Host susceptibility to snake fungal disease is highly dispersed across phylogenetic and functional trait space

Contribution of host species and pathogen clade to snake fungal disease hotspots in Europe

Infectious diseases are influenced by interactions between host and pathogen, and the number of infected hosts is rarely homogenous across the landscape. Areas with elevated pathogen prevalence can maintain a high force of infection and may indicate areas with disease impacts on host populations. However, isolating the ecological processes that result in increases in infection prevalence and intensity remains a challenge. Here we elucidate the contribution of pathogen clade and host species in disease hotspots caused by Ophidiomyces ophidiicola, the pathogen responsible for snake fungal disease, in 21 species of snakes infected with multiple pathogen strains across 10 countries in Europe. We found isolated areas of disease hotspots in a landscape where infections were otherwise low. O. ophidiicola clade had important effects on transmission, and areas with multiple pathogen clades had higher host infection prevalence. Snake species further influenced infection, with most positive detections coming from species within the Natrix genus. Our results suggest that both host and pathogen identity are essential components contributing to increased pathogen prevalence.

Characterisation, prevalence and severity of skin lesions caused by ophidiomycosis in a population of wild snakes

Ophidiomycosis is an emerging infectious disease affecting wild snakes in the Northern Hemisphere. Recently confirmed in Great Britain, the prevalence, severity and significance of ophidiomycosis has yet to be characterised in free-living snakes at a population level in Europe. Therefore, a population of barred grass snakes (Natrix helvetica) in eastern England was monitored for three seasons (May 2019 to October 2021), to investigate the prevalence (25.5%; 191/750 snakes) and severity of skin lesions and their aetiology. The most frequently observed skin lesion characteristics were changes in scale colour, crusting, and scale margin erosion. The majority of such lesions (96.9%; 185/191 snakes) was observed on the ventral surface along the length of the body. The severity of skin lesions was considered mild in more than half of the cases (53.1%; 98/191 snakes). Predominantly, skin lesions were observed in adult snakes (72.8%; 139/191 snakes). Combined histological examinations and qPCR tests of skin lesions from N. helvetica sloughs and/or carcasses confirmed a diagnosis of ophidiomycosis. Further targeted surveillance, supported by molecular and histological examinations to confirm skin lesion aetiology, is required to determine the extent to which our findings reflect the occurrence of ophidiomycosis in populations within wider landscapes.

Snake Fungal Disease in Free-Ranging Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in New Jersey: Lesions, Severity of Sores and Investigator's Perceptions

Ophidiomyces ophidiicola, the fungus causing snake fungal disease (SFD), has been identified in northern pine snakes (Pituophis melanoleucus) in New Jersey. In this paper, we (1) review the positivity rate of SFD on different locations on snakes' bodies, (2) determine the relationship between the sores and quantitative polymerase chain reaction (qPCR) positivity rates, and (3) explore the relationship between the investigators' clinical evaluation of the severity of sores, their evaluation of the likelihood of the sores being positive, and the qPCR positivity of SFD for the sores. Swabbing the sores was more effective at determining whether the snakes tested positive for O. ophidiicola than ventrum swabbing alone. The perception of the severity of the sores did not relate to qPCR positivity for O. ophidiicola. We suggest that the assessment of the rate of SFD among snakes in the wild needs to include the sampling of snakes with no clinical signs, as well as those with sores, and the swabbing of all the sores collectively. Clear terminology for sores, the identification of clinical signs of SFD, and distinguishing the rates of O. ophidiicola by PCR testing should be adopted. Overall, the pine snakes exhibited a higher rate of sores and positivity of O. ophidiicola swabs by PCR testing compared to the other snakes.

Genetic mechanisms and biological processes underlying host response to ophidiomycosis (snake fungal disease) inferred from tissue-specific transcriptome analyses

Emerging infectious diseases in wildlife species caused by pathogenic fungi are of growing concern, yet crucial knowledge gaps remain for diseases with potentially large impacts. For example, there is detailed knowledge about host pathology and mechanisms underlying response for chytridiomycosis in amphibians and white-nose syndrome in bats, but such information is lacking for other more recently described fungal infections. One such disease is ophidiomycosis, caused by the fungus Ophidiomyces ophidiicola, which has been identified in many species of snakes, yet the biological mechanisms and molecular changes occurring during infection are unknown. To gain this information, we performed a controlled experimental infection in captive Prairie rattlesnakes (Crotalus viridis) with O. ophidiicola at two different temperatures: 20 and 26°C. We then compared liver, kidney, and skin transcriptomes to assess tissue-specific genetic responses to O. ophidiicola infection. Given previous histopathological studies and the fact that snakes are ectotherms, we expected highest fungal activity on skin and a significant impact of temperature on host response. Although we found fungal activity to be localized on skin, most of the differential gene expression occurred in internal tissues. Infected snakes at the lower temperature had the highest host mortality whereas two-thirds of the infected snakes at the higher temperature survived. Our results suggest that ophidiomycosis is likely a systemic disease with long-term effects on host response. Our analysis also identified candidate protein coding genes that are potentially involved in host response, providing genetic tools for studies of host response to ophidiomycosis in natural populations.

CONTROLLED CLINICAL TRIAL USING TERBINAFINE NEBULIZATION TO TREAT WILD LAKE ERIE WATERSNAKES (NERODIA SIPEDON INSULARUM) WITH OPHIDIOMYCOSIS

Ophidiomycosis (snake fungal disease) is an important infectious disease caused by the fungus Ophidiomyces ophidiicola. To mitigate the disease's impact on individual snakes, a controlled clinical trial was conducted using terbinafine nebulization to treat snakes with ophidiomycosis. Fifty-three wild-caught Lake Erie watersnakes (Nerodia sipedon insularum) with apparent ophidiomycosis (skin lesions present, qPCR positive for O. ophidiicola) were divided into treatment and control groups: treatment snakes were nebulized with a 2 mg/ml terbinafine solution for 30 min daily for 30 d; control snakes received nebulization with 0.9% saline or no nebulization. Weekly physical exams were conducted to assign disease severity scores based on the number, type, location, and size of lesions, and qPCR was repeated after each 30-d course of treatment. Persistently qPCR-positive snakes received multiple nebulization courses. Terbinafine nebulization showed mixed results as a treatment for ophidiomycosis: 29.2% of animals treated with terbinafine showed molecular resolution of external disease, based on antemortem swabbing, following 3-6 mon of daily nebulization; this was significantly more than with saline nebulization (5%), but molecular resolution also occurred in 11.1% of snakes that received no treatment. Terbinafine nebulization did not significantly decrease clinical disease, as measured by disease severity scores. Evaluating molecular response to treatment using fungal quantities, terbinafine nebulization significantly reduced fungal quantity after three or more courses of treatment. These results indicate that, although terbinafine nebulization is a promising treatment for ophidiomycosis, snakes may require multiple nebulization courses and disease may not always resolve completely, despite treatment. This treatment may be most useful in snakes from managed populations that can be treated for several months, rather than wild snakes who are not releasable after multiple months in captivity.

Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis

Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O. ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O. ophidiicola, then apply that assay to swab-extracted DNA samples to investigate whether the multiple O. ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O. ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90-110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O. ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen's kappa = 0.360, 95% Confidence Interval = 0.154-0.567) with 67-77% sensitivity and 88-100% specificity, depending on clade/clonal lineage. Swab-extracted O. ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O. ophidiicola. Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake (Nerodia sipedon insularum). Overall, this assay represents a rapid, cost-effective genotyping method for O. ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.

Environmental temperature influences ophidiomycosis progression and survival in experimentally challenged prairie rattlesnakes (Crotalus viridis)

Ophidiomycosis is a prevalent and intermittently pervasive disease of snakes globally caused by the opportunistic fungal pathogen, Ophidiomyces ophidiicola. Host response has yet to be fully explored, including the role of temperature in disease progression and hematologic changes. This study enrolled twelve adult prairie rattlesnakes (Crotalus viridis) in an experimental challenge with O. ophidiicola at two temperatures, 26°C (n = 6) and 20°C (n = 6). Each temperature cohort included four inoculated and two control snakes. Assessments involving physical exams, lesion swabbing, and hematology were performed weekly. Differences were observed between inoculated and control snakes in survival, behavior, clinical signs, ultraviolet (UV) fluorescence, hematologic response, and histologic lesions. All inoculated snakes held at 20°C were euthanized prior to study end date due to severity of clinical signs while only one inoculated animal in the 26°C trial met this outcome. In both groups, qPCR positive detection preceded clinical signs with regards to days post inoculation (dpi). However, the earliest appearance of gross lesions occurred later in the 20°C snakes (20 dpi) than the 26°C snakes (13 dpi). Relative leukocytosis was observed in all inoculated snakes and driven by heterophilia in the 20°C snakes, and azurophilia in the 26°C group. Histologically, 20°C snakes had more severe lesions, a lack of appropriate inflammatory response, and unencumbered fungal proliferation and invasion. In contrast, 26°C snakes had marked granulomatous inflammation with encapsulation of fungi and less invasion and dissemination. The results of this study identified that O. ophidiicola-infected rattlesnakes exposed to lower temperatures have decreased survival and more robust hematologic change, though minimal and ineffective inflammatory response at site of infection. Ophidiomycosis is a complex disease with host, pathogen, and environmental factors influencing disease presentation, progression, and ultimately, survival. This study highlighted the importance of temperature as an element impacting the host response to O. ophidiicola.

A Cross-Inoculation Experiment Reveals that Ophidiomyces ophiodiicola and Nannizziopsis guarroi Can Each Infect Both Snakes and Lizards

Host range and specificity are key concepts in the study of infectious diseases. However, both concepts remain largely undefined for many influential pathogens, including many fungi within the Onygenales order. This order encompasses reptile-infecting genera (Nannizziopsis, Ophidiomyces, and Paranannizziopsis) formerly classified as the Chrysosporium anamorph of Nannizziopsis vriesii (CANV). The reported hosts of many of these fungi represent a narrow range of phylogenetically related animals, suggesting that many of these disease-causing fungi are host specific, but the true number of species affected by these pathogens is unknown. For example, to date, Nannizziopsis guarroi (the causative agent of yellow fungus disease) and Ophidiomyces ophiodiicola (the causative agent of snake fungal disease) have been documented only in lizards and snakes, respectively. In a 52-day reciprocal-infection experiment, we tested the ability of these two pathogens to infect currently unreported hosts, inoculating central bearded dragons (Pogona vitticeps) with O. ophiodiicola and corn snakes (Pantherophis guttatus) with N. guarroi. We confirmed infection by documenting both clinical signs and histopathological evidence of fungal infection. Our reciprocity experiment resulted in 100% of corn snakes and 60% of bearded dragons developing infections with N. guarroi and O. ophiodiicola, respectively, demonstrating that these fungal pathogens have a broader host range than previously thought and that hosts with cryptic infections may play a role in pathogen translocation and transmission. IMPORTANCE Our experiment using Ophidiomyces ophiodiicola and Nannizziopsis guarroi is the first to look more critically at these pathogens' host range. We are the first to identify that both fungal pathogens can infect both corn snakes and bearded dragons. Our findings illustrate that both fungal pathogens have a more general host range than previously known. Additionally, there are significant implications concerning the spread of snake fungal disease and yellow fungus disease in popular companion animals and the increased chance of disease spillover into other wild and naive populations.

Prevalence of Ophidiomyces ophidiicola and epizootiology of snake fungal disease in free-ranging Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in New Jersey

Snake fungal disease, caused by Ophidiomyces ophidiicola, is recognized as a potential concern for North American snakes. We tested skin swabs from Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in the New Jersey pinelands for the presence of O. ophidiicola before emergence from hibernation. We used qPCR to test the collected swabs for the presence of O. ophidiicola, then determined pathogen prevalence as a function of sampling year, sampling location (skin lesion, healthy ventral skin, healthy head skin) sex, and age. There were no temporal trends in O. ophidiicola detection percentages on snakes, which varied from 58 to 83% in different years. Ophidiomyces ophidiicola detection on snakes was highest in swabs of skin lesions (71%) and lowest in head swabs (29%). Males had higher prevalence than females (82% versus 62%). The fungus was not detected in hatchling snakes (age 0) in the fall, but 75% of juveniles tested positive at the end of hibernation (age 1 year). We also screened hibernacula soil samples for the presence of O. ophidiicola. Where snakes hibernated, 69% of soil samples were positive for O. ophidiicola, and 85% of snakes lying on positive soil samples also tested positive for the pathogen. Although a high proportion of snakes (73%) tested positive for O. ophidiicola during our 4-year study, the snakes appeared healthy except for small skin lesions. We conclude that O. ophidiicola prevalence is high on hibernating Northern Pine Snakes and in the hibernacula soil, with a strong association between snakes and positive adjacent soil. This is the first demonstration that snakes likely become infected during hibernation.

Ophidiomyces ophidiicola detection and infection: a global review on a potential threat to the world’s snake populations

Ophidiomyces ophidiicola (Oo) is one of the most relevant fungal pathogens for snakes. It is the etiological agent of ophidiomycosis, an emerging disease causing dysecdysis, skin abnormalities, crusting cutaneous lesions, and ulcerations. Despite this major tegumentary “tropism”, Oo infection can be systemic and it is capable of inducing visceral lesions. Moreover, ophidiomycosis may lead to abnormalities of reproductive physiology, hunting behavior, and thermoregulation, thus increasing the risks of sublethal effects and predation on affected snakes. Oo seems horizontally transmitted and can induce postnatal mortality. This article reviews published data on Oo detection and infection in all snake species in countries around the world and categorizes these data using new classification parameters. The presence of this fungus has been recorded in 11 states (considering the USA as a whole); however, in four states, the mycosis has only been reported in snakes held in captivity. Detection and/or infection of Oo has been ascertained in 62 snake species, divided into nine families. The taxa have been categorized with diagnostic criteria in order to report, for each species, the highest rank of categorization resulting from all cases. Therefore, 20 species have been included within the class “Ophidiomycosis and Oo shedder”, 11 within “Ophidiomycosis”, 16 in “Apparent ophidiomycosis”, and 15 within “Ophidiomyces ophidiicola present”. We also discuss the significance and limits of case classifications and Oo’s impact on wild populations, and we suggest methods for preliminary surveillance. Standardized methods, interdisciplinary studies, and cooperation between various research institutions may facilitate further Oo screening studies, elucidate the unclear aspects of the disease, and protect ophidiofauna from this emerging threat at the global level.

SEASONAL AND INTERSPECIFIC VARIATION IN THE PREVALENCE OF OPHIDIOMYCES OPHIDIICOLA AND OPHIDIOMYCOSIS IN A COMMUNITY OF FREE-RANGING SNAKES

Ophidiomycosis in snakes is caused by the fungus Ophidiomyces ophidiicola. Clinical signs associated with the disease range from minor skin lesions to severe swelling of the face. In some cases, the fungus invades the snake's underlying muscle and bone and internal organs; disease severity appears to peak during brumation. We quantified the prevalence of O. ophidiicola and ophidiomycosis in free-ranging snakes to explore seasonal variation in detection of the pathogen and disease. We collected skin swabs (n=464 samples) from seven species of free-ranging snakes (n=336) from Rondeau Provincial Park (Ontario, Canada) and tested the swabs for O. ophidiicola using quantitative PCR. We also assessed individuals for lesions consistent with ophidiomycosis and monitored changes in gross lesions over time in recaptured individuals. Eastern foxsnakes (Pantherophis vulpinus) had the highest prevalence of O. ophidiicola (24/84) and of lesions consistent with ophidiomycosis (34/84). On other species (Nerodia sipedon, Storeria dekayi, Thamnophis sirtalis, and Thamnophis sauritus), we detected the pathogen on only 4/229 snakes and observed gross lesions consistent with ophidiomycosis on 24/229 snakes. Body length of eastern foxsnakes was associated with detection of O. ophidiicola, suggesting that eastern foxsnakes' large size increases the risk of pathogen exposure relative to the other, smaller, species at our study site. Ophidiomyces ophidiicola and lesions consistent with ophidiomycosis were detected most frequently in eastern foxsnakes soon after emergence from brumation and less frequently later in the active season (O. ophidiicola: April=29.8%, October=3.9%; lesions: April=36.1%, October=5.5%). This decrease corresponded with resolution of lesions in 6/13 resampled eastern foxsnakes. Considering the seasonal cycle of O. ophidiicola and ophidiomycosis when planning disease surveillance research may improve detection probabilities for ophidiomycosis in Nearctic snakes.

Comparative host-pathogen associations of Snake Fungal Disease in sympatric species of water snakes (Nerodia)

The ascomycete fungus Ophidiomyces ophiodiicola (Oo) is the causative agent of ophidiomycosis (Snake Fungal Disease), which has been detected globally. However, surveillance efforts in the central U.S., specifically Texas, have been minimal. The threatened and rare Brazos water snake (Nerodia harteri harteri) is one of the most range restricted snakes in the U.S. and is sympatric with two wide-ranging congeners, Nerodia erythrogaster transversa and Nerodia rhombifer, in north central Texas; thus, providing an opportunity to test comparative host-pathogen associations in this system. To accomplish this, we surveyed a portion of the Brazos river drainage (~ 400 river km) over 29 months and tested 150 Nerodia individuals for the presence of Oo via quantitative PCR and recorded any potential signs of Oo infection. We found Oo was distributed across the entire range of N. h. harteri, Oo prevalence was 46% overall, and there was a significant association between Oo occurrence and signs of infection in our sample. Models indicated adults had a higher probability of Oo infection than juveniles and subadults, and adult N. h. harteri had a higher probability of infection than adult N. rhombifer but not higher than adult N. e. transversa. High Oo prevalence estimates (94.4%) in adult N. h. harteri has implications for their conservation and management owing to their patchy distribution, comparatively low genetic diversity, and threats from anthropogenic habitat modification.

Explosive networking: The role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly

Many species-rich ecological communities emerge from adaptive radiation events. Yet the effects of adaptive radiation on community assembly remain poorly understood. Here, we explore the well-documented radiations of African cichlid fishes and their interactions with the flatworm gill parasites Cichlidogyrus spp., including 10,529 reported infections and 477 different host-parasite combinations collected through a survey of peer-reviewed literature. We assess how evolutionary, ecological, and morphological parameters determine host-parasite meta-communities affected by adaptive radiation events through network metrics, host repertoire measures, and network link prediction. The hosts' evolutionary history mostly determined host repertoires of the parasites. Ecological and evolutionary parameters predicted host-parasite interactions. Generally, ecological opportunity and fitting have shaped cichlid-Cichlidogyrus meta-communities suggesting an invasive potential for hosts used in aquaculture. Meta-communities affected by adaptive radiations are increasingly specialised with higher environmental stability. These trends should be verified across other systems to infer generalities in the evolution of species-rich host-parasite networks.

The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA

Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations.

Snake fungal disease is an emerging disease in eastern North America, but the origins of the disease have been unclear. This study uses population genetic data to show that the fungus that causes the disease was introduced multiple times to North America over the last few hundred years.

INNATE IMMUNE FUNCTION IN LAKE ERIE WATERSNAKES (NERODIA SIPEDON INSULARUM) WITH OPHIDIOMYCOSIS

Ophidiomycosis, caused by the fungus Ophidiomyces ophidiicola, poses a threat to the health of wild and managed snakes worldwide. Variation in snake innate immunity, the primary defense against infection in reptiles, may explain the observed variation in ophidiomycosis clinical disease severity among snakes. In this study, two components of the innate immune response were examined in snake plasma. We investigated whether complement activity, as measured by sheep red blood cell hemolysis, and chitotriosidase activity were associated with ophidiomycosis disease severity and time in captivity in Lake Erie watersnakes (Nerodia sipedon insularum). There was no difference in complement-mediated hemolysis or chitotriosidase activities between snakes with varying levels of ophidiomycosis clinical severity sampled in the field. However, among snakes with skin lesions kept in captivity, chitotriosidase activity was significantly higher in snakes with mild disease, compared with snakes with severe disease, and hemolysis activity increased with time in captivity. Overall, Lake Erie watersnakes had higher complement activity, but lower chitotriosidase activity, compared with other reptile species. To our knowledge, this study is the first to describe chitotriosidase activity in a snake species. These results provide mixed evidence of associations between innate immune function and ophidiomycosis severity, and more work is needed to investigate differences among snake species.

Epidemiology of Ophidiomycosis In Lake Erie Watersnakes (Nerodia sipedon insularum)

Ophidiomycosis, caused by the fungus Ophidiomyces ophidiicola, is an infectious disease of wild and managed snakes worldwide. Lake Erie watersnakes (LEWS; Nerodia sipedon insularum) were listed as threatened under the US Endangered Species Act from 1999 to 2011 and were first diagnosed with ophidiomycosis in 2009. Our objective was to characterize the epidemiology of ophidiomycosis in LEWS. We hypothesized that the prevalence of skin lesions, O. ophidiicola DNA, and ophidiomycosis disease categories would show spatial and temporal variation and clustering, with higher prevalence at sites with greater human disturbance and prevalence increasing over time. Snakes were captured via visual encounter surveys at five sites across four islands and visually inspected for skin lesions suggestive of ophidiomycosis, and then body swabs were collected to detect O. ophidiicola DNA using the quantitative PCR assay. Each snake was assigned an ophidiomycosis category based on the presence of skin lesions and O. ophidiicola. We evaluated 837 LEWS between 2017 and 2020 and detected ophidiomycosis at all five sites. Logistic regression analysis showed temporal and spatial variation in disease, with higher risk of apparent ophidiomycosis (lesions present and O. ophidiicola detected) at Kelleys Island State Park, compared to all other sites; in May, compared to July; and in 2019, compared to 2018. The presence of emerging herbaceous wetlands, urban land change, and certain soil types increased the odds of both lesion presence and quantitative PCR detection of O. ophidiicola. Overall, ophidiomycosis epidemiology varied among sites: the disease appeared to be endemic at most sites and emerging at one site. Ongoing efforts to monitor population health and mortality associated with disease prevalence are needed to inform mitigation aimed at reducing the impact of ophidiomycosis in LEWS.

Testing the febrile response of snakes inoculated with Ophidiomyces ophidiicola, the causative agent of snake fungal disease

Snake Fungal Disease (SFD) negatively impacts wild snake populations in the eastern United States and Europe. Ophidiomyces ophidiicola causes SFD and manifests clinically by the formation of heterophilic granulomas around the mouth and eyes, weight loss, impaired vision, and sometimes death. Field observations have documented early seasonal basking behaviors in severely infected snakes, potentially suggesting induction of a behavioral febrile response to combat the mycosis. This study tested the hypothesis that snakes inoculated with Ophidiomyces ophidiicola would seek elevated basking temperatures to control body temperature and behaviorally induce a febrile response. Eastern ribbon snakes (Thamnophis saurita, n = 29) were experimentally or sham inoculated with O. ophidiicola. Seven days after inoculation, snakes were tested on a thermal gradient and the internal body temperature and substrate temperature of each snake was recorded over time. Quantitative PCR was used when snakes arrived, during pre-inoculation, and post-inoculation to test snakes for the presence of O. ophidiicola. Some snakes arrived with O. ophidiicola and were subsequently inoculated, allowing for an assessment of secondary exposure effects. Snake thermoregulatory behavior was compared between 1) O. ophidiicola inoculated vs. sham inoculated treatments, 2) infected vs. disease negative groups, and 3) disease naïve vs. pre-exposed immune response categories. Neither internal nor substrate temperatures differed among initially prescribed, and qPCR recovered disease states, although infected snakes tended to reach a preferred body temperature faster than disease negative snakes. Snakes experiencing their first exposure (disease naïve) sought higher substrate temperatures than snakes experiencing their second exposure (pre-exposed). Here, we recover no evidence for behaviorally induced fever in snakes with SFD but do elucidate a febrile immune response associated with secondary exposure.

Koch's postulates: Confirming Nannizziopsis guarroi as the cause of yellow fungal disease in Pogona vitticeps

Nannizziopsis guarroi is an ascomycete fungus associated with a necrotizing dermatitis in captive green iguanas (Iguana iguana) and bearded dragons (Pogona vitticeps) across both Europe and North America. Clinical signs of the disease include swelling and lesion formation. Lesions develop from white raised bumps on the skin and progress into crusty, yellow, discolored scales, eventually becoming necrotic. The clinical signs are the basis of a colloquial name yellow fungal disease (YFD). However, until now, N. guarroi has not been confirmed as the primary agent of the disease in bearded dragons. In this experiment, we fulfill Koch's postulates criteria of disease, demonstrating N. guarroi as the primary agent of YFD in bearded dragons.

First Report of Ophidiomycosis in a Free-Ranging California Kingsnake (Lampropeltis californiae) in California, USA

Ophidiomycosis (snake fungal disease) is an emerging threat to snake health worldwide. We report a case of disseminated ophidiomycosis in a California kingsnake (Lampropeltis californiae) from Plymouth, Amador County, California, US, which is the first report of the disease in this species and in a free-ranging snake in California.

Soil Reservoir Dynamics of Ophidiomyces ophidiicola, the Causative Agent of Snake Fungal Disease

Wildlife diseases pose an ever-growing threat to global biodiversity. Understanding how wildlife pathogens are distributed in the environment and the ability of pathogens to form environmental reservoirs is critical to understanding and predicting disease dynamics within host populations. Snake fungal disease (SFD) is an emerging conservation threat to North American snake populations. The causative agent, Ophidiomyces ophidiicola (Oo), is detectable in environmentally derived soils. However, little is known about the distribution of Oo in the environment and the persistence and growth of Oo in soils. Here, we use quantitative PCR to detect Oo in soil samples collected from five snake dens. We compare the detection rates between soils collected from within underground snake hibernacula and associated, adjacent topsoil samples. Additionally, we used microcosm growth assays to assess the growth of Oo in soils and investigate whether the detection and growth of Oo are related to abiotic parameters and microbial communities of soil samples. We found that Oo is significantly more likely to be detected in hibernaculum soils compared to topsoils. We also found that Oo was capable of growth in sterile soil, but no growth occurred in soils with an active microbial community. A number of fungal genera were more abundant in soils that did not permit growth of Oo, versus those that did. Our results suggest that soils may display a high degree of both general and specific suppression of Oo in the environment. Harnessing environmental suppression presents opportunities to mitigate the impacts of SFD in wild snake populations.

Revisiting Ophidiomycosis (Snake Fungal Disease) After a Decade of Targeted Research

Emerging infectious diseases (EIDs) are typically characterized by novelty (recent detection) and by increasing incidence, distribution, and/or pathogenicity. Ophidiomycosis, also called snake fungal disease, is caused by the fungus Ophidiomyces ophidiicola (formerly “ophiodiicola”). Ophidiomycosis has been characterized as an EID and as a potential threat to populations of Nearctic snakes, sparking over a decade of targeted research. However, the severity of this threat is unclear. We reviewed the available literature to quantify incidence and effects of ophidiomycosis in Nearctic snakes, and to evaluate whether the evidence supports the ongoing characterization of ophidiomycosis as an EID. Data from Canada remain scarce, so we supplemented the literature review with surveys for O. ophidiicola in the Canadian Great Lakes region. Peer-reviewed reports of clinical signs consistent with ophidiomycosis in free-ranging, Nearctic snakes date back to at least 1998, and retrospective molecular testing of samples extend the earliest confirmed record to 1986. Diagnostic criteria varied among publications (n = 33), confounding quantitative comparisons. Ophidiomycosis was diagnosed or suspected in 36/121 captive snakes and was fatal in over half of cases (66.7%). This result may implicate captivity-related stress as a risk factor for mortality from ophidiomycosis, but could also reflect reporting bias (i.e., infections are more likely to be detected in captive snakes, and severe cases are more likely to be reported). In contrast, ophidiomycosis was diagnosed or suspected in 441/2,384 free-ranging snakes, with mortality observed in 43 (9.8 %). Ophidiomycosis was only speculatively linked to population declines, and we found no evidence that the prevalence of the pathogen or disease increased over the past decade of targeted research. Supplemental surveys and molecular (qPCR) testing in Ontario, Canada detected O. ophidiicola on 76 of 657 free-ranging snakes sampled across ~136,000 km². The pathogen was detected at most sites despite limited and haphazard sampling. No large-scale mortality was observed. Current evidence supports previous suggestions that the pathogen is a widespread, previously unrecognized endemic, rather than a novel pathogen. Ophidiomycosis may not pose an imminent threat to Nearctic snakes, but further research should investigate potential sublethal effects of ophidiomycosis such as altered reproductive success that could impact population growth, and explore whether shifting environmental conditions may alter host susceptibility.

Effects of snake fungal disease on short-term survival, behavior, and movement in free-ranging snakes

Pathogenic fungi are increasingly associated with epidemics in wildlife populations. Snake fungal disease (SFD, also referred to as Ophidiomycosis) is an emerging threat to snakes, taxa that are elusive and difficult to sample. Thus, assessments of the effects of SFD on populations have rarely occurred. We used a field technique to enhance detection, Passive Integrated Transponder (PIT) telemetry, and a multi-state capture-mark-recapture model to assess SFD effects on short-term (within-season) survival, movement, and surface activity of two wild snake species, Regina septemvittata (Queensnake) and Nerodia sipedon (Common Watersnake). We were unable to detect an effect of disease state on short-term survival for either species. However, we estimated Bayesian posterior probabilities of >0.99 that R. septemvittata with SFD spent more time surface-active and were less likely to permanently emigrate from the study area. We also estimated probabilities of 0.98 and 0.87 that temporary immigration and temporary emigration rates, respectively, were lower in diseased R. septemvittata. We found evidence of elevated surface activity and lower temporary immigration rates in diseased N. sipedon, with estimated probabilities of 0.89, and found considerably less support for differences in permanent or temporary emigration rates. This study is the first to yield estimates for key demographic and behavioral parameters (survival, emigration, surface activity) of snakes in wild populations afflicted with SFD. Given the increase in surface activity of diseased snakes, future surveys of snake populations could benefit from exploring longer-term demographic consequences of SFD and recognize that disease prevalence in surface-active animals may exceed that of the population as a whole.

Host-shift as the cause of emerging infectious diseases: Experimental approaches using Drosophila-virus interactions

Host shifts, when a cross-species transmission of a pathogen can lead to successful infections, are the main cause of emerging infectious diseases, such as COVID-19. A complex challenge faced by the scientific community is to address the factors that determine whether the cross-species transmissions will result in spillover or sustained onwards infections. Here we review recent literature and present a perspective on current approaches we are using to understand the mechanisms underlying host shifts. We highlight the usefulness of the interactions between Drosophila species and viruses as an ideal study model. Additionally, we discuss how cross-infection experiments - when pathogens from a natural reservoir are intentionally injected in novel host species- can test the effect cross-species transmissions may have on the fitness of virus and host, and how the host phylogeny may influence this response. We also discuss experiments evaluating how cooccurrence with other viruses or the presence of the endosymbiont bacteria Wolbachia may affect the performance of new viruses in a novel host. Finally, we discuss the need of surveys of virus diversity in natural populations using next-generation sequencing technologies. In the long term, these approaches can contribute to a better understanding of the basic biology of host shifts.

Ophidiomycosis, an emerging fungal disease of snakes: Targeted surveillance on military lands and detection in the western US and Puerto Rico

Wildlife disease surveillance and pathogen detection are fundamental for conservation, population sustainability, and public health. Detection of pathogens in snakes is often overlooked despite their essential roles as both predators and prey within their communities. Ophidiomycosis (formerly referred to as Snake Fungal Disease, SFD), an emergent disease on the North American landscape caused by the fungus Ophidiomyces ophiodiicola, poses a threat to snake population health and stability. We tested 657 individual snakes representing 58 species in 31 states from 56 military bases in the continental US and Puerto Rico for O. ophiodiicola. Ophidiomyces ophiodiicola DNA was detected in samples from 113 snakes for a prevalence of 17.2% (95% CI: 14.4–20.3%), representing 25 species from 19 states/territories, including the first reports of the pathogen in snakes in Idaho, Oklahoma, and Puerto Rico. Most animals were ophidiomycosis negative (n = 462), with Ophidiomyces detected by qPCR (n = 64), possible ophidiomycosis (n = 82), and apparent ophidiomycosis (n = 49) occurring less frequently. Adults had 2.38 times greater odds than juveniles of being diagnosed with ophidiomycosis. Snakes from Georgia, Massachusetts, Pennsylvania, and Virginia all had greater odds of ophidiomycosis diagnosis, while snakes from Idaho were less likely to be diagnosed with ophidiomycosis. The results of this survey indicate that this pathogen is endemic in the eastern US and identified new sites that could represent emergence or improved detection of endemic sites. The direct mortality of snakes with ophidiomycosis is unknown from this study, but the presence of numerous individuals with clinical disease warrants further investigation and possible conservation action.

Mycological isolation from animal enclosures and environments in National Wildlife Rescue Centre and National Zoo, Malaysia

It is important to provide a baseline of fungal composition in the captive wildlife environment to better understand their role in overall wildlife health. The objectives were to identify species of fungi existing within wildlife animal enclosures and their environment at the National Wildlife Rescue Centre (NWRC) and the National Zoo, Malaysia and to describe their medical and veterinary importance. Samples of air, wall or floor swab, enrichment swab and soil were taken from the animal enclosures, exercise yard and enrichments at NWRC and National Zoo respectively. All samples including those pre-treated samples were plated onto Sabouraud’s Dextrose Agar (SDA). Numerous fungi were grown on all sampling SDA plates regardless by either single or multiple growth. Samples of air in both NWRC and National Zoo had the highest growth of Penicillium spp. with a prevalence of 31.2% and 83.7% respectively. Samples of swab from the wall, floor and enrichments were predominantly by Candida spp. (42.6%) in NWRC and Penicillium spp. (41.6%) in the National Zoo. Prevalence of multiple fungi isolated from the soil samples in NWRC were 57.9% and yeast species was the most common in National Zoo with a prevalence of 88.9%. Overall, 29 and 8 isolates were found in both samples from the NWRC and National Zoo with a predominant species of potential zoonotic fungi have been identified in both premises. The expected fungus Aspergillus spp. was not isolated in all samples in NWRC. Prevalent fungal species found in this study are known to cause disease in animals and humans as primary pathogen and also as opportunistic pathogens that may also cause infection. Thus, health safety precautions should be considered particularly in dealing with conservation of endangered wildlife species, along with personnel and public involvements.

Ophidiomycosis surveillance of snakes in Georgia, USA reveals new host species and taxonomic associations with disease

Ophidiomycosis (snake fungal disease) is caused by the fungus Ophidiomyces ophiodiicola and threatens snake health worldwide. It has been documented throughout the eastern United States and severe cases have recently been reported in Georgia, USA. To evaluate disease distribution and prevalence in this state, 786 free-ranging snakes were examined for skin lesions consistent with ophidiomycosis and swabbed to detect O. ophiodiicola DNA using qPCR. Sampled snakes represented 34 species and 4 families; 27.5% had skin lesions, 13.3% were positive for O. ophiodiicola DNA, and 77.8% of the qPCR positive individuals had skin lesions. This is the first report of O. ophiodiicola in five of the 22 species that were qPCR positive. Multinomial logistic regression modeling indicated that Drymarchon couperi had a higher relative risk of apparent ophidiomycosis (lesions present and qPCR positive), and the best models predicting qPCR result and ophidiomycosis category included individual factors and excluded temporal and spatial factors. Phylogeny-based bipartite network analysis showed that Nerodia erythrogaster, Nerodia taxispilota, and D. couperi had the highest prevalence of apparent ophidiomycosis; this category was more prevalent in the subfamily Colubrinae and less prevalent in Natricinae. These results provide important information about ophidiomycosis epidemiology, which has implications for snake conservation.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Field Diagnostics and Seasonality of Ophidiomyces ophiodiicola in Wild Snake Populations

Snake fungal disease (SFD) is an emerging disease caused by the fungal pathogen, Ophidiomyces ophiodiicola. Clinical signs of SFD include dermal lesions, including regional and local edema, crusts, and ulcers. Snake fungal disease is widespread in the Eastern United States, yet there are limited data on how clinical signs of SFD compare with laboratory diagnostics. We compared two sampling methods for O. ophiodiicola, scale clip collection and swabbing, to evaluate whether collection method impacted the results of polymerase chain reaction (PCR). In addition, we evaluated the use of clinical signs to predict the presence of O. ophiodiicola across seasons, snake habitat affiliation (aquatic or terrestrial) and study sites. We found no significant difference in PCR results between sampling methods. Clinical signs were a strong predictor of O. ophiodiicola presence in spring and summer seasons. Snakes occupying terrestrial environments had a lower overall probability of testing positive for O. ophiodiicola compared to snakes occupying aquatic environments. Although our study indicates that both clinical signs of SFD and prevalence of O. ophiodiicola vary seasonally and based on habitat preferences of the host, our analysis suggests that clinical signs can serve as a reliable indicator of O. ophiodiicola presence, especially during spring and summer.

Snake Fungal Disease in Colubridae Snakes in Connecticut, USA in 2015 and 2017

Snake fungal disease (SFD), caused by the fungus Ophidiomyces ophiodiicola, is an emerging threat to wild snake populations in the US. Data regarding its distribution, prevalence, and population-level impacts are sparse, and more information is needed to better manage SFD in the wild. In this study, we captured 38 wild snakes of five species in Connecticut in the summers of 2015 and 2017. Skin lesions were biopsied and evaluated histologically for fungal dermatitis. At least one individual from each species was positive for SFD, and 48% of snakes sampled in 2015 and 39% of snakes sampled in 2017 were positive for SFD. A Dekay's brownsnake (Storeria dekayi dekayi) with SFD lesions, captured in the summer of 2017, extended the host range of the disease. Thus, SFD was present in wild Connecticut snakes in 2015 and 2017, which demonstrated a wide-spread distribution throughout the state.

The Antifungal Properties of Epidermal Fatty Acid Esters: Insights from White-Nose Syndrome (WNS) in Bats

Numerous free fatty acids (FFAs) are known to have potent antifungal effects. The mammalian epidermis contains both FFAs and multiple classes of fatty acid esters, including 1-monoacylglycerols and wax esters. We thus hypothesized that wax esters and 1-monoacylglycerols composed of antifungal fatty acids would also have antifungal properties. We tested this hypothesis by examining the effects of 1-monoacylglycerols, 1,3-diacylglycerols, and wax esters on the growth of Pseudogymnoascus destructans (Pd), the fungus that causes White-nose Syndrome (WNS) in North American bats by invading their epidermis. Laboratory experiments with Pd cultures demonstrated that: (a) three 1-monoacylglycerols (1-monopalmitolein, 1-monoolein, and 1-monolinolein), as well as, (b) two wax esters, behenyl oleate and behenyl palmitoleate, profoundly inhibit Pd growth. The normal growth cycle of Pd was interrupted by addition of two cholesterol esters to the media as well. A bat species resistant to cutaneous Pd infections has these 1-monoacylglycerols in the epidermis, and another Pd resistant bat species has these wax esters in the sebum, thus cutaneous lipid composition is one factor which enables some bats to avoid WNS. Our experiments also revealed that the fatty acid esters which inhibit Pd growth are not hydrolyzed by the lipases secreted by this fungus, whereas the esters that do not inhibit Pd growth are hydrolyzed.