Dominique Pontier

Background: Antibiotic resistance is a major global health concern, yet its prevalence in wildlife remains poorly understood. Bats, due to their ecological diversity and mobility, can serve as indicators of environmental antimicrobial resistance. This study compares the diversity of Staphylococcus spp. and antibiotic resistance patterns between bats from a cave and an urban area in northeastern Gabon. Methods: A total of 655 bats were captured from Zadié Cave and Makokou City. Rectal and oral swabs were collected, and Staphylococcus spp. were isolated using mannitol media and identified via the APIstaph system. Antibiotic susceptibility was assessed by the disk-diffusion method. Statistical analyses, including Fisher’s exact test, Multiple Correspondence Analysis (MCA), and Random Forest classification, were applied to compare resistance patterns. Results: Among 257 Staphylococcus isolates, S. xylosus (32.5%), S. lentus (21.7%), and S. sciuri (14.9%) were the most prevalent. Clindamycin (74.0%–79.3%) and erythromycin/azithromycin (59.1%–72.4%) resistance were high in both environments. Multidrug resistance (MDR) was more frequent in cave bats (60.0%) than in urban bats (27.8%) (p < 0.001). MCA and Random Forest analyses highlighted a higher prevalence of chloramphenicol and rifampicin resistance in cave bats, while sulfamethoxazole/trimethoprim resistance was more common in urban bats. Conclusion: These results suggest that natural environments influence the emergence of antibiotic-resistant Staphylococcus spp. in bats. Given their ecological role and interactions with human habitats, bats should be integrated into One-Health surveillance programs to monitor antimicrobial resistance dissemination.

Context: Connectivity modelling is a powerful tool for strengthening the link between landscape and species conservation. This approach often relies on expert knowledge of connectivity indicators or limited, small numbers and small‐scale monitoring data, for example during animal foraging activities. However, integrating larger scale movement data, including dispersal or seasonal movements, is crucial to making conservation relevant by covering the entire life cycle of species. Approach and methods: Using Resource Selection Function, the movement patterns of greater horseshoe bats (GHB) studied on a local scale were transposed to a regional scale to model the connectivity in western France. GHB is highly sensitive to loss of connectivity and makes seasonal regional migrations. How the local landscape heterogeneity influenced the conductance parameters estimation for modelling was examined using the gap‐crossing method at four different sites with variable landscape composition. The inferred parameters were used to create a regional connectivity map based on circuit theory. To validate this map, acoustic monitoring was conducted during the autumn migration to assess its effectiveness in identifying connectivity gradients. Finally, the resulting connectivity map was superimposed on the Natura 2000 network. Results: First, it can be assumed that connectivity parameters are identical whatever the landscape context. Second, the regional connectivity model identified the main potential corridors connecting all the major sites in the region. Finally, based on acoustic sampling, the number of GHB in transit was significantly higher in areas of higher connectivity. In terms of overlap with conservation, the functional connectivity of the GHB has been variously addressed in the current Natura 2000 network, with an overall lack of representativeness. Policy implications: Studying pathways during high mobility periods is one of the main missing elements for effective conservation, particularly for small species such as bats. An acoustic, stratified sampling at both local and large scale provided sufficient spatial and temporal accuracy to model connectivity throughout the life cycle of bats. This framework can easily be applied to other bat species to improve our understanding of connectivity, in order to explicitly integrate this crucial aspect for highly mobile species into the protection network.

According to Bergmann's and Allen's rules, climate change may drive morphological shifts in species, affecting body size and appendage length. These rules predict that species in colder climates tend to be larger and have shorter appendages to improve thermoregulation. Bats are thought to be sensitive to climate and are therefore expected to respond to climatic changes across space and time. We conducted a phylogenetic meta‐analysis on > 27 000 forearm length (FAL) and body mass (BM) measurements from 20 sedentary European bat species to examine body size patterns. We assessed the relationships between body size and environmental variables (winter and summer temperatures, and summer precipitation) across geographic locations, and also analysed temporal trends in body size. We found sex‐specific morphological shifts in the body size of European bats in response to temperature and precipitation patterns across space, but no clear temporal changes due to high interspecific variability. Across Europe, male FAL decreased with increasing summer and winter temperatures, and BM increased with greater precipitation. In contrast, both FAL and BM of female bats increased with summer precipitation and decreased with winter temperatures. Our data can confirm Bergmann's rule for both males and females, while females' BM variations are also related to summer precipitation, suggesting a potential link to resource availability. Allen's rule is confirmed only in males in relation to summer temperature, while in females FAL and BM decrease proportionally with increasing temperature, maintaining a constant allometric relationship incompatible with Allen's rule. This study provides new insights into sex and species‐dependent morphological changes in bat body size in response to temperature and precipitation patterns. It highlights how body size variation reflects adaptations to temperature and precipitation patterns, thus providing insights into potential species‐level morphological responses to climate change across Europe.

Plusieurs espèces de chauves-souris hébergent de manière asymptomatique certains virus hautement pathogènes chez d’autres mammifères. Les mécanismes sous-jacents impliquent certainement une balance évolutive entre tolérance et résistance immunitaire aux infections virales. Toutefois, une grande partie de l’évolution de l’immunité innée des chauves-souris reste à élucider. Dans cette revue, nous présentons la caractérisation de la diversification de la protéine kinase R (PKR), une protéine antivirale majeure de la défense innée antivirale. Nos résultats récents indiquent que la PKR a évolué sous pression de sélection positive et a subi des duplications génomiques chez la chauve-souris, contrairement à tous les autres mammifères étudiés qui ne possèdent qu’une seule copie du gène. Ces changements génétiques dans la PKR des chauves-souris résulteraient en partie de conflits génétiques avec d’anciens poxvirus pathogènes, façonnant une interface hôte-virus spécifique aux chauves-souris. Par ailleurs, les PKR dupliquées chez les espèces du genre Myotis ont subi une diversification génétique qui leur permet d’échapper collectivement aux virus et d’en renforcer le contrôle. Ces résultats suggèrent que les adaptations de PKR contribuent à la spécificité des interactions modernes entre les virus et les chauves-souris et participent à expliquer ces mécanismes immunitaires uniques aux chauves-souris.

This study aimed to establish a baseline hematological profile and examine the influence of age, sex, and season on hematological parameters in captive chimpanzees (Pan troglodytes) living in a humid tropical climate. Hematological parameters are a useful tool for assessing health status and diagnosing diseases in animals. We analyzed 473 blood samples collected from 84 chimpanzees (43 females and 41 males) during annual health checks, conducted under anesthesia for a routine physical examination. The main findings revealed significant sex differences in some hematological parameters: males had higher hematocrit and red blood cell counts than females. Age‐related variations have also been noted, with adolescents and adults having lower lymphocyte counts but higher neutrophil and monocyte counts than infants. Adults, in particular, had significantly lower platelet counts compared to other age classes. Seasonal fluctuations were also observed: lymphocyte counts were higher in the rainy season, while neutrophil counts were higher in the dry season. In addition, the general trends in hematological parameters for this captive population of chimpanzees were similar to those reported in captive chimpanzees living in the United States. These results should provide animal health professionals, particularly those working with nonhuman primates, with data to compare and interpret. They will help improve practices for monitoring and managing the health of nonhuman primates in captivity.

Although antibiotic resistance is a major issue for both human and animal health, very few studies have investigated the role of the bacterial host spectrum in its dissemination within natural ecosystems. Here, we assessed the prevalence of methicillin resistance among Staphylococcus aureus (MRSA) isolates from humans, non-human primates (NHPs), micromammals and bats in a primatology center located in southeast Gabon, and evaluated the plausibility of four main predictions regarding the acquisition of antibiotic resistance in this ecosystem. MRSA strain prevalence was much higher in exposed species (i.e., humans and NHPs which receive antibiotic treatment) than in unexposed species (micromammals and bats), and in NHP species living in enclosures than those in captivity—supporting the assumption that antibiotic pressure is a risk factor in the acquisition of MRSA that is reinforced by the irregularity of drug treatment. In the two unexposed groups of species, resistance prevalence was high in the generalist strains that infect humans or NHPs, supporting the hypothesis that MRSA strains diffuse to wild species through interspecific transmission of a generalist strain. Strikingly, the generalist strains that were not found in humans showed a higher proportion of MRSA strains than specialist strains, suggesting that generalist strains present a greater potential for the acquisition of antibiotic resistance than specialist strains. The host spectrum is thus a major component of the issue of antibiotic resistance in ecosystems where humans apply strong antibiotic pressure.

Cryptic species diversity is known to be common in bats but remains challenging to study in these mammals, whose natural history traits render their sampling and monitoring challenging. For these animals, indirect genetic approaches provide a powerful tool to gain insight into the evolutionary history and ecology of cryptic bat species. The speciation history of the polyphyletic Chaerephon pumilus species group (Molossidae) is poorly understood, including those found on western Indian Ocean islands. Two species in this complex have been identified in the Comoros: C. pusillus and C. leucogaster. Here, we aim to genetically characterize these two species and investigate their spatial population genetic structure. Analyzing five nuclear microsatellite markers from 200 individuals and one mitochondrial DNA gene (Cyt‐b) from 161 (out of the 200) individuals sampled on Madagascar and the Comoros, our findings indicated that these species are genetically differentiated. We observed mitonuclear discordance in numerous individuals (33% of the 161 _mtDNA‐sequenced individuals). Based on ABC analyses, we found that this pattern could potentially be the result of asymmetric introgressive hybridization from C. leucogaster to C. pusillus and calls for further studies on the demographic history of these species. Moreover, at the intra‐specific level, analyses of the microsatellite loci suggested the evidence of a more pronounced, although weak, geographically based genetic structure in C. pusillus than in C. leucogaster. Altogether, our findings provide preliminary insights into the eco‐evolutionary aspects of this species complex and warrant further research to understand hybridization dynamics and mechanisms responsible for mitonuclear discordance.

Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.

Welfare and management decisions for unowned free-ranging cats in urban environments should no longer be based on knowledge about behavioural ecology of solitary cats living and breeding in more natural ‘wild’ environments. We provide evidence that urban free-ranging domestic cats in the Anthropocene have responded to rapidly changing environments, such as abundance of food and higher population densities of conspecifics by adapting their behaviour (behavioural plasticity—the ability of a genotype (individual) to express different behaviours according to its environment) and social organisation to living in complex social groups, especially those living in colonies. Urban free-ranging cats are now more social, as demonstrated by different breeding patterns, lower infanticide, more frequent affiliative interactions in general, and different spatial groupings. We argue that this knowledge should be disseminated widely, and inform future research and strategies used to manage free-ranging cats across environments. Understanding behavioural plasticity and other recently evolved traits of domestic cats may lead to management strategies that maximise health and welfare of cats, wildlife, and humans—otherwise domestic cat behaviour may be ‘misunderstood’. Importantly, interdisciplinary research using expertise from biological and social sciences, and engaging human communities, should evaluate these management strategies to ensure they maintain optimal welfare of free-ranging domestic cats while preserving biodiversity and protecting wildcats.

Several bat species act as asymptomatic reservoirs for many viruses that are instead highly pathogenic in other mammals. Here, we have characterized the functional diversification of the Protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats, in contrast to all studied mammals that possess a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. More importantly, we determined that duplicated PKRs of the Myotis species have undergone functional diversification allowing them to collectively escape from and enhance control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat specific immunity.