Use of site occupancy models to estimate prevalence of Myxobolus cerebralis infection in trout

ESTIMATING OCCURRENCE, PREVALENCE, AND DETECTION OF AMPHIBIAN PATHOGENS: INSIGHTS FROM OCCUPANCY MODELS

Understanding the distribution of pathogens across landscapes and their prevalence within host populations is a common aim of wildlife managers. Despite the need for unbiased estimates of pathogen occurrence and prevalence for planning effective management interventions, many researchers fail to account for imperfect pathogen detection. Instead raw data are often reported, which may lead to ineffective, or even detrimental, management actions. We illustrate the utility of occupancy models for generating unbiased estimates of disease parameters by 1) providing a written tutorial describing how to fit these models in Program PRESENCE and 2) presenting a case study with the pathogen ranavirus. We analyzed ranavirus detection data from a wildlife refuge (Maryland, US) using occupancy modeling, which yields unbiased estimates of pathogen occurrence and prevalence. We found ranavirus prevalence was underestimated by up to 30% if imperfect pathogen detection was ignored. The unbiased estimate of ranavirus prevalence in larval wood frog (Lithobates sylvaticus; 0.73) populations was higher than in larval spotted salamander (Ambystoma maculatum; 0.56) populations. In addition, the odds of detecting ranavirus in tail samples were 6.7 times higher than detecting ranavirus in liver samples. Therefore, tail samples presented a nonlethal sampling method for ranavirus that may be able to detect early (nonsystemic) infections.

Elimination of Myxobolus cerebralis in Placer Creek, a Native Cutthroat Trout Stream in Colorado

Placer Creek, a tributary of Sangre de Cristo Creek in Colorado's San Luis Valley, supported an allopatric core conservation population of native Rio Grande Cutthroat Trout Oncorhynchus clarkii virginalis during much of the 20th century. After the failure of gabion barriers in the late 1990s, Brook Trout Salvelinus fontinalis infected with Myxobolus cerebralis invaded from Sangre de Cristo Creek. By 2005, whirling disease (WD) and competition from Brook Trout reduced Rio Grande Cutthroat Trout numbers to less than 10% of the total trout population. New barriers were constructed in 2006 and the stream was treated with rotenone in 2007 and 2009 to eliminate all fish prior to the reintroduction of Rio Grande Cutthroat Trout. Results of WD research studies in Montana, California, and Colorado indicated it might be possible to break the life cycle of the parasite in some situations. Our management interventions included (1) reducing the fish population in the stream to zero for approximately 14 months, (2) introducing lineage V and VI Tubifex tubifex worms, which are not susceptible to M. cerebralis, and (3) eliminating a small off-channel pond that provided optimal habitat that sustained a localized high-density population of lineage III T. tubifex, the oligochaete host susceptible to M. cerebralis. Electrofishing during the fall of 2009 and spring of 2010 indicated the drainage was devoid of fish. Fry, juvenile, and adult Rio Grande Cutthroat Trout were stocked in September and October of 2010 and 2011. Approximately 975,000 lineage V and VI T. tubifex were introduced into Placer Creek between 2010 and 2012 as possible oligochaete competitors for the lineage III worms. The off-channel pond was filled in, and the surface was reseeded in April 2012. No evidence of M. cerebralis infection was detected among more than 280 Rio Grande Cutthroat Trout tested between July 2012 and July 2016, indicating the parasite had been eradicated from the Placer Creek basin upstream of the barriers.

Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics

Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmon Oncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population: Apophallus/echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus salmincola/ metacercariae, and Renibacterium salmoninarum. A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%.

Using site-occupancy models to prepare for the spread of chytridiomyosis and identify factors affecting detectability of a cryptic susceptible species, the Tasmanian tree frog

Context The global reduction of amphibian biodiversity as a result of the disease chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis; Bd) has highlighted the need to accurately detect local population declines in association with Bd presence. Although Bd has spread globally, some remote regions such as the Tasmanian Wilderness World Heritage Area (1.40 million ha; TWWHA) in Australia, remain largely, but not entirely, disease free. The Tasmanian tree frog (Litoria burrowsae) resides primarily within TWWHA boundaries, and is believed to be susceptible to chytridiomycosis. Aims In the absence of historical abundance data, we used a single-season multi-state site-occupancy model to investigate the impact of Bd on L. burrowsae populations, on factors affecting species detection and to inform ongoing surveillance and conservation. Methods We recorded frog detection and ranked call intensity (estimation of population size) from repeated independent surveys within a season to estimate the role of covariates, such as presence of Bd and environmental variables, on species occupancy and detection probability. Key results Modelling revealed large frog populations are more likely to be present at naturally formed than human-formed ponds, strong winds negatively affect detection of populations, and time after sunset affects detection of large populations. Large frog populations were more likely to be Bd-negative; however, models including Bd presence were not well supported, in part a result of the small number of Bd-positive sites recorded. Conclusions and Implications The utility of site-occupancy modelling in understanding the impact of disease on populations is little known, but has the potential to improve the accuracy and efficiency of many conservation programs.

Heterogeneous occupancy and density estimates of the pathogenic fungus Batrachochytrium dendrobatidis in waters of North America

Biodiversity losses are occurring worldwide due to a combination of stressors. For example, by one estimate, 40% of amphibian species are vulnerable to extinction, and disease is one threat to amphibian populations. The emerging infectious disease chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd), is a contributor to amphibian declines worldwide. Bd research has focused on the dynamics of the pathogen in its amphibian hosts, with little emphasis on investigating the dynamics of free-living Bd. Therefore, we investigated patterns of Bd occupancy and density in amphibian habitats using occupancy models, powerful tools for estimating site occupancy and detection probability. Occupancy models have been used to investigate diseases where the focus was on pathogen occurrence in the host. We applied occupancy models to investigate free-living Bd in North American surface waters to determine Bd seasonality, relationships between Bd site occupancy and habitat attributes, and probability of detection from water samples as a function of the number of samples, sample volume, and water quality. We also report on the temporal patterns of Bd density from a 4-year case study of a Bd-positive wetland. We provide evidence that Bd occurs in the environment year-round. Bd exhibited temporal and spatial heterogeneity in density, but did not exhibit seasonality in occupancy. Bd was detected in all months, typically at less than 100 zoospores L(-1). The highest density observed was ∼3 million zoospores L(-1). We detected Bd in 47% of sites sampled, but estimated that Bd occupied 61% of sites, highlighting the importance of accounting for imperfect detection. When Bd was present, there was a 95% chance of detecting it with four samples of 600 ml of water or five samples of 60 mL. Our findings provide important baseline information to advance the study of Bd disease ecology, and advance our understanding of amphibian exposure to free-living Bd in aquatic habitats over time.

Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

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A new field method was developed to study ectoparasite prevalence on hosts.

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We describe the approach using a study of fleas on prairie dogs.

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Data were analyzed with occupancy models to account for imperfect detection.

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There was a 99.3% probability of detecting a flea on a flea-occupied host.

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Flea occupancy varied among months, sites, sampling plots, and hosts.

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The field method can be used in the future to study ectoparasite communities.

Ectoparasites are often difficult to detect in the field. We developed a method that can be used with occupancy models to estimate the prevalence of ectoparasites on hosts, and to investigate factors that influence rates of ectoparasite occupancy while accounting for imperfect detection. We describe the approach using a study of fleas (Siphonaptera) on black-tailed prairie dogs (Cynomys ludovicianus). During each primary occasion (monthly trapping events), we combed a prairie dog three consecutive times to detect fleas (15 s/combing). We used robust design occupancy modeling to evaluate hypotheses for factors that might correlate with the occurrence of fleas on prairie dogs, and factors that might influence the rate at which prairie dogs are colonized by fleas. Our combing method was highly effective; dislodged fleas fell into a tub of water and could not escape, and there was an estimated 99.3% probability of detecting a flea on an occupied host when using three combings. While overall detection was high, the probability of detection was always <1.00 during each primary combing occasion, highlighting the importance of considering imperfect detection. The combing method (removal of fleas) caused a decline in detection during primary occasions, and we accounted for that decline to avoid inflated estimates of occupancy. Regarding prairie dogs, flea occupancy was heightened in old/natural colonies of prairie dogs, and on hosts that were in poor condition. Occupancy was initially low in plots with high densities of prairie dogs, but, as the study progressed, the rate of flea colonization increased in plots with high densities of prairie dogs in particular. Our methodology can be used to improve studies of ectoparasites, especially when the probability of detection is low. Moreover, the method can be modified to investigate the co-occurrence of ectoparasite species, and community level factors such as species richness and interspecific interactions.

Cryptic vector divergence masks vector-specific patterns of infection: an example from the marine cycle of Lyme borreliosis

Vector organisms are implicated in the transmission of close to a third of all infectious diseases. In many cases, multiple vectors (species or populations) can participate in transmission but may contribute differently to disease ecology and evolution. The presence of cryptic vector populations can be particularly problematic as differences in infection can be difficult to evaluate and may lead to erroneous evolutionary and epidemiological inferences. Here, we combine site-occupancy modeling and molecular assays to evaluate patterns of infection in the marine cycle of Lyme borreliosis, involving colonial seabirds, the tick Ixodes uriae, and bacteria of the Borrelia burgdorferi s.l. complex. In this cycle, the tick vector consists of multiple, cryptic (phenotypically undistinguishable but genetically distinct) host races that are frequently found in sympatry. Our results show that bacterial detection varies strongly among tick races leading to vector-specific biases if raw counts are used to calculate Borrelia prevalence. These differences are largely explained by differences in infection intensity among tick races. After accounting for detection probabilities, we found that overall prevalence in this system is higher than previously suspected and that certain vector-host combinations likely contribute more than others to the local dynamics and large-scale dispersal of Borrelia spirochetes. These results highlight the importance of evaluating vector population structure and accounting for detection probability when trying to understand the evolutionary ecology of vector-borne diseases.

Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis

Batrachochytrium dendrobatidis is a fungal pathogen that is receiving attention around the world for its role in amphibian declines. Study of its occurrence patterns is hampered by false negatives: the failure to detect the pathogen when it is present. Occupancy models are a useful but currently underutilized tool for analyzing detection data when the probability of detecting a species is <1. We use occupancy models to evaluate hypotheses concerning the occurrence and prevalence of B. dendrobatidis and discuss how this application differs from a conventional occupancy approach. We found that the probability of detecting the pathogen, conditional on presence of the pathogen in the anuran population, was related to amphibian development stage, day of the year, elevation, and human activities. Batrachochytrium dendrobatidis was found throughout our study area but was only estimated to occur in 53.4% of 78 populations of native amphibians and 66.4% of 40 populations of nonnative Rana catesbeiana tested. We found little evidence to support any spatial hypotheses concerning the probability that the pathogen occurs in a population, but did find evidence of some taxonomic variation. We discuss the interpretation of occupancy model parameters, when, unlike a conventional occupancy application, the number of potential samples or observations is finite.