Wildlife parasites are increasingly studied due to their importance in the ecology of mammals (Marathe et al., 2002) and their possible impact on public health as causative agents of zoonosis (Thompson, 2013). However, because wild animals can sometimes be nocturnal, secretive, and wide ranging (Prugh et al., 2005, Liccioli et al., 2015), accurate estimations of crucial characteristics such as parasite prevalence and host abundance or density are difficult to obtain (Pedersen et al., 2005, Wobeser, 2007).

Alveolar echinococcosis (AE) is a potentially fatal zoonotic disease caused by the parasite Echinococcus multilocularis. The parasite life cycle is primarily sylvatic in Europe and depends on predator-prey interactions between red foxes as definitive hosts (Hegglin et al., 2015) and small mammals as intermediate hosts (Oksanen et al., 2016, Beerli et al., 2017). Although domestic dogs and cats can also be infected, the red fox (Vulpes vulpes) is currently the main definitive host in the palearctic Eurasian region (Eckert and Deplazes, 2004) and responsible for most environmental contamination with E. multilocularis eggs in both rural and urban environments in Europe (Hegglin and Deplazes, 2013, Knapp et al., 2018). Foxes are recognised for their propensity to disperse, often over long distances exceeding tens of kilometres and more (Allen and Sargeant, 1993). Such spatiotemporal variation in dispersal patterns is influenced by factors such as population density, individual differences in age and sex, and the level of human activity and constraints on the foxes’ home ranges (Walton et al., 2018, Hagenlund et al., 2019, Zecchin et al., 2019). Juvenile foxes are more likely to disperse and disseminate E. multilocularis because they generally harbour a substantially higher worm burden than adults (Fischer et al., 2005, Robardet et al., 2008, Soulsbury et al., 2008). Both fox populations and the prevalence of E. multilocularis infection in foxes are expanding in endemic and previously non-endemic areas (Torgerson and Budke, 2003, Deplazes et al., 2017). Thus, understanding the structure and dynamics of the fox population to develop reliable estimates of parasite prevalence in this primary host may aid in predicting E. multilocularis dispersal patterns. This may allow for the development and implementation of appropriate control or prevention measures for both animal and human exposure to the parasite. Echinococcus multilocularis contamination of the environment in fox faeces is generally clustered within micro-foci, with seasonal variations likely due to changes in fox activity patterns and defecation behaviour (Giraudoux et al., 2002, Robardet et al., 2011, Raoul et al., 2015, Knapp et al., 2018, Da Silva et al., 2020). Distribution of the parasite among foxes is highly heterogeneous (Raoul et al., 2001, Fischer et al., 2005). Thus, knowing the specific defecation behaviour of only a few individuals (e.g., faecal over-marking of the home range, extensive foraging) in the local fox population may be critical in understanding the spatial aggregation of E. multilocularis.

The gold standard methodologies for the detection of E. multilocularis in foxes include post-mortem diagnosis by necropsy and methods to examine the intestinal content, such as the intestinal scraping technique (IST) or sedimentation and counting technique (SCT), followed by morphological identification of the adult parasitic stage (Rausch et al., 1990, Eckert, 2003). However, environmental contamination with E. multilocularis eggs occurs via faecal deposition. Thus, it is appropriate to analyse such biological material to trace the primary source of contamination for wild intermediate hosts and humans. In addition, this approach is non-invasive and does not disturb animal populations (Conraths and Deplazes, 2015, Knapp et al., 2018, Da Silva et al., 2020). Combining individual faecal genotyping and parasitological analysis allows individual determination of the parasitic status without confusion between samples from the same animal corresponding to the same infection event (Marathe et al., 2002, Zhang et al., 2011). Approaches based on host genetics enable determination of the size, sex ratio, genetic diversity, and structure of the population (Prugh et al., 2005, Valière et al., 2006, Liccioli et al., 2015). Although this integrated approach has several pitfalls (Taberlet, 1996, Taberlet and Luikart, 1999, Valière et al., 2006), it was successfully used in a Canadian urban setting with high E. multilocularis prevalence in coyotes to assess temporal patterns of infection and individual re-infection (Liccioli et al., 2015).

According to estimates, the prevalence of E. multilocularis in foxes in historically endemic areas in France is over 50% (Raoul et al., 2001, Combes et al., 2012).

In this study, we used a non-invasive faecal genetic sampling method to gather data on individual stools from foxes and track spatial and temporal variations in E. multilocularis infection. We aimed to understand how a red fox population is structured at the most local level in terms of population size and genetic structure, focusing on a rural village in the historic endemic area of AE in eastern France. Then, we attempted to link this structure with the distribution of E. multilocularis DNA-positive faeces. Because we conducted this study over 4 years, we used faecal genotyping and capture-recapture methods to assess inter-annual variations in the presence of E. multilocularis.