Search

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. [ABSTRACT FROM AUTHOR]

Dracunculus medinensis (Guinea worm) is a parasitic nematode that can cause the debilitating disease dracunculiasis (Guinea worm disease) in humans. The global Guinea Worm Eradication Program has led intervention and eradication efforts since the 1980s, and Guinea worm infections in people have decreased >99.99%. With the final goal of eradication drawing nearer, reports of animal infections from some remaining endemic countries pose unique challenges. Currently, confirmation of suspected Guinea worm infection relies on conventional molecular techniques such as polymerase chain reaction (PCR), which is not specific to Guinea worm and, therefore, requires sequencing of the PCR products to confirm the identity of suspect samples, a process that often takes a few weeks. To decrease the time required for species confirmation, we developed a quantitative PCR assay targeting the mitochondrial cytochrome b (cytb) gene of Guinea worm. Our assay has a limit of detection of 10 copies per reaction. The mean analytical parameters (± SE) were as follows: efficiency = 93.4 ± 7.7%, y-intercept = 40.93 ± 1.11, slope = -3.4896 ± 0.12, and the R2 = 0.999 ± 0.004. The assay did not amplify other nematodes found in Guinea worm-endemic regions and demonstrated 100% diagnostic sensitivity and specificity. Implementation of this quantitative PCR assay for Guinea worm identification could eliminate the need for DNA sequencing to confirm species. Thus, this approach can be implemented to provide more rapid confirmation of Guinea worm infections, leading to faster execution of Guinea worm interventions while increasing our understanding of infection patterns. Author summary: Guinea worm (Dracunculus medinensis) is a parasitic nematode that causes debilitating disease in humans. The Guinea Worm Eradication Program would benefit from having a rapid molecular test that can confirm species identification without time-consuming DNA sequencing. We developed a qPCR protocol targeting the mitochondrial cytochrome b (cytb) gene of Guinea worm. The assay was validated analytically over 12 experiments using a standard serial dilution as well as diagnostically on DNA samples from non-target host species and other parasites (n = 180) and Guinea worm samples (n = 200) from a diversity of hosts and geographic regions. This assay could reliably detect 10 copies of the target DNA sequence and had a mean efficiency of 93.4% with 100% diagnostic sensitivity and specificity. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]