The natural history, ecology, and epidemiology of Ophidiomyces ophiodiicola and its potential impact on free-ranging snake populations

Retrospective Detection of Ophidiomyces ophidiicola from Snake Moults Collected in Bieszczady Mountains, Poland

Ophidiomyces ophidiicola, the causative agent of ophidiomycosis, poses a potential threat to wild snakes worldwide. This study aimed to retrospectively investigate the prevalence of O. ophidiicola in archived snake moults collected from the San River Valley in the Bieszczady Mountains, Poland, from 2010 to 2012. Using qPCR for O. ophidiicola detection and conventional PCR for clade characterisation, we analysed 58 moults and one road-killed specimen of Zamenis longissimus and Natrix natrix. A novel combination of primers (ITS2L) was used to simultaneously confirm SYBR Green-based qPCR results and perform genotyping. O. ophidiicola has been detected from two Z. longissimus and one N. natrix specimens. The identified clade (I-B) is consistent with those found in wild snakes of eastern Europe and San River Valley, indicating that O. ophidiicola has been present in this region for at least a decade. This study underscores the value of historical samples in understanding the long-term presence of pathogens and highlights the potential role of environmental reservoirs in the persistence of O. ophidiicola. Our findings are crucial for informing conservation strategies for the endangered Aesculapian snake populations in Poland, emphasising the need for ongoing monitoring and habitat management to mitigate the potential impact of ophidiomycosis.

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.

Effects of ophidiomycosis on movement, survival, and reproduction of eastern foxsnakes (Pantherophis vulpinus)

Ophidiomycosis (snake fungal disease) is caused by the fungal pathogen Ophidiomyces ophidiicola, which causes dermal lesions, occasional systemic infections, and in some cases, mortality. To better understand potential conservation implications of ophidiomycosis (i.e., population-level effects), we investigated its impacts on individual fitness in a population of endangered eastern foxsnakes (Pantherophis vulpinus). We tracked 38 foxsnakes over 6 years and quantified body condition, movement patterns, oviposition rates, and survival. Body condition, distance travelled, and oviposition rates were similar between snakes with and without ophidiomycosis. Interestingly, snakes that tested positive for the pathogen travelled farther, suggesting that movement through a greater diversity of habitats increases risk of exposure. Ophidiomycosis did not negatively affect survival, and most apparently infected snakes persisted in a manner comparable to snakes without ophidiomycosis. Only one mortality was directly attributed to ophidiomycosis, although infected snakes were overrepresented in a sample of snakes killed by predators. Overall, our results suggest that ophidiomycosis may have sublethal effects on eastern foxsnakes, but do not suggest direct effects on survival, ovipositioning, or viability of the study population.

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.

Leveraging preserved specimens of Nerodia to infer the spatiotemporal dynamics of Ophidiomyces ophidiicola via quantitative polymerase chain reaction

Ophidiomyces ophidiicola (Oo) is a fungal pathogen and the causative agent of ophidiomycosis that has affected multiple snake taxa across the United States, Europe, and Asia. Ophidiomycosis has often been referred to as an emerging infectious disease (EID); however, its status as an EID has recently come under debate. Oo infections have been confirmed in wild snake populations in Texas; however, it is unknown if the pathogen is novel (i.e., invasive) or endemic to the state. To address this knowledge gap, we conducted surveys for Oo among preserved Nerodia deposited at three university museums in Texas. First, we visually assessed snakes for signs of infection (SOI), and if SOI were present, we sampled the affected area. We then used quantitative polymerase chain reaction to diagnose the presence of Oo DNA on areas with SOI and used these data to evaluate spatiotemporal patterns of Oo prevalence. We also tested for significant spatial clusters of Oo infenction using a Bernoulli probability model as implemented in the program SatScan. We found that the proportion of snakes exhibiting SOI was constant over time while the prevalence of Oo DNA among those SOI increased across space and time. Within these data, we detected an incidence pattern consistent with an introduction and then spread. We detected six spatial clusters of Oo infection, although only one was significant. Our results support the hypothesis that Oo is an emerging, novel pathogen to Texas snakes. These data narrow the knowledge gap regarding the history of Oo infections in Texas and establish a historical record of confirmed Oo detections in several counties across the state. Thus, our results will guide future research to those areas with evidence of past Oo infections but lacking confirmation in contemporary hosts.

Major Emerging Fungal Diseases of Reptiles and Amphibians

Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.

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.

Ten decadal advances in fungal biology leading towards human well-being

Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.

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.

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.

Metal(loid) pollution, not urbanisation nor parasites predicts low body condition in a wetland bioindicator snake

Urban ecosystems and remnant habitat 'islands' therein, provide important strongholds for many wildlife species including those of conservation significance. However, the persistence of these habitats can be undermined if their structure and function are too severely disrupted. Urban wetlands, specifically, are usually degraded by a monoculture of invasive vegetation, disrupted hydrology, and chronic-contamination from a suite of anthropogenic pollutants. Top predators-as bioindicators-can be used to assess and monitor the health of these ecosystems. We measured eight health parameters (e.g., parasites, wounds and scars, tail loss and body condition) in a wetland top predator, the western tiger snake, Notechis scutatus occidentalis. For three years, snakes were sampled across four wetlands along an urban gradient. For each site, we used GIS software to measure the area of different landscapes and calculate an urbanisation-landscape score. Previously published research on snake contamination informed our calculations of a metal-pollution index for each site. We used generalised linear mixed models to assess the relationship between all health parameters and site variables. We found the metal-pollution index to have the most significant association with poor body condition. Although parasitism, tail loss and wounds differed among sites, none of these parameters influenced body condition. Additionally, the suite of health parameters suggested differing health status among sites; however, our measure of contemporary landscape urbanisation was never a significant predictor variable. Our results suggest that the health of wetland predators surrounding a rapidly growing city may be offset by higher levels of environmental pollution.

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.

DETECTION OF OPHIDIOMYCES OPHIDIICOLA IN THREE FILE SNAKES (ACROCHORDUS GRANULATUS) IMPORTED FROM INDONESIA TO THE MOSCOW ZOO (RUSSIA)

Three file snakes (Acrochordus granulatus) were delivered to the Moscow Zoo (Russia) from Jakarta (Indonesia). Shortly after arrival, multiple white blisters were detected on their bodies. All three snakes died within a month of arrival. On microscopy, arthrospores and mycelium were seen in exudate from the lesions. Ophidiomyces ophidiicola was isolated from two of three snakes and identified by internal transcribed spacer sequencing. Dermatophyte test medium turned red in positive cultures and can be potentially employed for detection of O. ophidiicola, the causative agent of snake fungal disease. This is the first report of O. ophidiicola in Russia and the second reported case of ophidiomycosis in file snakes. The possible source of O. ophidiicola in snakes imported from Southeast Asia is discussed.

RETROSPECTIVE REVIEW OF OPHIDIOMYCOSIS (OPHIDIOMYCES OPHIODIICOLA) AT THE SMITHSONIAN'S NATIONAL ZOOLOGICAL PARK (1983-2017)

A retrospective review of systemic or localized mycotic infections in captive snakes confirmed via biopsy or necropsy from 1983 to 2017 was performed at the Smithsonian's National Zoological Park. Quantitative polymerase chain reaction (qPCR) confirmed infection with Ophidiomyces ophiodiicola (Oo) in 36.8% (n = 14) of the 38 mycotic infections. Infections with Oo were evenly distributed over the 35-y period and lacked a sex predilection. There was a period prevalence of 4.5% of completed snake necropsy or biopsy cases that were Oo positive. Species affected included green anaconda (Eunectes murinus, n = 4), garden tree boa (Corallus hortulanus, n = 1), false water cobra (Hydrodynastes gigas, n = 5), yellow anaconda (Eunectes notaeus, n = 1), eastern milksnake (Lampropeltis triangulum, n = 1), Brazilian rainbow boa (Epicrates cenchria cenchria, n = 1), and eastern diamondback rattlesnake (Crotalus adamanteus, n = 1). Histopathology demonstrated one or more of the following: heterophilic to necrotizing epidermitis with or without granulomatous dermatitis (n = 12), granulomatous pneumonia (n = 5), granulomatous endophthalmitis (n = 1), and subcutaneous-intramuscular fungal granuloma (n = 1). This study documents the presence of ophidiomycosis in a captive collection for almost 40 years, despite current literature designating it a recently emerging pathogen.

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.

ABSENCE OF BATRACHOCHYTRIUM SALAMANDRIVORANS IN A GLOBAL HOTSPOT FOR SALAMANDER BIODIVERSITY

Batrachochytrium salamandrivorans (Bsal) is an emerging fungal pathogen that affects salamander and newt populations in Asia and Europe. In the Western Hemisphere, Bsal represents a major threat to endemic amphibian populations, which have not evolved resistance to infection, and which could experience local extinction events such as those observed in European fire salamanders (Salamandra salamandra). We report findings of a survey focusing specifically on wild lungless salamanders in the southeastern US, the most biodiverse location for salamander species globally. Between May 2016 and July 2018, we conducted 25 surveys at 10 sites across three ecoregions in Tennessee, US. Using quantitative (q)PCR, we screened water samples and skin swabs from 137 salamanders in five plethodontid genera. Although single replicates of six samples amplified during qPCR cycling, no samples could be confirmed as positive for the presence of Bsal with 28S rRNA PCR and independent laboratory screening. It is probable that we found false positive results, as reported by other researchers using the same assay. We offer recommendations for future monitoring efforts.

Exposure to a fungal pathogen increases the critical thermal minimum of two frog species

The ability of an organism to tolerate seasonal temperature changes, such as extremely cold temperatures during the winter, can be influenced by their pathogens. We tested how exposure to a virulent fungal pathogen, Batrachochytrium dendrobatidis (Bd), affected the critical thermal minimum (CTmin) of two frog species, Hyla versicolor (gray treefrog) and Lithobates palustris (pickerel frog). The CTmin is the minimum thermal performance point of an organism, which we estimated via righting response trials. For both frog species, we compared the righting response of Bd-exposed and Bd-unexposed individuals in either a constant (15ºC) environment or with decreasing temperatures (-1°C/2.5 min) starting from 15°C. The CTmin for both species was higher for Bd-exposed frogs than unexposed frogs, and the CTmin of H. versicolor was higher than L. palustris. We also found that Bd-exposed frogs of both species righted themselves significantly fewer times in both decreasing and constant temperature trials. Our findings show that pathogen exposure can reduce cold tolerance and limit the thermal performance range of hosts, which may lead to increased overwintering mortality.

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.

A looming exotic reptile pet trade in India: patterns and knowledge gaps

Commercial trade of exotic reptiles through CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) in India is relatively recent (<2 decades).  Social media platforms and web portals are known to be used for pet trade.  Exotic pet trade is not legally regulated within India.  Therefore, little is known on the scale at which this trade is carried out in India.  We conducted a two-year study between 2018 and 2020 gathering information of exotic reptile pet trade online and summarized CITES documentation of the yearly import export records from 1976 to 2018 by CITES secretariat.  This manuscript provides a baseline for the extent of the trade, invasive species and the species traded in mainland India.  We found that there is an extensive trade of exotic reptiles in the country, comprising 84 species including the highly venomous species such as Bitis gabonica.  According to CITES records of 1976–2018, 98.6% of the reptile imports into India have not been reported to the CITES management authorities in India.  We also found some evidence of trade in protected native species through the exotic pet trade network.  Furthermore, some highly threatened reptile species including many listed in Appendix I of CITES are traded in India. 

Prevalence of Ophidiomyces ophiodiicola, the Causative Agent of Snake Fungal Disease, in the Interior Plateau Ecoregion of Tennessee, USA

The fungal pathogen Ophidiomyces ophiodiicola, the causative agent of snake fungal disease, has been implicated in declines of North American snake populations since 2006 and the geographic range of this pathogen is still not fully known. In Tennessee, US, O. ophiodiicola has been detected since 2012, but large portions of the state have not been surveyed for this pathogen. Our primary objective was to monitor the prevalence of O. ophiodiicola in the Interior Plateau ecoregion of Tennessee by swabbing all snakes that were encountered during road cruising survey efforts in 2017 and 2018. Eleven snakes of four species, copperhead (Agkistrodon contortrix), common water snake (Nerodia sipedon), black kingsnake (Lampropeltis nigra), and smooth earthsnake (Virginia valeriae), tested positive for the presence of O. ophiodiicola. Overall, 9.2% (11/120) of snakes sampled tested positive for the presence of O. ophiodiiola, and we further observed a seasonal trend in detections with summer months having the greatest frequency of detections. Our results extend the known geographic range of O. ophiodiicola in Tennessee by adding four previously unconfirmed O. ophiodiicola-positive counties. Further sampling will need to be conducted across west Tennessee because this is the most data-deficient region of the state. Our results offer additional evidence of the presence of this pathogen in Tennessee and will help researchers further understand the geographic distribution and host range.

POSTNATAL MORTALITY IN NEONATE RATTLESNAKES ASSOCIATED WITH OPHIDIOMYCES OPHIODIICOLA

Ophidiomycosis, historically referred to as snake fungal disease (SFD), caused by Ophidiomyces ophiodiicola, is a significant disease of snakes characterized by crusty scales, pustules, subcutaneous nodules, and death. Ophidiomycosis is a proposed threat to sustainability of free-ranging snake populations throughout the United States and Europe, but the clinical progression during periods of reproductive activity (gravid females, neonates) is unknown. In spring 2012, five apparently healthy gravid eastern massasauga (Sistrurus catenatus) rattlesnakes from Clinton County, Illinois, were brought into captivity to give birth and be returned into the population. While in captivity, one adult female and 21 neonates died. Five individuals were subsequently confirmed positive for O. ophiodiicola by using quantitative polymerase chain reaction (qPCR). In 2016, a gravid timber rattlesnake (Crotalus horridus) with ophidiomycosis from Jackson County, Illinois, gave birth in captivity to 13 neonates. Skin swabs were taken from all neonates immediately after birth and confirmed negative for O. ophiodiicola by using qPCR. The neonates remained housed with the positive female for 10 days before all animals were reswabbed and released back into the wild. One neonate was O. ophiodiicola positive at time of release. The initial negative result followed by a positive result several days postpartum suggests that the neonate was infected by the female after direct contact. Both case series represent natural infection of neonates after parturition and highlight the importance of this disease in a demographically important age class.

Niche Contraction of an Endangered Frog Driven by the Amphibian Chytrid Fungus

Introduced pathogens can alter the geographic distribution of susceptible host species. For example, Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has been linked to the global decline and extinction of numerous amphibian species during the last four decades. A growing number of studies have described the distribution of Bd and susceptible hosts across the globe; however, knowledge on how Bd may shape the climatic niche of susceptible species is still missing. We estimated the effect of Bd on the geographic distribution and niche dynamics of the critically endangered lowland robber frog (Craugastor ranoides) in Costa Rica. We found a reduction of 98% in the geographic range of this species by 1995, following the epizootic outbreaks of Bd that affected Costa Rica in the 1980 and early 1990s. We also quantified niche contraction and found that the species is currently restricted to dry and warm environments that have been considered unsuitable for Bd. Our results contribute to the understanding of how emerging pathogens shape the climatic niches and geographic distribution of susceptible species.

Infection with Nannizziopsis guarroi and Ophidiomyces ophiodiicola in reptiles in Taiwan

Fungal infection is an emerging threat to reptiles. The main pathogens are fungi of the genera Nannizziopsis, Paranannizziopsis and Ophidiomyces. The clinical symptoms range from mild skin lesions to the dissemination of internal organs and even death. Most of the reported cases are from Europe, North America and Australia. In this study, we report the Nannizziopsis guarroi infection in one captive inland bearded dragon (Pogona vitticeps), one captive green iguana (Iguana iguana) and Ophidiomyces ophiodiicola infection in one wild red-banded snake (Dinodon rufozonatum) and one wild Chinese cobra (Naja atra) in Taiwan. The infections were confirmed by the presence of fungal elements in the tissue. The pathogens were identified based on their morphological and DNA sequence characteristics. The susceptibility profiles of the fungal strains to nine antifungal drugs were obtained using broth microdilution methods. The presence of both fungal species in Asia highlights the urgent need for surveillance and close monitoring of reptile infections to prevent them from spreading and to the possible collapse of reptile populations in the wild.

Shell Lesions Associated With Emydomyces testavorans Infection in Freshwater Aquatic Turtles

A newly described onygenalean fungus, Emydomyces testavorans, has been isolated from ulcerative shell and skin lesions of freshwater aquatic chelonians. To investigate the shell lesions associated with infection and determine if any lesional features were unique to E. testavorans, tissues from turtles housed in zoological institutions (n = 45) in the United States and free-living turtles (n = 5) submitted for diagnostic biopsy or necropsy were examined. Free-living turtles were from geographically distinct habitats in Florida (n = 1) and Washington (n = 4) at the time of sampling. Histologic shell sections were evaluated for the presence or absence of specific lesional features. Infection with E. testavorans was evaluated in all cases by screening GMS (Grocott-Gomori's methenamine silver)-stained histologic sections for the presence of morphologically consistent fungi and by quantitative PCR (polymerase chain reaction) on representative frozen tissue or formalin-fixed paraffin-embedded sections. Additionally, culture was performed for 15 cases with available fresh/frozen tissue. In total, there were 17 PCR-confirmed E. testavorans cases, 29 cases with morphologically consistent fungi on GMS-stained sections, and 21 cases of shell lesions without histologic or molecular evidence of E. testavorans infection. Epithelial inclusion cysts, defined as cystic structures within the dermis lined by keratinized stratified squamous epithelium and containing necrotic bone and keratin debris, were significantly (P < .01) associated with E. testavorans infection. Other significantly associated shell lesions included squamous metaplasia, hyperkeratosis, inflammation, and osteonecrosis (P < .05). This study identified characteristic shell lesions associated with E. testavorans infection. Further studies to prove causality are needed.

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.

Selected Emerging Infectious Diseases of Squamata: An Update

This article details emerging infectious diseases that have devastating impacts on captive and wild squamates. Treatment advances have been attempted for Cryptosporidium infections in squamates. Gram-positive bacteria, Devriesea agamarum and Austwickia chelonae, are contributing to severe disease in captive and now in wild reptiles, some critically endangered. Nannizziposis, Paranannizziopsis, and Ophidiomyces continue to cause fatal disease as primary pathogens in wild and captive populations of squamates and sphenodontids. Nidovirus, bornavirus, paramyxovirus, sunshine virus, and arenavirus have emerged to be significant causes of neurorespiratory disease in snakes. Controlled studies evaluating environmental stability, disinfection, transmission control, and treatment are lacking.

Ophidiomycosis in Red Cornsnakes (Pantherophis guttatus): Potential Roles of Brumation and Temperature on Pathogenesis and Transmission

Ophidiomycosis (snake fungal disease) is caused by the fungus Ophidiomyces ophiodiicola. As ophidiomycosis is difficult to study in free-ranging snakes, a reliable experimental model is needed to investigate transmission, pathogenesis, morbidity, and mortality, and the effects of brumation and temperature on disease development. Our objective was to develop such a model via subcutaneous injection of O. ophiodiicola conidia in red cornsnakes (Pantherophis guttatus). The model was used to evaluate transmission and the effects of brumation and temperature in co-housed inoculated and noninoculated snakes. All 23 inoculated snakes developed lesions consistent with ophidiomycosis, including heterophilic and granulomatous dermatitis, cellulitis, and myositis, and embolic fungal granulomas throughout the liver and the coelomic connective tissue in 21/23 (91%). In the inoculated snakes, 21% of skin swabs, 37% of exuvia, and all liver samples tested positive by qPCR (quantitative polymerase chain reaction) for O. ophiodiicola. A post brumation skin swab from 1/12 noninoculated snakes that brumated in contact with inoculated snakes tested positive by qPCR, suggesting possible contact transmission. That snake had microscopic skin lesions consistent with ophidiomycosis, but no visible fungal elements. Of the 23 inoculated snakes, 20 (87%) died over the 70-day experiment, with ophidiomycosis considered the primary cause of death; 12 (52%) of the inoculated snakes died during brumation. Overall, this experimental model of ophidiomycosis reproduced skin lesions analogous to those of many natural cases, and internal lesions similar to the most severe natural cases. The study provides tentative experimental evidence for horizontal transmission in brumation, and offers a tool for future studies of this widespread snake disease.

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.

All tests are imperfect: Accounting for false positives and false negatives using Bayesian statistics

Tests with binary outcomes (e.g., positive versus negative) to indicate a binary state of nature (e.g., disease agent present versus absent) are common. These tests are rarely perfect: chances of a false positive and a false negative always exist. Imperfect results cannot be directly used to infer the true state of the nature; information about the method's uncertainty (i.e., the two error rates and our knowledge of the subject) must be properly accounted for before an imperfect result can be made informative. We discuss statistical methods for incorporating the uncertain information under two scenarios, based on the purpose of conducting a test: inference about the subject under test and inference about the population represented by test subjects. The results are applicable to almost all tests. The importance of properly interpreting results from imperfect tests is universal, although how to handle the uncertainty is inevitably case-specific. The statistical considerations not only will change the way we interpret test results, but also how we plan and carry out tests that are known to be imperfect. Using a numerical example, we illustrate the post-test steps necessary for making the imperfect test results meaningful.

Comparison of three different PCR protocols for the detection of ferlaviruses

Background

Ferlaviruses are important pathogens in snakes often associated with respiratory and neurological disease. The detection of ferlaviral RNA by PCR is considered to be the most reliable method for the diagnosis of infection. The PCRs that have been used most commonly for this purpose have not been properly assessed to determine their sensitivity, specificity and ability to detect the known genetic diversity of this group of viruses. The aim of this study was to compare three published PCR protocols so that a single method could be recommended to laboratories that perform this testing.

Results

Comparisons were carried out using cell culture isolates and tissues from snakes infected with specific virus genotypes. A single round PCR targeting a short segment of the viral polymerase (L) gene provided the highest sensitivity and specificity, and detected isolated ferlaviruses from all four described genogroups, as well as from tissues of infected snakes.

Conclusion

A broadly-reactive PCR for the detection of all known ferlaviruses was found to provide a good combination of detection limit, specificity and speed. Based on these criteria, this method is recommended for the diagnosis of ferlavirus infections.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-2028-0) contains supplementary material, which is available to authorized users.

Ophidiomycosis prevalence in Georgia's Eastern Indigo Snake (Drymarchon couperi) populations

Wildlife diseases have posed a significant challenge to the conservation of many species in recent years. Diseases have been implicated in population declines over large geographic areas, with severe disease outbreaks leading to either local or complete extinctions of wild populations. Ophidiomycosis, commonly known as snake fungal disease, is caused by the fungus Ophidiomyces ophiodiicola, which has been documented in snake populations across the eastern and southern United States. We collected swab samples from the federally threatened Eastern Indigo Snake (Drymarchon couperi) in populations across the species' Georgia range. We used quantitative PCR to determine the presence of O. ophiodiicola DNA and also recorded skin abnormalities characteristic of ophidiomycosis. From 1 September 2016 to 4 August 2018, Eastern Indigo Snakes tested positive for O. ophiodiicola DNA on 47 of 107 occasions (43.9%) and tested negative for fungal DNA but had skin lesions consistent with ophidiomycosis on 42 occasions (39.3%). Symptomatic and qPCR positive individuals were more likely to be encountered during January and February when compared to November and December. We found no effect of sex (p = 0.517), age-class (p = 0.106), or body size (snout-vent length: p = 0.083; mass: p = 0.206; body condition: p = 0.063) on ophidiomycosis status. Over the two-year study, we encountered individuals in which infection was clearly negatively impacting overall health and also documented individuals in which infection apparently cleared from one year to the next. These results demonstrate that O. ophiodiicola and lesions characteristic of ophidiomycosis are widespread in Georgia's Eastern Indigo Snake populations. However, there are many unanswered questions regarding this disease, including the effects of disease on populations and individuals, the presence of infection vectors, and the change in prevalence over time. More research is needed to address ophidiomycosis and understand its impacts on ongoing conservation efforts.

Variability in snake skin microbial assemblages across spatial scales and disease states

Understanding how biological patterns translate into functional processes across different scales is a central question in ecology. Within a spatial context, extent is used to describe the overall geographic area of a study, whereas grain describes the overall unit of observation. This study aimed to characterize the snake skin microbiota (grain) and to determine host–microbial assemblage–pathogen effects across spatial extents within the Southern United States. The causative agent of snake fungal disease, Ophidiomyces ophiodiicola, is a fungal pathogen threatening snake populations. We hypothesized that the skin microbial assemblage of snakes differs from its surrounding environment, by host species, spatial scale, season, and in the presence of O. ophiodiicola. We collected snake skin swabs, soil samples, and water samples across six states in the Southern United States (macroscale extent), four Tennessee ecoregions (mesoscale extent), and at multiple sites within each Tennessee ecoregion (microscale extent). These samples were subjected to DNA extraction and quantitative PCR to determine the presence/absence of O. ophiodiicola. High-throughput sequencing was also utilized to characterize the microbial communities. We concluded that the snake skin microbial assemblage was partially distinct from environmental microbial communities. Snake host species was strongly predictive of the skin microbiota at macro-, meso-, and microscale spatial extents; however, the effect was variable across geographic space and season. Lastly, the presence of the fungal pathogen O. ophiodiicola is predictive of skin microbial assemblages across macro- and meso-spatial extents, and particular bacterial taxa associate with O. ophiodiicola pathogen load. Our results highlight the importance of scale regarding wildlife host–pathogen–microbial assemblage interactions.

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.

Emydomyces testavorans, a New Genus and Species of Onygenalean Fungus Isolated from Shell Lesions of Freshwater Aquatic Turtles

The fungal order Onygenales includes many pathogens of humans and animals, and recent studies have shown some onygenalean fungi to be significant emerging pathogens of reptiles. Although many of these fungi have similar morphological features in histologic tissue sections, recent molecular analyses have revealed a genetically complex and diverse group of reptile pathogens comprising several genera, most notably Nannizziopsis, Ophidiomyces, and Paranannizziopsis Infections by members of these genera have been previously reported in a variety of reptile species, including crocodilians, lizards, snakes, and tuataras, with negative impacts on conservation efforts for some reptiles. Despite the well-documented pathogenicity of these fungi in all other extant reptile lineages, infection has not yet been reported in aquatic turtles. In this study, we report the isolation of an onygenalean fungus associated with shell lesions in freshwater aquatic turtles. The morphologic and genetic characteristics of multiple isolates (n = 21) are described and illustrated. Based on these features and results of a multigene phylogenetic analysis, a new genus and species, Emydomyces testavorans, are proposed for these fungi isolated from turtle shell lesions.