THE FITTING OF GENERAL FORCE-OF-INFECTION MODELS TO WILDLIFE DISEASE PREVALENCE DATA

Applications of VirScan to broad serological profiling of bat reservoirs for emerging zoonoses

Introduction

Bats are important providers of ecosystem services such as pollination, seed dispersal, and insect control but also act as natural reservoirs for virulent zoonotic viruses. Bats host multiple viruses that cause life-threatening pathology in other animals and humans but, themselves, experience limited pathological disease from infection. Despite bats' importance as reservoirs for several zoonotic viruses, we know little about the broader viral diversity that they host. Bat virus surveillance efforts are challenged by difficulties of field capture and the limited scope of targeted PCR- or ELISA-based molecular and serological detection. Additionally, virus shedding is often transient, thus also limiting insights gained from nucleic acid testing of field specimens. Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a broad serological tool used previously to comprehensively profile viral exposure history in humans, offers an exciting prospect for viral surveillance efforts in wildlife, including bats.

Methods

Here, for the first time, we apply PhIP-Seq technology to bat serum, using a viral peptide library originally designed to simultaneously assay exposures to the entire human virome.

Results

Using VirScan, we identified past exposures to 57 viral genera-including betacoronaviruses, henipaviruses, lyssaviruses, and filoviruses-in semi-captive Pteropus alecto and to nine viral genera in captive Eonycteris spelaea. Consistent with results from humans, we find that both total peptide hits (the number of enriched viral peptides in our library) and the corresponding number of inferred past virus exposures in bat hosts were correlated with poor bat body condition scores and increased with age. High and low body condition scores were associated with either seropositive or seronegative status for different viruses, though in general, virus-specific age-seroprevalence curves defied assumptions of lifelong immunizing infection, suggesting that many bat viruses may circulate via complex transmission dynamics.

Discussion

Overall, our work emphasizes the utility of applying biomedical tools, like PhIP-Seq, first developed for humans to viral surveillance efforts in wildlife, while highlighting opportunities for taxon-specific improvements.

The devil you know and the devil you don't: current status and challenges of bovine tuberculosis eradication in the United States

Having entered into its second century, the eradication program for bovine tuberculosis (bTB, caused by Mycobacterium bovis) in the United States of America occupies a position both enviable and daunting. Excepting four counties in Michigan comprising only 6109 km2 (0.06% of US land area) classified as Modified Accredited, as of April 2022 the entire country was considered Accredited Free of bTB by the US Department of Agriculture for cattle and bison. On the surface, the now well-described circumstances of endemic bTB in Michigan, where white-tailed deer (Odocoileus virginianus) serve as a free-ranging wildlife maintenance host, may appear to be the principal remaining barrier to national eradication. However, the situation there is unique in the U.S., and far-removed from the broader issues of bTB control in the remainder of the country. In Michigan, extensive surveillance for bTB in deer over the last quarter century, and regulatory measures to maximize the harvest of publicly-owned wildlife, have been implemented and sustained. Prevalence of bTB in deer has remained at a low level, although not sufficiently low to eliminate cattle herd infections. Public attitudes towards bTB, cattle and deer, and their relative importance, have been more influential in the management of the disease than any limitations of biological science. However, profound changes in the demographics and social attitudes of Michigan's human population are underway, changes which are likely to force a critical reevaluation of the bTB control strategies thus far considered integral. In the rest of the U.S. where bTB is not self-sustaining in wildlife, changes in the scale of cattle production, coupled with both technical and non-technical issues have created their own substantial challenges. It is against this diverse backdrop that the evolution of whole genome sequencing of M. bovis has revolutionized understanding of the history and ecology of bTB in Michigan, resolved previously undiscernible epidemiological puzzles, provided insights into zoonotic transmission, and unified eradication efforts across species and agencies. We describe the current status of bTB eradication in the U.S., how circumstances and management have changed, what has been learned, and what remains more elusive than ever.

Inter-epidemic Rift Valley fever virus infection incidence and risks for zoonotic spillover in northern Tanzania

Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that has caused epidemics involving people and animals across Africa and the Arabian Peninsula. A number of studies have found evidence for the circulation of RVFV among livestock between these epidemics but the population-level incidence of infection during this inter-epidemic period (IEP) is rarely reported. General force of infection (FOI) models were applied to age-adjusted cross-sectional serological data to reconstruct the annual FOI and population-level incidence of RVFV infection among cattle, goats, and sheep in northern Tanzania from 2009 through 2015, a period without reported Rift Valley fever (RVF) cases in people or animals. To evaluate the potential for zoonotic RVFV spillover during this period, the relationship between village-level livestock RVFV FOI and human RVFV seropositivity was quantified using multi-level logistic regression. The predicted average annual incidence was 72 (95% Credible Interval [CrI] 63, 81) RVFV infections per 10,000 animals and 96 (95% CrI 81, 113), 79 (95% CrI 62, 98), and 39 (95% CrI 28, 52) per 10,000 cattle, sheep, and goats, respectively. There was variation in transmission intensity between study villages, with the highest estimated village-level FOI 2.49% (95% CrI 1.89, 3.23) and the lowest 0.12% (95% CrI 0.02, 0.43). The human RVFV seroprevalence was 8.2% (95% Confidence Interval 6.2, 10.9). Human seropositivity was strongly associated with the village-level FOI in livestock, with the odds of seropositivity in an individual person increasing by around 1.2 times (95% CrI 1.1, 1.3) for each additional annual RVFV seroconversion per 1,000 animals. A history of raw milk consumption was also positively associated with human seropositivity. RVFV has circulated at apparently low levels among livestock in northern Tanzania in the period since the last reported epidemic. Although our data do not allow us to confirm human RVFV infections during the IEP, a strong association between human seropositivity and the FOI in cattle, goats, and sheep supports the hypothesis that RVFV circulation among livestock during the IEP poses a risk for undetected zoonotic spillover in northern Tanzania. We provide further evidence for the likely role of raw milk consumption in RVFV transmission from animals to people.

Examination of the interaction between age-specific predation and chronic disease in the Greater Yellowstone Ecosystem

Predators may create healthier prey populations by selectively removing diseased individuals. Predators typically prefer some ages of prey over others, which may, or may not, align with those prey ages that are most likely to be diseased. The interaction of age-specific infection and predation has not been previously explored and likely has sizable effects on disease dynamics. We hypothesize that predator cleansing effects will be greater when the disease and predation occur in the same prey age groups. We examine the predator cleansing effect using a model where both vulnerability to predators and pathogen prevalence vary with age. We tailor this model to chronic wasting disease (CWD) in mule deer and elk populations in the Greater Yellowstone Ecosystem, with empirical data from Yellowstone grey wolves and cougars. Model results suggest that under moderate, yet realistic, predation pressure from cougars and wolves independently, predators may decrease CWD outbreak size substantially and delay the accumulation of symptomatic deer and elk. The magnitude of this effect is driven by the ability of predators to selectively remove late-stage CWD infections that are likely the most responsible for transmission, but this may not be the age class they typically select. Thus, predators that select for infected young adults over uninfected juveniles have a stronger cleansing effect, and these effects are strengthened when transmission rates increase with increasing prey morbidity. There are also trade-offs from a management perspective-that is, increasing predator kill rates can result in opposing forces on prey abundance and CWD prevalence. Our modelling exploration shows that predators have the potential to reduce prevalence in prey populations when prey age and disease severity are considered, yet the strength of this effect is influenced by predators' selection for demography or body condition. Current CWD management focuses on increasing cervid hunting as the primary management tool, and our results suggest predators may also be a useful tool under certain conditions, but not necessarily without additional impacts on host abundance and demography. Protected areas with predator populations will play a large role in informing the debate over predator impacts on disease.

Optimal immune specificity at the intersection of host life history and parasite epidemiology

Hosts diverge widely in how, and how well, they defend themselves against infection and immunopathology. Why are hosts so heterogeneous? Both epidemiology and life history are commonly hypothesized to influence host immune strategy, but the relationship between immune strategy and each factor has commonly been investigated in isolation. Here, we show that interactions between life history and epidemiology are crucial for determining optimal immune specificity and sensitivity. We propose a demographically-structured population dynamics model, in which we explore sensitivity and specificity of immune responses when epidemiological risks vary with age. We find that variation in life history traits associated with both reproduction and longevity alters optimal immune strategies-but the magnitude and sometimes even direction of these effects depends on how epidemiological risks vary across life. An especially compelling example that explains previously-puzzling empirical observations is that depending on whether infection risk declines or rises at reproductive maturity, later reproductive maturity can select for either greater or lower immune specificity, potentially illustrating why studies of lifespan and immune variation across taxa have been inconclusive. Thus, the sign of selection on the life history-immune specificity relationship can be reversed in different epidemiological contexts. Drawing on published life history data from a variety of chordate taxa, we generate testable predictions for this facet of the optimal immune strategy. Our results shed light on the causes of the heterogeneity found in immune defenses both within and among species and the ultimate variability of the relationship between life history and immune specificity.

Host adaptation to novel pathogen introduction: Predicting conditions that promote evolutionary rescue

Novel pathogen introduction can have drastic consequences for naive host populations, and outcomes can be difficult to predict. Evolutionary rescue (ER) provides a foundation for understanding whether hosts are driven to extinction or survive via adaptation. Currently, patterns of host population dynamics alongside evidence of adaptation are used to infer ER. However, the gap between established ER theory and complexity inherent in natural systems makes interpreting empirical patterns difficult because they can be confounded with ecological drivers of survival under current theory. To bridge this gap, we expand ER theory to include biological selective agents, such as pathogens. We find birth processes to be more important than previously theorised in determining ER potential. We employ a novel framework evaluating ER potential within natural systems and gain ability to identify system characteristics that make ER possible. Identifying these characteristics allows a shift from retrospective observation to a predictive mindset, and our findings suggest that ER occurrence may be more limited than previously thought. We use the plague system of Yersinia pestis infecting Cynomys ludovicianus (black-tailed prairie dogs) and Spermophilus beecheyi (California ground squirrels) as a case study.

Trematode parasites exceed aquatic insect biomass in Oregon stream food webs

Although parasites are increasingly recognized for their ecosystem roles, it is often assumed that free-living organisms dominate animal biomass in most ecosystems and therefore provide the primary pathways for energy transfer. To examine the contributions of parasites to ecosystem energetics in freshwater streams, we quantified the standing biomass of trematodes and free-living organisms at nine sites in three streams in western Oregon, USA. We then compared the rates of biomass flow from snails Juga plicifera into trematode parasites relative to aquatic vertebrate predators (sculpin, cutthroat trout and Pacific giant salamanders). The trematode parasite community had the fifth highest dry biomass density among stream organisms (0.40 g/m² ) and exceeded the combined biomass of aquatic insects. Only host snails (3.88 g/m² ), sculpin (1.11 g/m² ), trout (0.73 g/m² ) and crayfish (0.43 g/m² ) had a greater biomass. The parasite 'extended phenotype', consisting of trematode plus castrated host biomass, exceeded the individual biomass of every taxonomic group other than snails. The substantial parasite biomass stemmed from the high snail density and infection prevalence, and the large proportional mass of infected hosts that consisted of trematode tissue (M = 31% per snail). Estimates of yearly biomass transfer from snails into trematodes were slightly higher than the combined estimate of snail biomass transfer into the three vertebrate predators. Pacific giant salamanders accounted for 90% of the snail biomass consumed by predators. These results demonstrate that trematode parasites play underappreciated roles in the ecosystem energetics of some freshwater streams.

Estimating disease prevalence and temporal dynamics using biased capture serological data in a wildlife reservoir: The example of brucellosis in Alpine ibex (Capra ibex)

The monitoring of the disease prevalence in a population is an essential component of its adaptive management. However, field data often lead to biased estimates. This is the case for brucellosis infection of ibex in the Bargy massif (France). A test-and-cull program is being carried out in this area to manage the infection: captured animals are euthanized when seropositive, and marked and released when seronegative. Because this mountainous species is difficult to capture, field workers tend to focus the capture effort on unmarked animals. Indeed, marked animals are less likely to be infected, as they were controlled and negative during previous years. As the proportion of marked animals in the population becomes large, captured animals can no longer be considered as an unbiased sample of the population. We designed an integrated Bayesian model to correct this bias, by estimating the seroprevalence in the population as the combination of the separate estimates of the seroprevalence among unmarked animals (estimated from the data) and marked animals (estimated with a catalytic infection model, to circumvent the scarcity of the data). As seroprevalence may not be the most responsive parameter to management actions, we also estimated the proportion of animals in the population with an active bacterial infection. The actual infection status of captured animals was thus inferred as a function of their age and their level of antibodies, using a model based on bacterial cultures carried out for a sample of animals. Focusing on the population of adult females in the core area of the massif, i.e. with the highest seroprevalence, this observational study shows that seroprevalence has been divided by two between 2013 (51%) and 2018 (21%). Moreover, the likely estimated proportion of actively infected females in the same population, though very imprecise, has decreased from a likely estimate of 34% to less than 15%, suggesting that the management actions have been effective in reducing infection prevalence.

Identifying Age Cohorts Responsible for Peste Des Petits Ruminants Virus Transmission among Sheep, Goats, and Cattle in Northern Tanzania

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in global sheep and goat populations. To better control this disease and inform eradication strategies, an improved understanding of how PPRV transmission risk varies by age is needed. Our study used a piece-wise catalytic model to estimate the age-specific force of infection (FOI, per capita infection rate of susceptible hosts) among sheep, goats, and cattle from a cross-sectional serosurvey dataset collected in 2016 in Tanzania. Apparent seroprevalence increased with age, reaching 53.6%, 46.8%, and 11.6% (true seroprevalence: 52.7%, 52.8%, 39.2%) for sheep, goats, and cattle, respectively. Seroprevalence was significantly higher among pastoral animals than agropastoral animals across all ages, with pastoral sheep and goat seroprevalence approaching 70% and 80%, respectively, suggesting pastoral endemicity. The best fitting piece-wise catalytic models merged age groups: two for sheep, three for goats, and four for cattle. The signal of these age heterogeneities were weak, except for a significant FOI peak among 2.5-3.5-year-old pastoral cattle. The subtle age-specific heterogeneities identified in this study suggest that targeting control efforts by age may not be as effective as targeting by other risk factors, such as production system type. Further research should investigate how specific husbandry practices affect PPRV transmission.

Inferring seasonal infection risk at population and regional scales from serology samples

Accurate estimates of seasonal infection risk can be used by animal health officials to predict future disease risk and improve understanding of the mechanisms driving disease dynamics. It can be difficult to estimate seasonal infection risk in wildlife disease systems because surveillance assays typically target antibodies (serosurveillance), which are not necessarily indicative of current infection, and serosurveillance sampling is often opportunistic. Recently developed methods estimate past time of infection from serosurveillance data using quantitative serological assays that indicate the amount of antibodies in a serology sample. However, current methods do not account for common opportunistic and uneven sampling associated with serosurveillance data. We extended the framework of survival analysis to improve estimates of seasonal infection risk from serosurveillance data across population and regional scales. We found that accounting for the right-censored nature of quantitative serology samples greatly improved estimates of seasonal infection risk, even when sampling was uneven in time. Survival analysis can also be used to account for common challenges when estimating infection risk from serology data, such as biases induced by host demography and continually elevated antibodies following infection. The framework developed herein is widely applicable for estimating seasonal infection risk from serosurveillance data in humans, wildlife, and livestock.

Feline immunodeficiency virus in puma: Estimation of force of infection reveals insights into transmission

Determining parameters that govern pathogen transmission (such as the force of infection, FOI), and pathogen impacts on morbidity and mortality, is exceptionally challenging for wildlife. Vital parameters can vary, for example across host populations, between sexes and within an individual's lifetime.Feline immunodeficiency virus (FIV) is a lentivirus affecting domestic and wild cat species, forming species-specific viral-host associations. FIV infection is common in populations of puma (Puma concolor), yet uncertainty remains over transmission parameters and the significance of FIV infection for puma mortality. In this study, the age-specific FOI of FIV in pumas was estimated from prevalence data, and the evidence for disease-associated mortality was assessed.We fitted candidate models to FIV prevalence data and adopted a maximum likelihood method to estimate parameter values in each model. The models with the best fit were determined to infer the most likely FOI curves. We applied this strategy for female and male pumas from California, Colorado, and Florida.When splitting the data by sex and area, our FOI modeling revealed no evidence of disease-associated mortality in any population. Both sex and location were found to influence the FOI, which was generally higher for male pumas than for females. For female pumas at all sites, and male pumas from California and Colorado, the FOI did not vary with puma age, implying FIV transmission can happen throughout life; this result supports the idea that transmission can occur from mothers to cubs and also throughout adult life. For Florida males, the FOI was a decreasing function of puma age, indicating an increased risk of infection in the early years, and a decreased risk at older ages.This research provides critical insight into pathogen transmission and impact in a secretive and solitary carnivore. Our findings shed light on the debate on whether FIV causes mortality in wild felids like puma, and our approach may be adopted for other diseases and species. The methodology we present can be used for identifying likely transmission routes of a pathogen and also estimating any disease-associated mortality, both of which can be difficult to establish for wildlife diseases in particular.

Disentangling serology to elucidate henipa- and filovirus transmission in Madagascar fruit bats

Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa- and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat populations and (c) compare mechanistic hypotheses for possible transmission dynamics underlying these data. To this end, we amassed and analysed a unique dataset documenting longitudinal serological henipa- and filovirus dynamics in three Madagascar fruit bat species. We uncovered serological evidence of exposure to Hendra-/Nipah-related henipaviruses in Eidolon dupreanum, Pteropus rufus and Rousettus madagascariensis, to Cedar-related henipaviruses in E. dupreanum and R. madagascariensis and to Ebola-related filoviruses in P. rufus and R. madagascariensis. We demonstrated significant seasonality in population-level seroprevalence and individual serostatus for multiple viruses across these species, linked to the female reproductive calendar. An age-structured subset of the data highlighted evidence of waning maternal antibodies in neonates, increasing seroprevalence in young and decreasing seroprevalence late in life. Comparison of mechanistic epidemiological models fit to these data offered support for transmission hypotheses permitting waning antibodies but retained immunity in adult-age bats. Our findings suggest that bats may seasonally modulate mechanisms of pathogen control, with consequences for population-level transmission. Additionally, we narrow the field of candidate transmission hypotheses by which bats are presumed to host and transmit potentially zoonotic viruses globally.

Babesial infection in the Madagascan flying fox, Pteropus rufus É. Geoffroy, 1803

Background

Babesiae are erythrocytic protozoans, which infect the red blood cells of vertebrate hosts to cause disease. Previous studies have described potentially pathogenic infections of Babesia vesperuginis in insectivorous bats in Europe, the Americas and Asia. To date, no babesial infections have been documented in the bats of Madagascar, or in any frugivorous bat species worldwide.

Results

We used standard microscopy and conventional PCR to identify babesiae in blood from the endemic Madagascan flying fox (Pteropus rufus). Out of 203 P. rufus individuals captured between November 2013 and January 2016 and screened for erythrocytic parasites, nine adult males (4.43%) were infected with babesiae. Phylogenetic analysis of sequences obtained from positive samples indicates that they cluster in the Babesia microti clade, which typically infect felids, rodents, primates, and canids, but are distinct from B. vesperuginis previously described in bats. Statistical analysis of ecological trends in the data suggests that infections were most commonly observed in the rainy season and in older-age individuals. No pathological effects of infection on the host were documented; age-prevalence patterns indicated susceptible-infectious (SI) transmission dynamics characteristic of a non-immunizing persistent infection.

Conclusions

To our knowledge, this study is the first report of any erythrocytic protozoan infecting Madagascan fruit bats and the first record of a babesial infection in a pteropodid fruit bat globally. Given the extent to which fruit bats have been implicated as reservoirs for emerging human pathogens, any new record of their parasite repertoire and transmission dynamics offers notable insights into our understanding of the ecology of emerging pathogens.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3300-7) contains supplementary material, which is available to authorized users.

Evidence of multiple intraspecific transmission routes for Leptospira acquisition in Norway rats (Rattus norvegicus)

Infectious diseases frequently have multiple potential routes of intraspecific transmission of pathogens within wildlife and other populations. For pathogens causing zoonotic diseases, knowing whether these transmission routes occur in the wild and their relative importance, is critical for understanding maintenance, improving control measures and ultimately preventing human disease. The Norway rat (Rattus norvegicus) is the primary reservoir of leptospirosis in the urban slums of Salvador, Brazil. There is biological evidence for potentially three different transmission routes of leptospire infection occurring in the rodent population. Using newly obtained prevalence data from rodents trapped at an urban slum field site, we present changes in cumulative risk of infection in relation to age-dependent transmission routes to infer which intra-specific transmission routes occur in the wild. We found that a significant proportion of animals leave the nest with infection and that the risk of infection increases throughout the lifetime of Norway rats. We did not observe a significant effect of sexual maturity on the risk of infection. In conclusion, our results suggest that vertical and environmental transmission of leptospirosis both occur in wild populations of Norway rats.

Estimating Loss of Brucella Abortus Antibodies from Age-Specific Serological Data In Elk

Serological data are one of the primary sources of information for disease monitoring in wildlife. However, the duration of the seropositive status of exposed individuals is almost always unknown for many free-ranging host species. Directly estimating rates of antibody loss typically requires difficult longitudinal sampling of individuals following seroconversion. Instead, we propose a Bayesian statistical approach linking age and serological data to a mechanistic epidemiological model to infer brucellosis infection, the probability of antibody loss, and recovery rates of elk (Cervus canadensis) in the Greater Yellowstone Ecosystem. We found that seroprevalence declined above the age of ten, with no evidence of disease-induced mortality. The probability of antibody loss was estimated to be 0.70 per year after a five-year period of seropositivity and the basic reproduction number for brucellosis to 2.13. Our results suggest that individuals are unlikely to become re-infected because models with this mechanism were unable to reproduce a significant decline in seroprevalence in older individuals. This study highlights the possible implications of antibody loss, which could bias our estimation of critical epidemiological parameters for wildlife disease management based on serological data.

Elucidating transmission dynamics and host-parasite-vector relationships for rodent-borne Bartonella spp. in Madagascar

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At least five distinct species of Bartonella infect R. rattus rodents and their ectoparasites in Madagascar.

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Infection dynamics for zoonotic B. elizabethae are consistent with an SIS or SIR model in rodent hosts.

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Infection dynamics for non-zoonotic B. phoceensis & rattimassiliensis are consistent with an SI model in rodent hosts.

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Transmission of B. elizabethae and B. phoceensis & rattimassiliensis, respectiviely, are affected by S. fonquerniei & X. cheopsis fleas and Polyplax spp. lice.

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S. fonquerniei/X. cheopsis fleas may vector B. elizabethae and Polyplax spp. lice vector B. phoceensis/rattimassiliensis.

Bartonella spp. are erythrocytic bacteria transmitted via arthropod vectors, which infect a broad range of vertebrate hosts, including humans. We investigated transmission dynamics and host-parasite-vector relationships for potentially zoonotic Bartonella spp. in invasive Rattus rattus hosts and associated arthropod ectoparasites in Madagascar. We identified five distinct species of Bartonella (B. elizabethae 1, B. elizabethae 2, B. phoceensis 1, B. rattimassiliensis 1, and B. tribocorum 1) infecting R. rattus rodents and their ectoparasites. We fit standard epidemiological models to species-specific age-prevalence data for the four Bartonella spp. with sufficient data, thus quantifying age-structured force of infection. Known zoonotic agents, B. elizabethae 1 and 2, were best described by models exhibiting high forces of infection in early age class individuals and allowing for recovery from infection, while B. phoceensis 1 and B. rattimassiliensis 1 were best fit by models of lifelong infection without recovery and substantially lower forces of infection. Nested sequences of B. elizabethae 1 and 2 were recovered from rodent hosts and their Synopsyllus fonquerniei and Xenopsylla cheopsis fleas, with a particularly high prevalence in the outdoor-dwelling, highland-endemic S. fonquerniei. These findings expand on force of infection analyses to elucidate the ecological niche of the zoonotic Bartonella elizabethae complex in Madagascar, hinting at a potential vector role for S. fonquerniei. Our analyses underscore the uniqueness of such ecologies for Bartonella species, which pose a variable range of potential zoonotic threats.

Inferring infection hazard in wildlife populations by linking data across individual and population scales

Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease.

Reconstruction of Rift Valley fever transmission dynamics in Madagascar: estimation of force of infection from seroprevalence surveys using Bayesian modelling

The force of infection (FOI) is one of the key parameters describing the dynamics of transmission of vector-borne diseases. Following the occurrence of two major outbreaks of Rift Valley fever (RVF) in Madagascar in 1990-91 and 2008-09, recent studies suggest that the pattern of RVF virus (RVFV) transmission differed among the four main eco-regions (East, Highlands, North-West and South-West). Using Bayesian hierarchical models fitted to serological data from cattle of known age collected during two surveys (2008 and 2014), we estimated RVF FOI and described its variations over time and space in Madagascar. We show that the patterns of RVFV transmission strongly differed among the eco-regions. In the North-West and Highlands regions, these patterns were synchronous with a high intensity in mid-2007/mid-2008. In the East and South-West, the peaks of transmission were later, between mid-2008 and mid-2010. In the warm and humid northwestern eco-region favorable to mosquito populations, RVFV is probably transmitted all year-long at low-level during inter-epizootic period allowing its maintenance and being regularly introduced in the Highlands through ruminant trade. The RVF surveillance of animals of the northwestern region could be used as an early warning indicator of an increased risk of RVF outbreak in Madagascar.

Intensive Circulation of Japanese Encephalitis Virus in Peri-urban Sentinel Pigs near Phnom Penh, Cambodia

Despite the increased use of vaccination in several Asian countries, Japanese Encephalitis (JE) remains the most important cause of viral encephalitis in Asia in humans with an estimated 68,000 cases annually. Considered a rural disease occurring mainly in paddy-field dominated landscapes where pigs are amplifying hosts, JE may nevertheless circulate in a wider range of environment given the diversity of its potential hosts and vectors. The main objective of this study was to assess the intensity of JE transmission to pigs in a peri-urban environment in the outskirt of Phnom Penh, Cambodia. We estimated the force of JE infection in two cohorts of 15 sentinel pigs by fitting a generalised linear model on seroprevalence monitoring data observed during two four-month periods in 2014. Our results provide evidence for intensive circulation of JE virus in a periurban area near Phnom Penh, the capital and most populated city of Cambodia. Understanding JE virus transmission in different environments is important for planning JE virus control in the long term and is also an interesting model to study the complexity of vector-borne diseases. Collecting quantitative data such as the force of infection will help calibrate epidemiological model that can be used to better understand complex vector-borne disease epidemiological cycles.

Chronic wasting disease in white-tailed deer: infection, mortality, and implications for heterogeneous transmission

Chronic wasting disease (CWD) is a fatal neurodegenerative disease affecting free-ranging and captive cervids that now occurs in 24 U.S. states and two Canadian provinces. Despite the potential threat of CWD to deer populations, little is known about the rates of infection and mortality caused by this disease. We used epidemiological models to estimate the force of infection and disease-associated mortality for white-tailed deer in the Wisconsin and Illinois CWD outbreaks. Models were based on age-prevalence data corrected for bias in aging deer using the tooth wear and replacement method. Both male and female deer in the Illinois outbreak had higher corrected age-specific prevalence with slightly higher female infection than deer in the Wisconsin outbreak. Corrected ages produced more complex models with different infection and mortality parameters than those based on apparent prevalence. We found that adult male deer have a more than threefold higher risk of CWD infection than female deer. Males also had higher disease mortality than female deer. As a result, CWD prevalence was twofold higher in adult males than females. We also evaluated the potential impacts of alternative contact structures on transmission dynamics in Wisconsin deer. Results suggested that transmission of CWD among male deer during the nonbreeding season may be a potential mechanism for producing higher rates of infection and prevalence characteristically found in males. However, alternatives based on high environmental transmission and transmission from females to males during the breeding season may also play a role.

Pathogen exposure varies widely among sympatric populations of wild and domestic felids across the United States

Understanding how landscape, host, and pathogen traits contribute to disease exposure requires systematic evaluations of pathogens within and among host species and geographic regions. The relative importance of these attributes is critical for management of wildlife and mitigating domestic animal and human disease, particularly given rapid ecological changes, such as urbanization. We screened > 1000 samples from sympatric populations of puma (Puma concolor), bobcat (Lynx rufus), and domestic cat (Felis catus) across urban gradients in six sites, representing three regions, in North America for exposure to a representative suite of bacterial, protozoal, and viral pathogens (Bartonella sp., Toxoplasma gondii, feline herpesvirus-1, feline panleukopenea virus, feline calicivirus, and feline immunodeficiency virus). We evaluated prevalence within each species, and examined host trait and land cover determinants of exposure; providing an unprecedented analysis of factors relating to potential for infections in domesticated and wild felids. Prevalence differed among host species (highest for puma and lowest for domestic cat) and was greater for indirectly transmitted pathogens. Sex was inconsistently predictive of exposure to directly transmitted pathogens only, and age infrequently predictive of both direct and indirectly transmitted pathogens. Determinants of pathogen exposure were widely divergent between the wild felid species. For puma, suburban land use predicted increased exposure to Bartonella sp. in southern California, and FHV-1 exposure increased near urban edges in Florida. This may suggest interspecific transmission with domestic cats via flea vectors (California) and direct contact (Florida) around urban boundaries. Bobcats captured near urban areas had increased exposure to T. gondii in Florida, suggesting an urban source of prey Bobcats captured near urban areas in Colorado and Florida had higher FIV exposure, possibly suggesting increased intraspecific interactions through pile-up of home ranges. Beyond these regional and pathogen specific relationships, proximity to the wildland-urban interface did not generally increase the probability of disease exposure in wild or domestic felids, empha- sizing the importance of local ecological determinants. Indeed, pathogen exposure was often negatively associated with the wildland-urban interface for all felids. Our analyses suggest cross-species pathogen transmission events around this interface may be infrequent, but followed by self-sustaining propagation within the new host species. virus; puma (Puma concolor); Toxoplasma gondii; urbanization.

Interacting Effects of Newcastle Disease Transmission and Illegal Trade on a Wild Population of White-Winged Parakeets in Peru: A Modeling Approach

Illegal wildlife-pet trade can threaten wildlife populations directly from overharvest, but also indirectly as a pathway for introduction of infectious diseases. This study evaluated consequences of a hypothetical introduction of Newcastle disease (ND) into a wild population of Peru's most trafficked psittacine, the white-winged parakeet (Brotogeris versicolurus), through release of infected confiscated individuals. We developed two mathematical models that describe ND transmission and the influence of illegal harvest in a homogeneous (model 1) and age-structured population of parakeets (model 2). Infection transmission dynamics and harvest were consistent for all individuals in model 1, which rendered it mathematically more tractable compared to the more complex, age-structured model 2 that separated the host population into juveniles and adults. We evaluated the interaction of ND transmission and harvest through changes in the basic reproduction number (R0) and short-term host population dynamics. Our findings demonstrated that ND introduction would likely provoke considerable disease-related mortality, up to 24% population decline in two years, but high harvest rates would dampen the magnitude of the outbreak. Model 2 produced moderate differences in disease dynamics compared to model 1 (R0 = 3.63 and 2.66, respectively), but highlighted the importance of adult disease dynamics in diminishing the epidemic potential. Therefore, we suggest that future studies should use a more realistic, age-structured model. Finally, for the presumptive risk that illegal trade of white-winged parakeets could introduce ND into wild populations, our results suggest that while high harvest rates may have a protective effect on the population by reducing virus transmission, the combined effects of high harvest and disease-induced mortality may threaten population survival. These results capture the complexity and consequences of the interaction between ND transmission and harvest in a wild parrot population and highlight the importance of preventing illegal trade.

Unknown age in health disorders: A method to account for its cumulative effect and an application to feline viruses interactions

Parasite interactions have been widely evidenced experimentally but field studies remain rare. Such studies are essential to detect interactions of interest and access (co)infection probabilities but face methodological obstacles. Confounding factors can create statistical associations, i.e. false parasite interactions. Among them, host age is a crucial covariate. It influences host exposition and susceptibility to many infections, and has a mechanical effect, older individuals being more at risk because of a longer exposure time. However, age is difficult to estimate in natural populations. Hence, one should be able to deal at least with its cumulative effect. Using a SI type dynamic model, we showed that the cumulative effect of age can generate false interactions theoretically (deterministic modeling) and with a real dataset of feline viruses (stochastic modeling). The risk to wrongly conclude to an association was maximal when parasites induced long-lasting antibodies and had similar forces of infection. We then proposed a method to correct for this effect (and for other potentially confounding shared risk factors) and made it available in a new R package, Interatrix. We also applied the correction to the feline viruses. It offers a way to account for an often neglected confounding factor and should help identifying parasite interactions in the field, a necessary step towards a better understanding of their mechanisms and consequences.

Integrated survival analysis using an event-time approach in a Bayesian framework

Event-time or continuous-time statistical approaches have been applied throughout the biostatistical literature and have led to numerous scientific advances. However, these techniques have traditionally relied on knowing failure times. This has limited application of these analyses, particularly, within the ecological field where fates of marked animals may be unknown. To address these limitations, we developed an integrated approach within a Bayesian framework to estimate hazard rates in the face of unknown fates. We combine failure/survival times from individuals whose fates are known and times of which are interval-censored with information from those whose fates are unknown, and model the process of detecting animals with unknown fates. This provides the foundation for our integrated model and permits necessary parameter estimation. We provide the Bayesian model, its derivation, and use simulation techniques to investigate the properties and performance of our approach under several scenarios. Lastly, we apply our estimation technique using a piece-wise constant hazard function to investigate the effects of year, age, chick size and sex, sex of the tending adult, and nesting habitat on mortality hazard rates of the endangered mountain plover (Charadrius montanus) chicks. Traditional models were inappropriate for this analysis because fates of some individual chicks were unknown due to failed radio transmitters. Simulations revealed biases of posterior mean estimates were minimal (≤ 4.95%), and posterior distributions behaved as expected with RMSE of the estimates decreasing as sample sizes, detection probability, and survival increased. We determined mortality hazard rates for plover chicks were highest at <5 days old and were lower for chicks with larger birth weights and/or whose nest was within agricultural habitats. Based on its performance, our approach greatly expands the range of problems for which event-time analyses can be used by eliminating the need for having completely known fate data.

Revisiting Rayong: shifting seroprofiles of dengue in Thailand and their implications for transmission and control

Dengue virus has traditionally caused substantial morbidity and mortality among children less than 15 years of age in Southeast Asia. Over the last 2 decades, a significant increase in the mean age of cases has been reported, and a once pediatric disease now causes substantial burden among the adult population. An age-stratified serological study (n = 1,736) was conducted in 2010 among schoolchildren in the Mueang Rayong district of Thailand, where a similar study had been conducted in 1980/1981. Serotype-specific forces of infection (λ(t)) and basic reproductive numbers (R0) of dengue were estimated for the periods 1969-1980 and 1993-2010. Despite a significant increase in the age at exposure and a decrease in λ(t) from 0.038/year to 0.019/year, R0 changed only from 3.3 to 3.2. Significant heterogeneity was observed across subdistricts and schools, with R0 ranging between 1.7 and 6.8. These findings are consistent with the idea that the observed age shift might be a consequence of the demographic transition in Thailand. Changes in critical vaccination fractions, estimated by using R0, have not accompanied the increase in age at exposure. These results have implications for dengue control interventions because multiple countries in Southeast Asia are undergoing similar demographic transitions. It is likely that dengue will never again be a disease exclusively of children.

Ecological Approaches to Studying Zoonoses

Concern over emerging infectious diseases (EIDs) and a better understanding of their causes has resulted in increasing recognition of the linkages among human, animal, and ecosystem health. It is now well recognized that human activities can promote the emergence of infectious diseases through the large-scale modification of natural environments and inadvertent vectoring (e.g., international trade and travel). These perturbations can alter the ecological and evolutionary relationships among humans, wildlife, and the pathogens that move between them, resulting in disease emergence. In recent years, the rise in zoonotic EIDs has not only increased our awareness of the need for cross-sectoral collaborations, but has also highlighted the disconnect between current ecological theory and biological reality. As the One Health movement continues to gain steam, further integration of ecological approaches into the One Health framework will be required. We discuss the importance of ecological methods and theory to the study of zoonotic diseases by (i) discussing key ecological concepts and approaches, (ii) reviewing methods of studying wildlife diseases and their potential applications for zoonoses, and (iii) identifying future directions in the One Health movement.

Deciphering serology to understand the ecology of infectious diseases in wildlife

The ecology of infectious disease in wildlife has become a pivotal theme in animal and public health. Studies of infectious disease ecology rely on robust surveillance of pathogens in reservoir hosts, often based on serology, which is the detection of specific antibodies in the blood and is used to infer infection history. However, serological data can be inaccurate for inference to infection history for a variety of reasons. Two major aspects in any serological test can substantially impact results and interpretation of antibody prevalence data: cross-reactivity and cut-off thresholds used to discriminate positive and negative reactions. Given the ubiquitous use of serology as a tool for surveillance and epidemiological modeling of wildlife diseases, it is imperative to consider the strengths and limitations of serological test methodologies and interpretation of results, particularly when using data that may affect management and policy for the prevention and control of infectious diseases in wildlife. Greater consideration of population age structure and cohort representation, serological test suitability and standardized sample collection protocols can ensure that reliable data are obtained for downstream modeling applications to characterize, and evaluate interventions for, wildlife disease systems.

Emerging prion disease drives host selection in a wildlife population

Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.

Infection dynamics of endemic malaria in a wild bird population: parasite species-dependent drivers of spatial and temporal variation in transmission rates

1. Investigating the ecological context in which host-parasite interactions occur and the roles of biotic and abiotic factors in forcing infection dynamics is essential to understanding disease transmission, spread and maintenance. 2. Despite their prominence as model host-pathogen systems, the relative influence of environmental heterogeneity and host characteristics in influencing the infection dynamics of avian blood parasites has rarely been assessed in the wild, particularly at a within-population scale. 3. We used a novel multievent modelling framework (an extension of multistate mark-recapture modelling) that allows for uncertainty in disease state, to estimate transmission parameters and assess variation in the infection dynamics of avian malaria in a large, longitudinally sampled data set of breeding blue tits infected with two divergent species of Plasmodium parasites. 4. We found striking temporal and spatial heterogeneity in the disease incidence rate and the likelihood of recovery within this single population and demonstrate marked differences in the relative influence of environmental and host factors in forcing the infection dynamics of the two Plasmodium species. 5. Proximity to a permanent water source greatly influenced the transmission rates of P. circumflexum, but not of P. relictum, suggesting that these parasites are transmitted by different vectors. 6. Host characteristics (age/sex) were found to influence infection rates but not recovery rates, and their influence on infection rates was also dependent on parasite species: P. relictum infection rates varied with host age, whilst P. circumflexum infection rates varied with host sex. 7. Our analyses reveal that transmission of endemic avian malaria is a result of complex interactions between biotic and abiotic components that can operate on small spatial scales and demonstrate that knowledge of the drivers of spatial and temporal heterogeneity in disease transmission will be crucial for developing accurate epidemiological models and a thorough understanding of the evolutionary implications of pathogens.

Identifying the age cohort responsible for transmission in a natural outbreak of Bordetella bronchiseptica

Identifying the major routes of disease transmission and reservoirs of infection are needed to increase our understanding of disease dynamics and improve disease control. Despite this, transmission events are rarely observed directly. Here we had the unique opportunity to study natural transmission of Bordetella bronchiseptica--a directly transmitted respiratory pathogen with a wide mammalian host range, including sporadic infection of humans--within a commercial rabbitry to evaluate the relative effects of sex and age on the transmission dynamics therein. We did this by developing an a priori set of hypotheses outlining how natural B. bronchiseptica infections may be transmitted between rabbits. We discriminated between these hypotheses by using force-of-infection estimates coupled with random effects binomial regression analysis of B. bronchiseptica age-prevalence data from within our rabbit population. Force-of-infection analysis allowed us to quantify the apparent prevalence of B. bronchiseptica while correcting for age structure. To determine whether transmission is largely within social groups (in this case litter), or from an external group, we used random-effect binomial regression to evaluate the importance of social mixing in disease spread. Between these two approaches our results support young weanlings--as opposed to, for example, breeder or maternal cohorts--as the age cohort primarily responsible for B. bronchiseptica transmission. Thus age-prevalence data, which is relatively easy to gather in clinical or agricultural settings, can be used to evaluate contact patterns and infer the likely age-cohort responsible for transmission of directly transmitted infections. These insights shed light on the dynamics of disease spread and allow an assessment to be made of the best methods for effective long-term disease control.

Probable causes of increasing brucellosis in free-ranging elk of the Greater Yellowstone Ecosystem

While many wildlife species are threatened, some populations have recovered from previous overexploitation, and data linking these population increases with disease dynamics are limited. We present data suggesting that free-ranging elk (Cervus elaphus) are a maintenance host for Brucella abortus in new areas of the Greater Yellowstone Ecosystem (GYE). Brucellosis seroprevalence in free-ranging elk increased from 0-7% in 1991-1992 to 8-20% in 2006-2007 in four of six herd units around the GYE. These levels of brucellosis are comparable to some herd units where elk are artificially aggregated on supplemental feeding grounds. There are several possible mechanisms for this increase that we evaluated using statistical and population modeling approaches. Simulations of an age-structured population model suggest that the observed levels of seroprevalence are unlikely to be sustained by dispersal from supplemental feeding areas with relatively high seroprevalence or an older age structure. Increases in brucellosis seroprevalence and the total elk population size in areas with feeding grounds have not been statistically detectable. Meanwhile, the rate of seroprevalence increase outside the feeding grounds was related to the population size and density of each herd unit. Therefore, the data suggest that enhanced elk-to-elk transmission in free-ranging populations may be occurring due to larger winter elk aggregations. Elk populations inside and outside of the GYE that traditionally did not maintain brucellosis may now be at risk due to recent population increases. In particular, some neighboring populations of Montana elk were 5-9 times larger in 2007 than in the 1970s, with some aggregations comparable to the Wyoming feeding-ground populations. Addressing the unintended consequences of these increasing populations is complicated by limited hunter access to private lands, which places many ungulate populations out of administrative control. Agency-landowner hunting access partnerships and the protection of large predators are two management strategies that may be used to target high ungulate densities in private refuges and reduce the current and future burden of disease.

Impact and dynamics of disease in species threatened by the amphibian chytrid fungus, Batrachochytrium dendrobatidis

Estimating disease-associated mortality and transmission processes is difficult in free-ranging wildlife but important for understanding disease impacts and dynamics and for informing management decisions. In a capture-mark-recapture study, we used a PCR-based diagnostic test in combination with multistate models to provide the first estimates of disease-associated mortality and detection, infection, and recovery rates for frogs endemically infected with the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the pandemic amphibian disease chytridiomycosis. We found that endemic chytridiomycosis was associated with a substantial reduction (approximately 38%) in apparent monthly survival of the threatened rainforest treefrog Litoria pearsoniana despite a long period of coexistence (approximately 30 years); detection rate was not influenced by disease status; improved recovery and reduced infection rates correlated with decreased prevalence, which occurred when temperatures increased; and incorporating changes in individuals' infection status through time with multistate models increased effect size and support (98.6% vs. 71% of total support) for the presence of disease-associated mortality when compared with a Cormack-Jolly-Seber model in which infection status was restricted to the time of first capture. Our results indicate that amphibian populations can face significant ongoing pressure from chytridiomycosis long after epidemics associated with initial Bd invasions subside, an important consideration for the long-term conservation of many amphibian species worldwide. Our findings also improve confidence in estimates of disease prevalence in wild amphibians and provide a general framework for estimating parameters in epidemiological models for chytridiomycosis, an important step toward better understanding and management of this disease.

Spatial and temporal patterns of chronic wasting disease: fine-scale mapping of a wildlife epidemic in Wisconsin

Emerging infectious diseases threaten wildlife populations and human health. Understanding the spatial distributions of these new diseases is important for disease management and policy makers; however, the data are complicated by heterogeneities across host classes, sampling variance, sampling biases, and the space-time epidemic process. Ignoring these issues can lead to false conclusions or obscure important patterns in the data, such as spatial variation in disease prevalence. Here, we applied hierarchical Bayesian disease mapping methods to account for risk factors and to estimate spatial and temporal patterns of infection by chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus) of Wisconsin, U.S.A. We found significant heterogeneities for infection due to age, sex, and spatial location. Infection probability increased with age for all young deer, increased with age faster for young males, and then declined for some older animals, as expected from disease-associated mortality and age-related changes in infection risk. We found that disease prevalence was clustered in a central location, as expected under a simple spatial epidemic process where disease prevalence should increase with time and expand spatially. However, we could not detect any consistent temporal or spatiotemporal trends in CWD prevalence. Estimates of the temporal trend indicated that prevalence may have decreased or increased with nearly equal posterior probability, and the model without temporal or spatiotemporal effects was nearly equivalent to models with these effects based on deviance information criteria. For maximum interpretability of the role of location as a disease risk factor, we used the technique of direct standardization for prevalence mapping, which we develop and describe. These mapping results allow disease management actions to be employed with reference to the estimated spatial distribution of the disease and to those host classes most at risk. Future wildlife epidemiology studies should employ hierarchical Bayesian methods to smooth estimated quantities across space and time, account for heterogeneities, and then report disease rates based on an appropriate standardization.

Upper respiratory tract disease, force of infection, and effects on survival of gopher tortoises

Upper respiratory tract disease (URTD) caused by Mycoplasma agassizii has been hypothesized to contribute to the decline of some wild populations of gopher tortoises (Gopherus polyphemus). However, the force of infection (FOI) and the effect of URTD on survival in free-ranging tortoise populations remain unknown. Using four years (2003-2006) of mark-recapture and epidemiological data collected from 10 populations of gopher tortoises in central Florida, USA, we estimated the FOI (probability per year of a susceptible tortoise becoming infected) and the effect of URTD (i.e., seropositivity to M. agassizii) on apparent survival rates. Sites with high (> or = 25%) seroprevalence had substantially higher FOI (0.22 +/- 0.03; mean +/- SE) than low (< 25%) seroprevalence sites (0.04 +/- 0.01). Our results provide the first quantitative evidence that the rate of transmission of M. agassizii is directly related to the seroprevalence of the population. Seropositive tortoises had higher apparent survival (0.99 +/- 0.0001) than seronegatives (0.88 +/- 0.03), possibly because seropositive tortoises represent individuals that survived the initial infection, developed chronic disease, and experienced lower mortality during the four-year span of our study. However, two lines of evidence suggested possible effects of mycoplasmal URTD on tortoise survival. First, one plausible model suggested that susceptible (seronegative) tortoises in high seroprevalence sites had lower apparent survival rates than did susceptible tortoises in low seroprevalence sites, indicating a possible acute effect of infection. Second, the number of dead tortoise remains detected during annual site surveys increased significantly with increasing site seroprevalence, from approximately 1 to approximately 5 shell remains per 100 individuals. If (as our results suggest) URTD in fact reduces adult survival, it could adversely influence the population dynamics and persistence of this late- maturing, long-lived species.

Chronic wasting disease in a Wisconsin white-tailed deer farm

In September 2002, chronic wasting disease (CWD), a prion disorder of captive and wild cervids, was diagnosed in a white-tailed deer (Odocoileus virginianus) from a captive farm in Wisconsin. The facility was subsequently quarantined, and in January 2006 the remaining 76 deer were depopulated. Sixty animals (79%) were found to be positive by immunohistochemical staining for the abnormal prion protein (PrP(CWD)) in at least one tissue; the prevalence of positive staining was high even in young deer. Although none of the deer displayed clinical signs suggestive of CWD at depopulation, 49 deer had considerable accumulation of the abnormal prion in the medulla at the level of the obex. Extraneural accumulation of the abnormal protein was observed in 59 deer, with accumulation in the retropharyngeal lymph node in 58 of 59 (98%), in the tonsil in 56 of 59 (95%), and in the rectal mucosal lymphoid tissue in 48 of 58 (83%). The retina was positive in 4 deer, all with marked accumulation of prion in the obex. One deer was considered positive for PrP(CWD) in the brain but not in the extraneural tissue, a novel observation in white-tailed deer. The infection rate in captive deer was 20-fold higher than in wild deer. Although weakly related to infection rates in extraneural tissues, prion genotype was strongly linked to progression of prion accumulation in the obex. Antemortem testing by biopsy of recto-anal mucosal-associated lymphoid tissue (or other peripheral lymphoid tissue) may be a useful adjunct to tonsil biopsy for surveillance in captive herds at risk for CWD infection.

Mycobacteriosis-associated mortality in wild striped bass (Morone saxatilis) from Chesapeake Bay, U.S.A

The striped bass (Morone saxatilis) is an economically and ecologically important finfish species along the Atlantic seaboard of the United States. Recent stock assessments in Chesapeake Bay (U.S.A.) indicate that non-fishing mortality in striped bass has increased since 1999, concomitant with very high (>50%) prevalence of visceral and dermal disease caused by Mycobacterium spp. Current fishery assessment models do not differentiate between disease and other components of non-fishing mortality (e.g., senescence, predation); therefore, disease impact on the striped bass population has not been established. Specific measurement of mortality associated with mycobacteriosis in wild striped bass is complicated because the disease is chronic and mortality is cryptic. Epidemiological models have been developed to estimate disease-associated mortality from cross-sectional prevalence data and have recently been generalized to represent disease processes more realistically. Here, we used this generalized approach to demonstrate disease-associated mortality in striped bass from Chesapeake Bay. To our knowledge this is the first demonstration of cryptic mortality associated with a chronic infectious disease in a wild finfish. This finding has direct implications for management and stock assessment of striped bass, as it demonstrates population-level negative impacts of a chronic disease. Additionally, this research provides a framework by which disease-associated mortality may be specifically addressed within fisheries models for resource management.

West Nile virus and greater sage-grouse: estimating infection rate in a wild bird population

Understanding impacts of disease on wild bird populations requires knowing not only mortality rate following infection, but also the proportion of the population that is infected. Greater sage-grouse (Centrocercus urophasianus) in western North America are known to have a high mortality rate following infection with West Nile virus (WNv), but actual infection rates in wild populations remain unknown. We used rates of WNv-related mortality and seroprevalence from radiomarked females to estimate infection rates in a wild greater sage-grouse population in the Powder River basin (PRB) of Montana and Wyoming from 2003 to 2005. Minimum WNv-related mortality rates ranged from 2.4% to 13.3% among years and maximum possible rates ranged from 8.2% to 28.9%. All live-captured birds in 2003 and 2004 tested seronegative. In spring 2005 and spring 2006, 10.3% and 1.8% respectively, of newly captured females tested seropositive for neutralizing antibodies to WNv. These are the first documented cases of sage-grouse surviving infection with WNv. Low to moderate WNv-related mortality in summer followed by low seroprevalence the following spring in all years indicates that annual infection rates were between 4% and 29%. This suggests that most sage-grouse in the PRB have not yet been exposed and remain susceptible. Impacts of WNv in the PRB in the near future will likely depend more on annual variation in temperature and changes in vector distribution than on the spread of resistance. Until the epizootiology of WNv in sagebrush-steppe ecosystems is better understood, we suggest that management to reduce impacts of WNv focus on eliminating man-made water sources that support breeding mosquitoes known to vector the virus. Our findings also underscore problems with using seroprevalence as a surrogate for infection rate and for identifying competent hosts in highly susceptible species.

Adjusting age and stage distributions for misclassification errors

Ecologists often use samples from the age or stage structure of a population to make inferences about population-level processes and to parameterize matrix models. Typically, researchers make a simplifying assumption that age and stage classes are determined without error, when in fact some level of misclassification often can be expected. If unaccounted for, misclassification will lead to overly optimistic levels of precision and can cause biased estimates of age or stage structure. Although several studies have used information from known-age individuals to quantify errors in age or stage distribution, the problem of estimating the age or stage structure in face of such errors has received comparably little attention. In this paper, we describe a general statistical framework for estimating the true stage distribution of a sample when misclassification rates can be estimated. The estimation process requires auxiliary information on misclassification rates, such as data from individuals of known age. We analyze age-structured harvest records from black bears in Pennsylvania to illustrate how incorporating misclassification errors leads to changes in point estimates and provides a measure of precision.