure to environmental contaminants in shaping zoonotic hazards within rodent reservoirs; and (iii) inform interventions and policy while identifying locally adapted, actionable measures for urban policymakers, public health operators and local communities.
Project managers: Gauthier Dobigny & Karine Mouline (IRD, UMR Mivegec)
Funding: Défi Clé Riv’Oc
The aim of EctoPeste is to establish proof of concept for the efficacy and optimum conditions for formulating rodent baits enriched with a systemic insecticide to control their flea, Xenopsyllla cheopis, the main vector of plague in Madagascar.
Project manager: Guillaume Castel
Funding: PNR Est (ANSES)
The aim of HANTARIS is to study the circulation of the Seoul virus hantavirus in rats in the port city of Cotonou (Benin). The genetic variability of the strains detected will be characterised and any human contamination will be investigated among port workers.
Project manager: Nathalie Charbonnel
Funfing: ExposUM
Our project proposes an integrative study of the leptospires exposome within a strong One Health framework. By integrating human, animal (coypu and dog), and environmental dimensions, it will clarify each compartment’s role in leptospires circulation, identify exposure risk factors, and support prevention strategies. The study focuses on two watersheds near Montpellier, the Lez and Or, covering urban and peri-urban zones where human–dog–coypu interactions are frequent, varied, and understudied. By integrating ecology, epidemiology, environmental health, social sciences, and mathematical modeling, this interdisciplinary and transdisciplinary project will generate new insights into leptospires transmission in urban areas and species interactions under global change.
Project manager: Carine Brouat & Franck Prugnolles, IRL REHABS
Funding: ANR
The MICETRAL project aims to understand how murine malaria parasites may have changed host (from a native rodent to an invasive exotic rodent: the house mouse in Gabon). Following problems with parasite sampling, the project is currently refocusing on studying the dynamics of the invasion of the house mouse in Africa, and its health consequences.
Projet manager : J. Louvrier (contact Julien Pradel & Nathalie Charbonnel)
Funding: Univ. Montpellier, INRAE-SA
This project aims to assess the dynamics of biodiversity, pathogen transmission, and their vectors in and around domestic sheep farms located along an urbanization gradient in the Montpellier region. Through the installation of camera traps, the collection of biological samples (blood, feces, vector arthropods), and the analysis of these samples to detect pathogens, we will explore wildlife-livestock interactions and their health implications.
Project manager: Gauthier Dobigny
Funding: Agence Nationale de la Recherche (AAP 2024)
Plague is endemic in Madagascar, where it is generally regarded as an essentially rural disease. However, recurrent cases of human bubonic plague in Malagasy cities suggest the possible existence of an urban cycle of the disease, which could open the door to future large-scale epidemics that are difficult to control. Unfortunately, no study of the factors suspected of strongly influencing the persistence and emergence of plague in rural Madagascar has ever been carried out in an urban environment.
Bringing together teams from CBGP, SESSTIM, TETIS and the Instituts Pasteur in Paris and Madagascar, PLAY-MAD aims to bring together health ecology, population genomics, bacteriology and geography to produce the first assessment of the risk of plague in an urban socio-ecosystem, in this case in Antananarivo, the capital of the Grande Ile.
Project leader: Gauthier Dobigny
Funding: Enabel (Belgique) & Port Autonome de Cotonou
In Africa, data on socio-environmental and economic consequences of invasive species remain rare. Accordingly, the involvement of operational and political stakeholders is low, when not inexistent. In Cotonou, Benin, collaborative pluridisciplinary researches were conducted by French and Beninese academics, thus highlighting invasive species associated risks as well as providing practical recommendations for a better preventive management of biological invasions.
From there, the Cotonou International Seaport authorities have engaged into a partnership-based process with French (IRD), Beninese (UAC, CREC) and international (IITA) scientific groups in order to set up the first Portuary Platform of Environmental Surveillance (PPES) in Africa. PPES activities are currently run by a team of young beninese researchers who:
Project managers: Laurent Granjon & Christophe Diagne
Funding: Agence française de développement (AFD)
The general objective is to co-construct locally an integrated information system to help identify, reduce and prevent episodes of emergence and spread of zoonotic diseases at the human-animal-environment interface, while taking into account the socio-economic impact and sustainability of the solutions identified.
Project manager: Gauthier Dobigny
Funding: ANR and Région Occitanie via Institut Expos’UM
The project RoCoCity aims to investigate the impacts of rodent management on spatial and temporal changes in zoonotic exposome through several case studies conducted in French (Montpellier and Lyon zoos) and African (city markets in Senegal and Madagascar; an international seaport in Benin) urban socio-ecosystems.
Project manager: Djelouadji Zorée (contact Nathalie Charbonnel)
Funding: DGAL – Ecoantibio
The project aims to study the carriage of multidrug-resistant bacteria (MDRB) in rodents found in urban areas, as part of a localized One Health approach (Lyon metropolitan area). More specifically, it will enable us to analyze, on the one hand, the potential of rodents as reservoirs, sentinels, vectors, and evolutionary hubs for AMR, and, on the other hand, to assess the value of implementing surveillance in these species in light of the AMR patterns detected in humans, dogs, and the environment at the same study sites. Finally, it will provide new insights into the dynamics of transmission and/or spread of antibiotic resistance.
Project manager: Gauthier Dobigny
Funding : GESCOD (AFD, decentralised cooperation)
Project « Santé et Environnement à Mahajanga » (SEM) forms part of the decentralised cooperation initiative between the city of Mulhouse and the Urban Municipality of Mahajanga, through the multi-stakeholder network Grand Est Solidarités et Coopérations pour le Développement. It aims to improve the health of Mahajanga’s residents and protect their environment by strengthening sanitation policies, supporting healthcare facilities and promoting civil protection.
This project is a continuation of the project ASSMA (Assainissement à Mahajanga) carried out between 2013 and 2018, which involved the installation of sanitation infrastructure and an assessment of the impact of the facilities on public health. For this study, an action research component (vRA) will be led by the Pasteur Institute of Madagascar and its institutional partners (the University of Antananarivo, IRD and CIRAD). vRA-SEM involves monitoring the impact on the target populations of the actions undertaken as part of the SEm project.
