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.

En tant que réservoirs, les petits mammifères et notamment les rongeurs représentent une cible importante pour contrôler de nombreuses maladies zoonotiques qui touchent l’humain. Ainsi, plusieurs de nos chantiers visent à proposer et évaluer des stratégies de gestion de ces réservoirs en concertation avec les différentes parties prenantes incluant les organisations internationales, les acteurs politiques et socio-économiques, les habitants et les publics à risque.

À titre d’exemple, plusieurs projets en cours en Europe et en Afrique visent à comprendre le risque d’exposition de certains publics à des pathogènes transmis par les micromammifères. Pour cela, nous essayons de déterminer à l’échelle d’un écosystème la distribution spatio-temporelle d’agents zoonotiques (ex. Leptospira, hantavirus, Borrelia crocidurae, Yersinia pestis, Schistosoma spp.) en lien avec les facteurs socio-environnementaux (ex. paysage, élevage, usages). Ces approches nous permettent de cartographier le risque dans le temps et dans l’espace (ex. suivi du virus Puumala en France), d’alerter les autorités sanitaires (ex. leptospirose et hantavirus Séoul au Bénin) et d’orienter en conséquence la surveillance (ex. mise en place d’une plateforme portuaire de surveillance environnementale au Bénin) ou les stratégies de contrôle (ex. projet pilote de gestion environnementale des rongeurs urbains – Ecologically-Based Rodent Management – au Niger, au Bénin, en Éthiopie et à Madagascar).

Pour mener à bien l’ensemble de ces travaux, nous nous appuyons largement sur les expertises de nos plateaux techniques de biologie moléculaire, collections et informatique. Nous avons également développé un vaste réseau de collaborateurs en France, en Europe et en Afrique, tant académiques (ex. UMRs et universités partenaires, ANSES, Instituts Pasteur, Centres Nationaux de Référence de l’OMS) qu’opérationnels (ex. hôpitaux, entreprises, services santé-environnement de différentes villes, ONF), politiques (ex. ministères) ou de la société civile (ex. ONG, groupements participatifs, associations).