Threat Characterization of an Invasive Lung Parasite and a Longstanding Fungal Pathogen to Florida Pygmy Rattlesnake Populations

Jenna Noel Palmisano

University of Central Florida

November 2023

Figure 1. A Sistrurus miliarius barbouri, the dusky pygmy rattlesnake in a loose coil.

Background—Snake species native to the southeastern United States face many conservation threats including habitat loss, invasive species, persecution, and infectious diseases. Two emerging invasive pathogens, Ophidiomyces ophiodiicola (Oo) (the causative agent of Snake Fungal Disease) and Raillietiella orientalis (Ro) are prevalent in snake populations of the southeastern U.S. and may contribute to local extinctions (1,2). Oo, a fungal pathogen, and Ro, a lung parasite, utilize an array of snake taxa as hosts, survive wide environmental conditions, and cause chronic and lethal disease outcomes. In the pygmy rattlesnake (Sistrurus miliarius), Oo infections can alter reproductive schedules and increase metabolic rate, febrile responses, and evaporative water loss (3,4). These energetically expensive coping mechanisms may leave snakes with less energy to allocate towards reproduction. Therefore, the sublethal mechanisms of Oo infections indirectly impact populations and coinfections with other pathogens, like Ro, could exacerbate these effects.

The dependence of pygmy rattlesnakes on ectothermic prey makes them vulnerable to Ro infection because this parasite utilizes frogs and lizards as intermediate hosts (5). Pygmy rattlesnakes are also an immunologically naïve host and this lack of an evolutionary history with Ro could augment adverse health impacts. Ro belongs to an understudied class of crustaceans that as adults mostly parasitize the lungs of carnivorous reptiles (6). Ro originated in Southeast Asia and has subsequently invaded Australian and North American snake populations. In North America, Burmese pythons have been supported as the introduction pathway both spatiotemporally and molecularly (2). In native snakes, the infections are more intense than in pythons. The adult parasites grow to over 100 mm in native snakes and the infections can often include over 100 adult parasites in the lungs. Infections cause chronic inflammation, lesions of the lungs, anemia, and pneumonia, all of which are documented in pygmy rattlesnakes, banded water snakes, and indigo snakes (7,8,9). The threat of Ro is a conservation concern as its use of numerous hosts and presence in the pet trade increases the likelihood of rapid dispersal. Precipitous declines of pygmy rattlesnake populations that are spatially and temporally consistent with the initial invasion of Ro indicate population level consequences of infections. For informed habitat management and disease control strategies, I am documenting the host-pathogen dynamics of Oo and Ro in pygmy rattlesnake populations across Florida and assessing the influence of disease on the genomic structure within and between these populations.

Figure 2. A deceased pygmy rattlesnake with Ro individuals that crawled out of the mouth (left). Clinical representation of snake fungal disease on the tail of a pygmy rattlesnake (right).

Methods—In June 2023, I started my field expeditions to 13 locations with pygmy rattlesnakes across Florida. When I capture individuals, I take their cloacal temperatures, conduct body (Oo detection) and cloacal swabs (Ro detection), and collect fecal samples. I determine their sex, take scale clips (DNA), insert PIT tags, and measure the masses and snout vent lengths. At the location of capture, I record the ground and ambient temperature and humidity as well as the GPS coordinates. I visit three of these 13 locations monthly to assess growth rate and survival in individuals with infections over time. Each of the mark-recapture locations vary in their current prevalence of Oo and Ro as well as the initial detection dates of each pathogen. I visit the other 10 sites for 2-day periods 4–6 times a year to describe prevalence of these diseases over time and collect a minimum genetic sample size of 24.

Figure 3. Taking the internal body temperature of a pygmy rattlesnake for comparative analyses of behavioral fever in infected versus noninfected snakes (left). Measuring a dusky pygmy rattlesnake in a clear newspaper bag with a spring scale for accurate mass and reduced contamination (right).

Figure 4. Swabbing the dorsal and ventral surfaces for detection of Oo.

Preliminary findings—Since June, I have captured 195 snakes with 178 individuals and 16 recaptures across 11 locations. The funds granted by the Orianne Society have made PIT tagging these individuals possible and will support tagging of 205 more snakes over the next year. It’s critical that I have ways to identify the individual, so I can accurately assess the genomic diversity across all locations and the growth rate and survival at the mark-recapture locations. Out of the 11 sites that I have visited, 5 have individuals with symptoms of snake fungal disease and 4 have symptoms of pentastomiasis caused by Ro. Given the seasonality of snake fungal disease, I will likely find a higher prevalence once I sample in the winter and spring. I also expect the prevalence of pentastomiasis to increase with increased sample sizes. For the current data set, I have only calculated prevalence for the individuals I have obtained fecal samples from.

Figure 5 and 6. The prevalence of pentastomiasis (left) and snake fungal disease (right) across sampled counties with the bars representing prevalence and the points representing sample size. Note that these figures only include the locations that have been sampled.

Future of the research—I will sample all 13 locations over the next 3 years. For the mark-recapture locations, the intensive monthly sampling will allow me to study the growth rate and survival of individuals with Ro and Oo infections. For the other 10 locations, the four to six annual sampling events will allow me to assess the prevalence and severity of these diseases over time. Once I have at least 24 individual’s DNA from each location, I will characterize neutral population genetic diversity and structure using a ddRADseq approach to generate thousands of loci distributed throughout the genome. This neutral dataset will be contrasted with genetic polymorphisms of adaptive genetic markers (major histocompatibility class II alleles) generated from an amplicon sequencing approach that I am currently optimizing for snakes. Together, studies of pathogen distribution and the population and genetic structure of pygmy rattlesnake populations will better characterize the threat of disease caused by Oo (Ophidiomycosis or Snake Fungal Disease) and Ro (Pentastomiasis), which is essential to the implementation of proper species, land, and biosecurity management.

Figure 7. (Left) A female pygmy rattlesnake in early pregnancy in June on the west coast of Florida. (Right) A young female pygmy rattlesnake in ambush. The red paint dot is my marking system to avoid capturing individuals more than once within a month.


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  5. Palmisano, J.N., et al. 2022. Infection experiments indicate common Florida anurans and lizards serve as intermediate hosts for the invasive pentastome parasite, Raillietiella orientalis. Journal of Herpetology.
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