Ecology and evolution of zoonoses

Health ecology must be based first and foremost on the precise characterisation of infectious systems. To do this, we use integrative taxonomy and genomics approaches to identify the taxa that make up mammalian reservoir assemblages, their microbiome and some of their ectoparasite vectors of zoonotic agents, such as fleas. We are increasingly internalising molecular and serological tools to detect and characterise pathogens such as leptospires, trypanosomes, hantaviruses and schistosomes. In addition, we have developed considerable expertise in describing microbial compartments as a whole, whether pathogenic or commensal, using high-throughput sequencing approaches.

This work is most often carried out as part of spatio-temporal monitoring carried out in a variety of ecosystems: towns, agro-ecosystems, forests and natural habitats. This enables us to gain a better understanding of the impact of major anthropogenic upheavals (e.g. transport, urbanisation, forest management methods, ecological transition) on small mammal faunas and the associated zoonotic risks.

Our expertise in population genetics and genomics also enables us to describe the spatial structuring of reservoirs and vectors, infer their demographic dynamics and test biological invasion scenarios. To do this, we use approaches based on molecular markers such as microsatellite genotyping, sequencing and high-throughput genotyping, as well as innovative analytical approaches such as random forest, DIY-ABC and MAPPI.

It is now well established that pathogens evolve within diverse microbial communities, both commensal and pathogenic, on both intra- and inter-host scales. Describing the biotic environment of pathogens and their reservoirs is an essential prerequisite for studying the influence of interactions on the severity of diseases, as well as on their epidemiological and evolutionary dynamics. One of our aims is therefore to characterise the host-parasite-microbiota interaction networks in populations and natural communities of small mammals. To do this, we are developing approaches to study the stability, vulnerability or resilience of these interaction networks in the face of global change, and to identify the key elements in the transmission dynamics of pathogens.

Our research also aims to gain a better understanding of the ecological and evolutionary processes that shape host-pathogen interactions and explain the persistence, emergence and re-emergence of zoonoses. This work involves immunoecology and phylogenomics, population genomics and transcriptomics approaches, carried out on natural populations (or in controlled environments via collaborations). This involves, for example, assessing whether intra- and inter-host viral diversity affects the transmission of hantaviruses, or studying the variability of the host immune phenotype and its response (sensitivity, resistance or tolerance) to different pathogens (hantavirus; murine Plasmodium; Yersinia pestis). Here again, we are relying on the development of « omics » approaches to simultaneously analyse different immune pathways and characterise the genetic architecture of the response. This involves identifying the genetic characteristics of hosts and pathogens that are involved in virulence, particularly in the case of the Puumala hantavirus. We are also studying the evolution of this virulence, for example in the context of a change of host for Toxoplasma or murine Plasmodium, or a change in the small mammal community or microbiome for Puumala hantavirus.

As reservoirs, small mammals, particularly rodents, are an important target for controlling many zoonotic diseases affecting humans. Several of our projects are therefore aimed at proposing and evaluating strategies for managing these reservoirs in consultation with the various stakeholders, including international organisations, political and socio-economic players, local residents and at-risk groups.

For example, several ongoing projects in Europe and Africa aim to understand the risk of exposure of certain sections of the public to pathogens transmitted by small mammals. To do this, we are trying to determine the spatio-temporal distribution of zoonotic agents (e.g. Leptospira, hantavirus, Borrelia crocidurae, Yersinia pestis, Schistosoma spp.) on an ecosystem scale, in relation to socio-environmental factors (e.g. landscape, livestock farming, uses). These approaches enable us to map the risk over time and space (e.g. monitoring of the Puumala virus in France), to alert the health authorities (e.g. leptospirosis and hantavirus Seoul in Benin) and to direct surveillance accordingly (e.g. monitoring of the Hantavirus in the Netherlands). (e.g. setting up a port environmental monitoring platform in Benin) or control strategies – Ecologically-Based Rodent Management pilot project in Niger, Benin, Ethiopia and Madagascar).

To carry out all this work, we draw heavily on the expertise of our molecular biology, collections and IT technical platforms. We have also developed a vast network of collaborators in France, Europe and Africa, both academic (e.g. partner UMRs and universities, ANSES, Instituts Pasteur, WHO National Reference Centres) and operational (e.g. hospitals, companies, health-environment departments of various towns, ONF), political (e.g. ministries) or civil society (e.g. NGOs, participatory groups, associations).