Analysis of a multi-type resurgence of Mycobacterium bovis in cattle and badgers in Southwest France, 2007-2019.

Although control measures to tackle bovine tuberculosis (bTB) in cattle have been successful in many parts of Europe, this disease has not been eradicated in areas where Mycobacterium bovis circulates in multi-host systems. Here we analyzed the resurgence of 11 M. bovis genotypes (defined based on spoligotyping and MIRU-VNTR) detected in 141 farms between 2007 and 2019, in an area of Southwestern France where wildlife infection was also detected from 2012 in 65 badgers. We used a spatially-explicit model to reconstruct the simultaneous diffusion of the 11 genotypes in cattle farms and badger populations. Effective reproduction number R was estimated to be 1.34 in 2007-2011 indicating a self-sustained M. bovis transmission by a maintenance community although within-species Rs were both < 1, indicating that neither cattle nor badger populations acted as separate reservoir hosts. From 2012, control measures were implemented, and we observed a decrease of R below 1. Spatial contrasts of the basic reproduction ratio suggested that local field conditions may favor (or penalize) local spread of bTB upon introduction into a new farm. Calculation of generation time distributions showed that the spread of M. bovis has been more rapid from cattle farms (0.5-0.7 year) than from badger groups (1.3-2.4 years). Although eradication of bTB appears possible in the study area (since R < 1), the model suggests it is a long-term prospect, because of the prolonged persistence of infection in badger groups (2.9-5.7 years). Supplementary tools and efforts to better control bTB infection in badgers (including vaccination for instance) appear necessary.

Population genomics of Corsican wildcats: Paving the way toward a new subspecies within the Felis silvestris spp. complex?

In the context of the current extinction crisis, identifying new conservation units is pivotal to the development of sound conservation measures, especially in highly threatened taxa such as felids. Corsican wildcats are known by Corsican people since a very long time but have been little studied. Meaningful information about their phylogenetic position is lacking. We used ddRADseq to genotype phenotypically homogenous Corsican wildcats at 3671 genome-wide SNPs and reported for the first time their genetic identity. We compared this genomic information to domestic cats Felis silvestris catus from Corsica and mainland France, European wildcats F. s. silvestris and Sardinian wildcats F. s. lybica. Our premise was that if the Corsican wildcat, as a phenotypic entity, also represents a genetic entity, it deserves conservation measures and to be recognized as a conservation unit. Corsican wildcats appeared highly genetically differentiated from European wildcats and genetically closer to Sardinian wildcats than to domestic cats. Domestic cats from Corsica and mainland France were closer to each other and Sardinian wildcats were intermediate between Corsican wildcats and domestic cats. This suggested that Corsican wildcats do not belong to the F. s. silvestris or catus lineages. The inclusion of more high-quality Sardinian samples and Near-Eastern mainland F. s. lybica would constitute the next step toward assessing the status of Corsican wildcat as a subspecies and/or evolutionarily significant unit and tracing back wildcat introduction history of in Corsica.

"BACACIX", a spatial index combining proxies of bovine and badger space use associated with extended Mycobacterium bovis circulation in France.

To better prevent and control multi-host pathogen circulation over large areas, it is essential to identify patterns of disease persistence within host communities involved in pathogen circulation at a macroscale. The aim of this study was to design and calculate "BACACIX", a spatial index of indirect contacts between cattle and badgers, two species involved in the circulation of Mycobacterium bovis, one of the main causative agents of bovine tuberculosis (bTB), in some areas of France. The index combined spatial models of land use distribution (the probable distribution defining animal use of space) based on pasture location for cattle, and based on land cover for badgers, with proxies for animal density for both species. For badgers, we used two series of census data of badger setts in two regions of France to evaluate our model of badger space use distribution (also known as utilization distribution), and analyzed the relationship between BACACIX and the upsurge of bovine tuberculosis observed in several regions of France during the decade after the country obtained the officially bTB-free status in 2001. We observed high values of BACACIX from the southwest to the northeast of France and from Brittany to the Channel coast. Conversely, in two areas (north-central area and Mediterranean coast), index values were low, suggesting that indirect cattle-badger contacts were unlikely. In the two series of census data of badger setts that we analyzed, 96.5% and 87% of the global positioning system (GPS) locations of badger setts, respectively were located in the calculated badger space use distribution. A logistic regression model showed that after controlling bTB over the previous decade, the value of the index was positively associated with the risk of cattle outbreaks between 2001 and 2010 (OR = 1.57). In addition, the risk of bTB occurrence in cattle decreased when the pasture area outside the badger space use distribution increased. In the future, the spatial index of indirect cattle-badger contacts we propose could help to better target bTB surveillance and control in France.

Estimation of Bait Uptake by Badgers, Using Non-invasive Methods, in the Perspective of Oral Vaccination Against Bovine Tuberculosis in a French Infected Area.

Although France is officially declared free of bovine tuberculosis (TB), Mycobacterium bovis infection is still observed in several regions in cattle and wildlife, including badgers (Meles meles). In this context, vaccinating badgers should be considered as a promising strategy for the reduction in M. bovis transmission between badgers and other species, and cattle in particular. An oral vaccine consisting of live Bacille Calmette-Guérin (BCG) contained in bait is currently under assessment for badgers, for which testing bait deployment in the field and assessing bait uptake by badgers are required. This study aimed to evaluate the bait uptake by badgers and determine the main factors influencing uptake in a TB-infected area in Burgundy, north-eastern France. The baits were delivered at 15 different setts located in the vicinity of 13 pastures within a TB-infected area, which has been subject to intense badger culling over the last decade. Pre-baits followed by baits containing a biomarker (Rhodamine B; no BCG vaccine) were delivered down sett entrances in the spring (8 days of pre-baiting and 4 days of baiting) and summer (2 days of pre-baiting and 2 days of baiting) of 2018. The consumption of the marked baits was assessed by detecting fluorescence, produced by Rhodamine B, in hair collected in hair traps positioned at the setts and on the margins of the targeted pastures. Collected hairs were also genotyped to differentiate individuals using 24 microsatellites markers and one sex marker. Bait uptake was estimated as the proportion of badgers consuming baits marked by the biomarker over all the sampled animals (individual level), per badger social group, and per targeted pasture. We found a bait uptake of 52.4% (43 marked individuals of 82 genetically identified) at the individual level and a mean of 48.9 and 50.6% at the social group and pasture levels, respectively. The bait uptake was positively associated with the presence of cubs (social group level) and negatively influenced by the intensity of previous trapping (social group and pasture levels). This study is the first conducted in France on bait deployment in a badger population of intermediate density after several years of intensive culling. The results are expected to provide valuable information toward a realistic deployment of oral vaccine baits to control TB in badger populations.

Breaking down population density into different components to better understand its spatial variation.

BACKGROUND: Population size and densities are key parameters in both fundamental and applied ecology, as they affect population resilience to density-dependent processes, habitat changes and stochastic events. Efficient management measures or species conservation programs thus require accurate estimates of local population densities across time and space, especially for continuously distributed species. For social species living in groups, population density depends on different components, namely the number of groups and the group size, for which relative variations in space may originate from different environmental factors. Whether resulting spatial variations in density are mostly triggered by one component or the other remains poorly known. Here, we aimed at determining the magnitude of the spatial variation in population densities of a social, group-living species, i.e. the European badger Meles meles, in 13 different sites of around 50 km2 across France, to decipher whether sett density, group size or proportion of occupied sett variation is the main factor explaining density variation. Besides the intrinsic factors of density variation, we also assessed whether habitat characteristics such as habitat fragmentation, urbanisation, and resource availability, drove both the spatial variation of density components and local population densities. RESULTS: We proposed a new standardised approach combining use of multiple methods, namely distance sampling for estimating the density of occupied sett clusters, i.e. group density, and camera and hair trapping for genetic identification to determine the mean social group size. The density of adult badgers was on average 3.8 per km2 (range 1.7-7.9 per km2) and was positively correlated with the density of sett clusters. The density of adult badgers per site was less related to the social group size or to the proportion of occupied sett clusters. Landscape fragmentation also explained the spatial variation of adult badger density, with highly fragmented landscapes supporting lower adult densities. Density components were linked differently to environmental variables. CONCLUSIONS: These results underline the need to break down population density estimates into several components in group-living species to better understand the pattern of temporal and spatial variation in population density, as different components may vary due to different ecological factors.

Detection of DNA from the zoonotic raccoon roundworm Baylisascaris procyonis in a French wolf.

Baylisascaris procyonis is a zoonotic nematode whose main definitive host is the raccoon, an invasive carnivore in Europe introduced from the United States. B. procyonis causes larva migrans with poor prognosis in humans. This parasite was unexpectedly detected in France for the first time upon molecular screening of wolf faecal samples. Because no patent infection was found, the wolf cannot be considered as a definitive host. This discovery of B. procyonis in France nonetheless raises questions about the parasite status of the expanding raccoon populations in the country, which will be investigated in the future.

Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species.

AIM: Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes, and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France. LOCATION: The whole metropolitan France. METHODS: We used (a) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (b) a Bayesian modeling approach to identify the main environmental determinants influencing badger abundance. RESULTS: Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (<400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruit crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e., soil texture and climate) drove the variation in badger relative abundance. MAIN CONCLUSIONS: These results underline the importance of mapping the abundance of wildlife species based on environmental suitability and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic vs. abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.

The spatial distribution of Mustelidae in France.

We estimated the spatial distribution of 6 Mustelidae species in France using the data collected by the French national hunting and wildlife agency under the "small carnivorous species logbooks" program. The 1500 national wildlife protection officers working for this agency spend 80% of their working time traveling in the spatial area in which they have authority. During their travels, they occasionally detect dead or living small and medium size carnivorous animals. Between 2002 and 2005, each car operated by this agency was equipped with a logbook in which officers recorded information about the detected animals (species, location, dead or alive, date). Thus, more than 30000 dead or living animals were detected during the study period. Because a large number of detected animals in a region could have been the result of a high sampling pressure there, we modeled the number of detected animals as a function of the sampling effort to allow for unbiased estimation of the species density. For dead animals -- mostly roadkill -- we supposed that the effort in a given region was proportional to the distance traveled by the officers. For living animals, we had no way to measure the sampling effort. We demonstrated that it was possible to use the whole dataset (dead and living animals) to estimate the following: (i) the relative density -- i.e., the density multiplied by an unknown constant -- of each species of interest across the different French agricultural regions, (ii) the sampling effort for living animals for each region, and (iii) the relative detection probability for various species of interest.

Environmental determinants of spatial and temporal variations in the transmission of Toxoplasma gondii in its definitive hosts.

Toxoplasmosis is a major zoonosis, and its prevention requires multiple approaches due to the complex life-cycle of its causative agent, Toxoplasma gondii. Environmental contamination by oocysts is a key factor in the transmission of T. gondii to both humans and meat-producing animals; however, its spatial and temporal variations are poorly understood. We analysed the distribution of T. gondii seropositivity in a sample of 210 cats, including the European wildcat (Felis silvestris silvestris), the domestic cat (Felis silvestris catus) and their hybrids that were collected in Central and Eastern France between 1996 and 2006. We searched for spatial variability among communes and temporal variations among years to relate this variability to landscape and meteorological conditions, which can affect the population dynamics of rodent hosts and the survival of oocysts. The overall seroprevalence was 65.2% (95% CI: 58.6-71.4). As expected, adults were more often infected than young individuals, while the occurrence of infection was not related to cat genotypes. Seroprevalence correlated significantly with farm density and the North-Atlantic Oscillation index, which describes temporal variations of meteorological conditions at the continental scale. The highest seroprevalence values were obtained in areas with high farm densities and during years with cool and moist winters. These results suggest that both farming areas and years with cool and wet winters are associated with increased T. gondii seroprevalence in cats. As cat infection determines the environmental contamination by oocysts, climate and landscape characteristics should be taken into account to improve the risk analysis and prevention of T. gondii.

The epidemiology of the highly pathogenic H5N1 avian influenza in Mute Swan (Cygnus olor) and other Anatidae in the Dombes region (France), 2006.

In February 2006, a highly pathogenic avian influenza (HPAI) H5N1 virus was isolated from Common Pochards (Aythia ferina) in the Dombes region of France, an important migrating and wintering waterfowl area. Thereafter, HPAI H5N1 virus was isolated from 39 swab pools collected from dead waterfowl found in the Dombes, but only from three pooled samples collected outside of this area but located on the same migration flyway. A single turkey farm was infected in the Dombes. The epizootic lasted 2 mo and was restricted to the Dombes area. Virus-positive pools were detected in 20 of 1,200 ponds and infected Mute Swans (Cygnus olor) represented 82% of the virus-positive pools. Other infected species included Common Pochard (n=4), Grey Heron (Ardea cinerea, n=1), Eurasian Buzzard (Buteo buteo, n=1), and Greylag Goose (Anser anser, n=1). Despite intensive monitoring during and after the outbreak, HPAI H5N1 virus was not isolated from healthy wild birds. Our results are consistent with an HPAI H5N1-virus introduction into the Dombes via migrating ducks. These birds could have been pushed west by a severe cold spell in central Europe where the virus had already been detected. The Mute Swan served as an excellent epidemiologic sentinel during this outbreak; swans appear to be highly sensitive to infection with these viruses and swan mortality was easy to detect. During the outbreak, the mortality rates for wild birds remained moderate and the virus affected a limited number of species.