Vector-Borne Disease in Wild Mammals Impacted by Urban Expansion and Climate Change.

Ecologies of zoonotic vector-borne diseases may shift with climate and land use change. As many urban-adapted mammals can host ectoparasites and pathogens of human and animal health concern, our goal was to compare patterns of arthropod-borne disease among medium-sized mammals across gradients of rural to urban landscapes in multiple regions of California. DNA of Anaplasma phagocytophilum was found in 1-5% of raccoons, coyotes, and San Joaquin kit foxes; Borrelia burgdorferi in one coyote, rickettsiae in two desert kit foxes, and Yersinia pestis in two coyotes. There was serological evidence of rickettsiae in 14-37% of coyotes, Virginia opossums, and foxes; and A. phagocytophilum in 6-40% of coyotes, raccoons, Virginia opossums, and foxes. Of six flea species, one Ctenocephalides felis from a raccoon was positive for Y. pestis, and Ct. felis and Pulex simulans fleas tested positive for Rickettsia felis and R. senegalensis. A Dermacentor similis tick off a San Joaquin kit fox was PCR-positive for A. phagocytophilum. There were three statistically significant risk factors: risk of A. phagocytophilum PCR-positivity was threefold greater in fall vs the other three seasons; hosts adjacent to urban areas had sevenfold increased A. phagocytophilum seropositivity compared with urban and rural areas; and there was a significant spatial cluster of rickettsiae within greater Los Angeles. Animals in areas where urban and rural habitats interconnect can serve as sentinels during times of change in disease risk.

Cutaneous Histiocytic Sarcoma with Giant Cells in a Free-ranging Brush Rabbit (Sylvilagus bachmani).

A cutaneous mass in a free-ranging brush rabbit (Sylvilagus bachmani) was composed of neoplastic spindle to polygonal cells with multinucleated giant cells, which were positive for CD204 and negative for smooth muscle actin and desmin. Histiocytic sarcoma with giant cells was diagnosed; this neoplasm has not been reported previously in free-ranging lagomorphs.

MOVEMENTS BY SAN JOAQUIN KIT FOXES (VULPES MACROTIS MUTICA) BETWEEN URBAN AND NONURBAN HABITATS: IMPLICATIONS FOR INTERPOPULATION DISEASE TRANSFER.

Sarcoptic mange epidemics erupted in two of the remaining populations of endangered San Joaquin kit foxes (Vulpes macrotis mutica). Both populations are in urban habitats in the cities of Bakersfield and Taft, California, USA. The risk of disease spread from the two urban populations to nearby nonurban populations, and then throughout the species range, is of considerable conservation concern. To date, mange has not been detected in any nonurban populations despite considerable surveillance effort. The reasons for the lack of detections of mange among nonurban foxes are unknown. We monitored urban kit fox movements using geographic positioning system (GPS) collars to test the hypothesis that urban foxes were not venturing into nonurban habitats. Of 24 foxes monitored December 2018 to November 2019, 19 (79%) made excursions from urban into nonurban habitats from 1-124 times. The mean number of excursions per 30 d was 5.5 (range 0.1-13.9 d). The mean proportion of locations in nonurban habitats was 29.0% (range 0.6-99.7%). The mean maximum distance that foxes traveled into nonurban areas from the urban-nonurban interface was 1.1 km (range 0.1-2.9 km). Mean number of excursions, proportion of nonurban locations, and maximum distance into nonurban habitats were similar between Bakersfield and Taft, females and males, and adults and juveniles. At least eight foxes apparently used dens in nonurban habitats; shared use of dens may be an important mode of mange mite transmission between conspecifics. Two of the collared foxes died of mange during the study and two others had mange when captured at the end of the study. Three of these four foxes had made excursions into nonurban habitats. These results confirm a significant potential for mange to spread from urban to nonurban kit fox populations. We recommend continued surveillance in nonurban populations and continued treatment efforts in the affected urban populations.

Spatio-temporal and transmission dynamics of sarcoptic mange in an endangered New World kit fox.

Sarcoptic mange poses a serious conservation threat to endangered San Joaquin kit foxes (Vulpes macrotis mutica). After first appearing in Bakersfield, California in spring 2013, mange reduced the kit fox population approximately 50% until the epidemic ended with minimally detectable endemic cases after 2020. Mange is lethal and thus, with such a high force of infection and lack of immunity, it remains unclear why the epidemic did not burn itself out rapidly and how it persisted so long. Here we explored spatio-temporal patterns of the epidemic, analyzed historical movement data, and created a compartment metapopulation model (named "metaseir") to evaluate whether movement of foxes among patches and spatial heterogeneity would reproduce the eight years epidemic with 50% population reduction observed in Bakersfield. Our main findings from metaseir were that: 1) a simple metapopulation model can capture the Bakersfield-like disease epidemic dynamics even when there is no environmental reservoir or external spillover host, 2) the most impactful parameter on persistence and magnitude of the epidemic is the projection, ß/αß (transmission over decay rate of transmission over space), 3) heterogeneity in patch carrying capacities changes the critical value of the projection needed to achieve an epidemic but makes little difference to epidemic persistence time, and 4) the epidemic is relatively insensitive to birth rates and density vs. frequency-dependent transmission. Our model can help guide management and assessment of metapopulation viability of this vulpid subspecies, while the exploratory data analysis and model will also be valuable to understand mange in other, particularly den-occupying, species.

Feline Leukemia Virus Frequently Spills Over from Domestic Cats to North American Pumas.

Feline leukemia virus (FeLV) is a gammaretrovirus with horizontally transmitted and endogenous forms. Domestic cats are the primary reservoir species, but FeLV outbreaks in endangered Florida panthers and Iberian lynxes have resulted in mortalities. To assess prevalence and interspecific/intraspecific transmission, we conducted an extensive survey and phylogenetic analysis of FeLV infection in free-ranging pumas (n = 641) and bobcats (n = 212) and shelter domestic cats (n = 304). Samples were collected from coincident habitats across the United States between 1985 and 2018. FeLV infection was detected in 3.12% of the puma samples, 0.47% of the bobcat samples, and 6.25% of the domestic cat samples analyzed. Puma prevalence varied by location, with Florida having the highest rate of infection. FeLV env sequences revealed variation among isolates, and we identified two distinct clades. Both progressive and regressive infections were identified in cats and pumas. Based on the time and location of sampling and phylogenetic analysis, we inferred 3 spillover events between domestic cats and pumas; 3 puma-to-puma transmissions in Florida were inferred. An additional 14 infections in pumas likely represented spillover events following contact with reservoir host domestic cat populations. Our data provide evidence that FeLV transmission from domestic cats to pumas occurs widely across the United States, and puma-to-puma transmission may occur in genetically and geographically constrained populations. IMPORTANCE Feline leukemia virus (FeLV) is a retrovirus that primarily affects domestic cats. Close interactions with domestic cats, including predation, can lead to the interspecific transmission of the virus to pumas, bobcats, or other feline species. Some infected individuals develop progressive infections, which are associated with clinical signs of disease and can result in mortality. Therefore, outbreaks of FeLV in wildlife, including the North American puma and the endangered Florida panther, are of high conservation concern. This work provides a greater understanding of the dynamics of the transmission of FeLV between domestic cats and wild felids and presents evidence of multiple spillover events and infections in all sampled populations. These findings highlight the concern for pathogen spillover from domestic animals to wildlife but also identify an opportunity to understand viral evolution following cross-species transmissions more broadly.

Multi-population puma connectivity could restore genomic diversity to at-risk coastal populations in California.

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 pumas sampled broadly across the state. Our analyses indicated support for 4-10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer-scale genetic clusters, some of which exhibited fixed alleles and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at risk populations are typically nested within a broader-scale group of interconnected populations that collectively retain high genetic diversity and heterogenous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.

Sarcoptic mange outbreak decimates South American wild camelid populations in San Guillermo National Park, Argentina.

Sarcoptic mange epidemics can devastate wildlife populations. In 2014, mange was first detected in vicuñas (Vicugna vicugna) and guanacos (Lama guanicoe) in San Guillermo National Park (SGNP), Argentina. This study describes the temporal dynamics of the outbreak, its effects on the park's wild camelid populations between 2017-2019, and investigates the potential source of the epidemic. From May 2017 to June 2018, transect surveys indicated a sharp decrease in the density of living vicuñas and guanacos by 68% and 77%, respectively. By April 2019 no vicuñas or guanacos were recorded on transect surveys, suggesting their near-extinction in the park. Clinical signs consistent with mange (e.g., intense scratching, hyperkeratosis, alopecia) were observed in 24% of living vicuñas (n = 478) and 33% of living guanacos (n = 12) during surveys, as well as in 94% of vicuña carcasses (n = 124) and 85% of guanaco carcasses (n = 20) examined. Sarcoptes scabiei was identified as the causal agent by skin scrapings, and the cutaneous lesions were characterized by histopathology (n = 15). Genetic characterization revealed that mites recovered from seven vicuñas (n = 13) and three guanacos (n = 11) shared the same genotype, which is consistent with a single source and recent origin of the epidemic. Tracing the potential source, we identified a governmental livestock incentive program which introduced llamas (Lama glama) in areas adjacent to SGNP in 2009, some of which had alopecic scaling consistent with sarcoptic mange. Though at the time of our study no llamas with mange were available for confirmatory sampling, we hypothesize that the introduction of mange-infected llamas may have triggered the outbreak in wild camelids. This unprecedented event in SGNP had devastating effects on dominating herbivores with potentially profound cascading effects at the community and ecosystem levels.

Generalized dermatophytosis caused by Trichophyton equinum in 8 juvenile black bears in California.

From 2014-2019, 8 juvenile black bears (Ursus americanus) from different geographic regions were presented to the California Department of Fish and Wildlife because of emaciation, alopecia, and exfoliative dermatitis that resulted in death or euthanasia. Autopsy and histopathology revealed that all 8 bears had generalized hyperkeratotic dermatitis, folliculitis, and furunculosis. Skin structures were heavily colonized by fungal hyphae and arthrospores; fungal cultures of skin from 7 bears yielded Trichophyton equinum, a zoophilic dermatophyte reported only rarely in non-equid species. Additional skin conditions included mites (5), ticks (2), and coagulase-negative Staphylococcus sp. infections (2). No other causes of morbidity or mortality were identified. Molecular comparisons performed at the University of Texas Fungal Reference Laboratory determined that all isolates produced identical banding patterns, potentially representing a clonal population. Dermatophytosis is commonly localized and limited to the stratum corneum of the epidermis and hair follicles. Generalized disease with dermal involvement is rare in immunocompetent individuals; illness, malnutrition, age, or immunosuppression may increase susceptibility. Underlying causes for the severe disease impact in these bears were not evident after physical or postmortem examination. The mechanism by which bears from different geographic locations had severe, T. equinum-associated dermatophytosis from a potentially clonal dermatophyte could not be explained and warrants further investigation.

LEPTOSPIRA PREVALENCE AND ITS ASSOCIATION WITH RENAL PATHOLOGY IN MOUNTAIN LIONS (PUMA CONCOLOR) AND BOBCATS (LYNX RUFUS) IN CALIFORNIA, USA.

Leptospirosis is reported infrequently in wild and domestic felids. We estimated the prevalence of Leptospira spp. infection and exposure using real-time PCR and serology, respectively, in 136 mountain lions (Puma concolor) and 39 bobcats (Lynx rufus) that died or were euthanized between 2009 and 2017 from several regions of California, US. Felids were classified as Leptospira-positive if they were test-positive using real-time PCR targeting the LipL32 gene of pathogenic Leptospira spp. or microscopic agglutination test for six serovars of Leptospira spp. The overall Leptospira spp. prevalence was 46% (63/136) for mountain lions and 28% (11/39) for bobcats. The most common serovar detected in both felid species was Leptospira interrogans serovar Pomona. Age class and geographic location were significantly associated with Leptospira spp. in mountain lions, but not in bobcats. Interstitial nephritis, predominately lymphocytic, was diagnosed in 39% (41/106) of mountain lions and 16% (4/25) of bobcats evaluated histologically and was significantly associated with being Leptospira spp.-positive in both species. Our findings suggest that Leptospira spp. infection is common and widespread in California's wild felids and may have clinical impacts on renal and overall health of individuals. Key words: Bobcat, Leptospira spp., leptospirosis, Lynx rufus, mountain lion, nephritis, pathology, Puma concolor.

Molecular epidemiology of a fatal sarcoptic mange epidemic in endangered San Joaquin kit foxes (Vulpes macrotis mutica).

BACKGROUND: In 2013, sarcoptic mange, caused by Sarcoptes scabiei mites, precipitated a catastrophic decline of the formerly stable urban population of endangered San Joaquin kit foxes (Vulpes macrotis mutica) in Bakersfield, California, USA. In 2019, a smaller sarcoptic mange outbreak affected kit foxes 58 km southwest of Bakersfield in the town of Taft, California. To determine whether the Taft outbreak could have occurred as spillover from the Bakersfield outbreak and whether epidemic control efforts must involve not only kit foxes but also sympatric dogs (Canis lupus familiaris), coyotes (Canis latrans), and red foxes (Vulpes vulpes), we evaluated genotypes and gene flow among mites collected from each host species. METHODS: We used 10 Sarcoptes microsatellite markers (SARM) to perform molecular typing of 445 S. scabiei mites collected from skin scrapings from twenty-two infested kit foxes, two dogs, five coyotes, and five red foxes from Bakersfield, Taft, and other nearby cities. RESULTS: We identified 60 alleles across all SARM loci; kit fox- and red fox-derived mites were relatively monomorphic, while genetic variability was greatest in Bakersfield coyote- and dog-derived mites. AMOVA analysis documented distinct mite populations unique to hosts, with an overall FST of 0.467. The lowest FST (i.e. closest genetic relationship, FST = 0.038) was between Bakersfield and Taft kit fox-derived mites while the largest genetic difference was between Ventura coyote- and Taft kit fox-derived mites (FST = 0.843). CONCLUSIONS: These results confirm the close relationship between the Taft and Bakersfield outbreaks. Although a spillover event likely initiated the kit fox mange outbreak, mite transmission is now primarily kit fox-to-kit fox. Therefore, any large-scale population level intervention should focus on treating kit foxes within the city.

USE OF FLUMETHRIN-IMPREGNATED COLLARS TO MANAGE AN EPIDEMIC OF SARCOPTIC MANGE IN AN URBAN POPULATION OF ENDANGERED SAN JOAQUIN KIT FOXES (VULPES MACROTIS MUTICA).

Sarcoptic mange epidemics can have long-lasting impacts on susceptible wildlife populations, potentially contributing to local population declines and extirpation. Since 2013, there have been 460 reported cases of sarcoptic mange in an urban population of endangered San Joaquin kit foxes (Vulpes macrotis mutica) in Bakersfield, CA, with many of them resulting in fatality. As part of a multifaceted response to mitigate mange-caused mortalities and reduce this conservation threat, a 2-yr randomized field trial was conducted to assess the efficacy of long-acting flumethrin collars against sarcoptic mange in kit foxes. Thirty-five kit foxes living in a high-density population on a college campus were captured, examined, administered selamectin, and each fox randomly assigned to either receive a flumethrin collar placed within a VHF radio collar or a VHF radio collar without flumethrin. The survival and mange-infestation status of study animals was monitored via radio telemetry, remote cameras, and periodic recapture examinations and compared among treated and control kit foxes using a Cox proportional hazards model. The average time to onset of mange for treated kit foxes (176 days) was similar to controls (171 days) and treatment with flumethrin did not significantly reduce mange risk for all kit foxes. Kit foxes that had a mild mange infestation at the beginning of the study were four times more likely to develop mange again, regardless of flumethrin treatment, compared with kit foxes that had no signs at initial recruitment. This study demonstrates an approach to evaluating population-level protection and contributes to the limited literature on efficacy, safety, and practicality of acaricides in free-ranging wildlife.

Assessing the role of dens in the spread, establishment and persistence of sarcoptic mange in an endangered canid.

Sarcoptic mange is a skin disease caused by the mite Sarcoptes scabiei that can devastate populations of wild species. S. scabiei can survive off-host and remain infective for specific periods. In den-dwelling species, dislodged mites could be protected from the environmental conditions that impair their survival thus supporting pathogen transmission. To assess the potential role of dens in the spread, establishment, and persistence of sarcoptic mange in a population of hosts, we constructed an agent-based model of the endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) population in Bakersfield, California, that explicitly considered the denning ecology and behavior of this species. We focused on this SJKF urban population because of their vulnerability and because a sarcoptic mange epizootic is currently ongoing. Further, SJKF is a social species that lives in family groups year-round and contact between individuals from different family groups is rare, but they will occupy the same dens intermittently. If mites remain infective in dens, they could support intra-family disease transmission via direct (den sharing) and indirect (contaminated den) contact, but also inter-family transmission if susceptible individuals from different families occupy contaminated dens. Simulations showed that den-associated transmission significantly increases the chances for the mite to spread, to establish and to persist. These findings hold for different within-den S. scabiei off-host survival periods assessed. Managers dealing with S. scabiei in this species as well as in other den-dwelling species should consider den-associated transmission as they could be targeted as part of the control strategies against this mite.

Hematologic and Serum Chemistry values of Endangered San Joaquin Kit Foxes ( Vulpes macrotis mutica) with Sarcoptic Mange.

A fatal outbreak of sarcoptic mange caused by Sarcoptes scabiei in San Joaquin kit foxes ( Vulpes macrotis mutica) in Bakersfield, California, US is causing the once-stable population to decline. Given the fatality of the disease in this already-endangered species experiencing continued population declines, city-wide interventions are underway. To optimize medical management of mange-infested kit foxes, we documented serum biochemistry and hematology values for 11 kit foxes with mange collected from January-May 2015 and compared them to historical data from 18 healthy Bakersfield kit foxes. Results from kit foxes with mange were consistent with chronic illness and inflammation, protein loss, hypoglycemia, and dehydration. These findings contribute to our understanding of this debilitating, multisystemic disease that can progress to death in individuals without intervention and will aid in the treatment and care of rehabilitated individuals.

Comparison of Flea (Siphonaptera) Burdens on the Endangered San Joaquin Kit Fox (Vulpes macrotis mutica (Carnivora, Canidae)) Inhabiting Urban and Nonurban Environments in Central Valley, California.

The San Joaquin kit fox (Vulpes macrotis mutica Merriam (Carnivora, Canidae)) is an endangered small carnivore endemic to the San Joaquin Valley of California. Commercial and agricultural land expansion has contributed to the species' decline and invasion of more cosmopolitan species, providing means for potential ecological shifts in disease vector and host species. Fleas are common ectoparasites that can serve as important indicators of cross-species interactions and disease risk. We compared flea load and species composition on kit foxes inhabiting urban and nonurban habitats to determine how urbanization affects flea diversity and potential disease spillover from co-occurring species. We identified Echidnophaga gallinacea (Westwood) (Siphonaptera, Pulicidae) and Pulex spp. (L.) in both urban and nonurban populations, and Ctenocephalides felis (Bouche) (Siphonaptera, Pulicidae) only in the urban population. Flea load scores differed significantly across capture sites and with respect to concomitant sarcoptic mange infestation in the urban population, with milder flea infestations more typical of healthy foxes. All observed flea species are known vectors for pathogens that have been detected in mesocarnivores. Further examination of kit fox fleas and their associated pathogens will help to direct conservation and disease preventive measures for both wildlife and humans in the region.

SARCOPTIC MANGE IN ENDANGERED KIT FOXES (VULPES MACROTIS MUTICA): CASE HISTORIES, DIAGNOSES, AND IMPLICATIONS FOR CONSERVATION.

The San Joaquin kit fox ( Vulpes macrotis mutica) is a federally endangered small carnivore whose distribution is limited to the San Joaquin Valley in central California. Population decline is due to profound habitat loss, and conservation of all remaining populations is critical. A robust urban population occurs in the city of Bakersfield. In spring of 2013, putative cases of mange were reported in this population. Mites from affected animals were confirmed to be Sarcoptes scabiei morphologically and by DNA sequencing. By the end of 2014, 15 cases of kit foxes with mange had been confirmed. As with other species, sarcoptic mange in kit foxes is characterized by intense pruritus and dermatitis, caused by mites burrowing into the epidermal layers, as well as alopecia, hyperkeratosis, and encrustations, secondary bacterial infections, and finally extreme morbidity and death. Of the 15 cases, six foxes were found dead, six were captured but died during attempted rehabilitation, and three were successfully treated. We have no evidence that untreated kit foxes can recover from mange. Sarcoptic mange constitutes a significant threat to the Bakersfield kit fox population and could pose an even greater threat to this imperiled species if it spreads to populations in nearby natural lands.

Serum chemistry, hematologic, and post-mortem findings in free-ranging bobcats (Lynx rufus) with notoedric mange.

Notoedric mange was responsible for a population decline of bobcats ( Lynx rufus ) in 2 Southern California counties from 2002-2006 and is now reported to affect bobcats in Northern and Southern California. With this study we document clinical laboratory and necropsy findings for bobcats with mange. Bobcats in this study included free-ranging bobcats with mange (n = 34), a control group of free-ranging bobcats without mange (n = 11), and a captive control group of bobcats without mange (n = 19). We used 2 control groups to evaluate potential anomalies due to capture stress or diet. Free-ranging healthy and mange-infected bobcats were trapped or salvaged. Animals were tested by serum biochemistry, complete blood count, urine protein and creatinine, body weight, necropsy, and assessment for anticoagulant rodenticide residues in liver tissue. Bobcats with severe mange were emaciated, dehydrated, and anemic with low serum creatinine, hyperphosphatemia, hypoglycemia, hypernatremia, and hyperchloremia, and sometimes septicemic when compared to control groups. Liver enzymes and leukocyte counts were elevated in free-ranging, recently captured bobcats whether or not they were infested with mange, suggesting capture stress. Bobcats with mange had lower levels of serum cholesterol, albumin, globulin, and total protein due to protein loss likely secondary to severe dermatopathy. Renal insufficiency was unlikely in most cases, as urine protein:creatinine ratios were within normal limits. A primary gastrointestinal loss of protein or blood was possible in a few cases, as evidenced by elevated blood urea nitrogen, anemia, intestinal parasitism, colitis, gastric hemorrhage, and melena. The prevalence of exposure to anticoagulant rodenticides was 100% (n = 15) in bobcats with mange. These findings paint a picture of debilitating, multisystemic disease with infectious and toxic contributing factors that can progress to death in individuals and potential decline in populations.