Parameter inference for an individual based model of chytridiomycosis in frogs

Individual based models (IBMs) and Agent based models (ABMs) have become widely used tools to understand complex biological systems. However, general methods of parameter inference for IBMs are not available. In this paper we show that it is possible to address this problem with a traditional likelihood-based approach, using an example of an IBM developed to describe the spread of chytridiomycosis in a population of frogs as a case study. We show that if the IBM satisfies certain criteria we can find the likelihood (or posterior) analytically, and use standard computational techniques, such as MCMC, for parameter inference.

Impact of the experimental removal of lizards on Lyme disease risk

The distribution of vector meals in the host community is an important element of understanding and predicting vector-borne disease risk. Lizards (such as the western fence lizard; Sceloporus occidentalis) play a unique role in Lyme disease ecology in the far-western United States. Lizards rather than mammals serve as the blood meal hosts for a large fraction of larval and nymphal western black-legged ticks (Ixodes pacificus--the vector for Lyme disease in that region) but are not competent reservoirs for the pathogen, Borrelia burgdorferi. Prior studies have suggested that the net effect of lizards is to reduce risk of human exposure to Lyme disease, a hypothesis that we tested experimentally. Following experimental removal of lizards, we documented incomplete host switching by larval ticks (5.19%) from lizards to other hosts. Larval tick burdens increased on woodrats, a competent reservoir, but not on deer mice, a less competent pathogen reservoir. However, most larvae failed to find an alternate host. This resulted in significantly lower densities of nymphal ticks the following year. Unexpectedly, the removal of reservoir-incompetent lizards did not cause an increase in nymphal tick infection prevalence. The net result of lizard removal was a decrease in the density of infected nymphal ticks, and therefore a decreased risk to humans of Lyme disease. Our results indicate that an incompetent reservoir for a pathogen may, in fact, increase disease risk through the maintenance of higher vector density and therefore, higher density of infected vectors.

Influence of abiotic and environmental factors on the density and infection prevalence of Ixodes pacificus (Acari:Ixodidae) with Borrelia burgdorferi

The abiotic and biotic factors that govern the spatial distribution of Lyme disease vectors are poorly understood. This study addressed the influence of abiotic and biotic environmental variables on Ixodes pacificus Cooley & Kohls (Acari:Ixodidae) nymphs, because it is the primary vector of Borrelia burgdorferi Johnson, Schmidt, Hyde, Steigerwaldt & Brenner in the far-western United States. Three metrics of Lyme disease risk were evaluated: the density of nymphs, the density of infected nymphs, and the nymphal infection prevalence. This study sampled randomly located plots in oak (Quercus spp.) woodland habitat in Sonoma County, CA. Each plot was drag-sampled for nymphal ticks and tested for B. burgdorferi infection. Path analysis was used to evaluate the direct and indirect relationship between topographic, forest structure and microclimatic variables on ticks. Significant negative correlations were found between maximum temperature in the dry season and the density of infected ticks in 2006 and tick density in 2007, but we did not find a significant relationship with nymphal infection prevalence in either year. Tick density and infected tick density had an indirect, positive correlation with elevation, mediated through temperature. This study found that in certain years but not others, temperature maxima in the dry season may constrain the density and density of infected I. pacificus nymphs. In other years, biotic or stochastic factors may play a more important role in determining tick density.

Effects of an invasive forest pathogen on abundance of ticks and their vertebrate hosts in a California Lyme disease focus

Invasive species, including pathogens, can have important effects on local ecosystems, including indirect consequences on native species. This study focuses on the effects of an invasive plant pathogen on a vertebrate community and Ixodes pacificus, the vector of the Lyme disease pathogen (Borrelia burgdorferi) in California. Phytophthora ramorum, the causative agent of sudden oak death, is a non-native pathogen killing trees in California and Oregon. We conducted a multi-year study using a gradient of SOD-caused disturbance to assess the impact on the dusky-footed woodrat (Neotoma fuscipes) and the deer mouse (Peromyscus maniculatus), two reservoir hosts of B. burgdorferi, as well as the impact on the Columbian black-tailed deer (Odocoileus hemionus columbianus) and the western fence lizard (Sceloporus occidentalis), both of which are important hosts for I. pacificus but are not pathogen reservoirs. Abundances of P. maniculatus and S. occidentalis were positively correlated with greater SOD disturbance, whereas N. fuscipes abundance was negatively correlated. We did not find a change in space use by O. hemionus. Our data show that SOD has a positive impact on the density of nymphal ticks, which is expected to increase the risk of human exposure to Lyme disease all else being equal. A positive correlation between SOD disturbance and the density of nymphal ticks was expected given increased abundances of two important hosts: deer mice and western fence lizards. However, further research is needed to integrate the direct effects of SOD on ticks, for example via altered abiotic conditions with host-mediated indirect effects.

Life-history trade-offs influence disease in changing climates: strategies of an amphibian pathogen

Life-history trade-offs allow many animals to maintain reproductive fitness across a range of climatic conditions. When used by parasites and pathogens, these strategies may influence patterns of disease in changing climates. The chytrid fungus, Batrachochytrium dendrobatidis, is linked to global declines of amphibian populations. Short-term growth in culture is maximal at 17 degrees-25 degrees C. This has been used in an argument that global warming, which increases the time that amphibians spend at these temperatures in cloud-covered montane environments, has led to extinctions. Here we show that the amphibian chytrid responds to decreasing temperatures with trade-offs that increase fecundity as maturation rate slows and increase infectivity as growth decreases. At 17 degrees-25 degrees C, infectious zoospores encyst (settle and develop a cell wall) and develop into the zoospore-producing stage (zoosporangium) faster, while at 7 degrees-10 degrees C, greater numbers of zoospores are produced per zoosporangium; these remain infectious for a longer period of time. We modeled the population growth of B. dendrobatidis through time at various temperatures using delayed differential equations and observational data for four parameters: developmental rate of thalli, fecundity, rate of zoospore encystment, and rate of zoospore survival. From the models, it is clear that life-history trade-offs allow B. dendrobatidis to maintain a relatively high long-term growth rate at low temperatures, so that it maintains high fitness across a range of temperatures. When a seven-day cold shock is simulated, the outcome is intermediate between the two constant temperature regimes, and in culture, a sudden drop in temperature induces zoospore release. These trade-offs can be ecologically important for a variety of organisms with complex life histories, including pathogenic microorganisms. The effect of temperature on amphibian mortality will depend on the interaction between fungal growth and host immune function and will be modified by host ecology, behavior, and life history. These results demonstrate that B. dendrobatidis populations can grow at high rates across a broad range of environmental temperatures and help to explain why it is so successful in cold montane environments.

Spatial dynamics of lyme disease: a review

Lyme disease (LD), the most frequently reported vector-borne disease in the United States, requires that humans, infected vector ticks, and infected hosts all occur in close spatial proximity. Understanding the spatial dynamics of LD requires an understanding of the spatial determinants of each of these organisms. We review the literature on spatial patterns and environmental correlates of human cases of LD and the vector ticks, Ixodes scapularis in the northeastern and midwestern United States and Ixodes pacificus in the western United States. The results of this review highlight a need for a more standardized and comprehensive approach to studying the spatial dynamics of the LD system. Specifically, we found that the only environmental variable consistently associated with increased LD risk and incidence was the presence of forests. However, the reasons why some forests are associated with higher risk and incidence than others are still poorly understood. We suspect that the discordance among studies is due, in part, to the rapid developments in both conceptual and technological aspects of spatial ecology hastening the obsolescence of earlier approaches. Significant progress in identifying the determinants of spatial variation in LD risk and incidence requires that: (1) existing knowledge of the biology of the individual components of each LD system is utilized in the development of spatial models; (2) spatial data are collected over longer periods of time; (3) data collection and analysis among regions are more standardized; and (4) the effect of the same environmental variables is tested at multiple spatial scales.

Predators, parasitoids, and pathogens: a cross-cutting examination of intraguild predation theory

Although the canonical concept of intraguild predation evokes images of predators and prey, several subdisciplines within ecology have developed theory not specifically framed in terms of predation and competition and often using system-specific terminology, yet functionally quite similar. Here, we formulate models combining exploitation and competition in predator-prey, host-parasitoid, and host-pathogen communities to compare dynamics, food web structure, and coexistence criteria for these disparate communities. Although dynamic stability in the coexistence region varies strongly among systems, in all cases coexistence of two consumers on a single resource occurs only if the intraguild prey species is more efficient than the intraguild predator at suppressing the abundance of the basal resource, and if the intraguild predator accrues a sufficient gain from attacking the intraguild prey. In addition, equilibrial abundances of all species in all three formulations respond similarly to increases in productivity of the basal resource. Our understanding of predator-prey and parasitoid-host communities has benefited from explicit examination of intraguild predation (IGP) theory, and we suggest that future research examining pathogen communities, in particular, will benefit substantially from explicit recognition of predictions from IGP theory.

Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis

Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geography, local frog extirpation by a single fungal genotype, and evidence of human-assisted fungus migration. In support of endemism, at a local scale, we find some diverse, recombining populations. Therefore neither epidemic spread nor endemism alone explains this particular amphibian decline. Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen.

Multiple sources of isotopic variation in a terrestrial arthropod community: challenges for disentangling food webs

Documenting trophic links in a food web has traditionally required complex exclusion experiments coupled with extraordinarily labor-intensive direct observations of predator foraging. Newer techniques such as stable isotope analysis (SIA) may facilitate relatively quick and accurate assessments of consumer feeding behavior. Ratios of N and C isotopes are thought to be useful for determining species' trophic position (e.g., 1 degrees consumer, 2 degrees consumer, or omnivore) and their original carbon source (e.g., C3 or C4 plants; terrestrial or marine nutrients). Thus far, however, applications of stable isotopes to terrestrial arthropod food webs have suggested that high taxon-specific variation may undermine the effectiveness of this method. We applied stable isotope analysis to a pear orchard food web, in which biological control of a dominant pest, pear psylla (Cacopsylla pyricola), involves primarily generalist arthropod predators with a high frequency of omnivory. We found multiple sources of isotopic variation in this food web, including differences among plant tissues; time, stage, and taxon-specific differences among herbivores (despite similar feeding modes); and high taxon-specific variation among predators (with no clear evidence of omnivory). Collectively, these multiple sources of isotopic variation blur our view of the structure of this food web. Idiosyncrasies in consumer trophic shifts make ad hoc application of SIA to even moderately complex food webs intractable. SIA may not be a generally applicable "quick and dirty" method for delineating terrestrial food web structure-not without calibration of specific consumer food trophic shifts.

Quantifying the disease transmission function: effects of density on Batrachochytrium dendrobatidis transmission in the mountain yellow-legged frog Rana muscosa

1. Chytridiomycosis is an emerging infectious disease of amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis, which has been implicated recently in population declines and possible extinctions throughout the world. 2. The transmission rate of this pathogen was quantified in the mountain yellow-legged frog Rana muscosa through laboratory and field experiments, and a maximum likelihood approach was used to determine the form of the transmission function that was best supported by the experimental data. 3. The proportion of R. muscosa tadpole hosts that became infected increased with the number of previously infected R. muscosa tadpoles to which they were exposed, as would be expected in an infectious disease. 4. The laboratory experiment revealed some support for a transmission function in which the transmission rate levels off as the density of infected individuals increases. However, there was not enough power to distinguish between a frequency-dependent form and several other asymptotic forms of the transmission function. 5. The impacts of crowding and temperature on transmission were also investigated; however, neither of these factors significantly affected the transmission rate.

Effect of microenvironment on development of a gall midge

This study assessed the influence of microenvironment on the establishment and relative reproductive success of the gall-forming midge Rhopalomyia californica Felt on its host plant Baccharis pilularis De Candolle in Marin County, CA. Mesh cages were used to alter the microenvironment, which also allowed us to assess the validity of using these types of experimental manipulations in this system. Temperature, light intensity, wind speed, and stem growth were compared in caged and uncaged B. pilularis plots in two sites during three seasons. Cage presence significantly altered the microenvironment of R. californica but did not affect development. R. californica establishment was greater when growing on host plants with increased stem growth. Season had the largest impact on gall establishment and reproductive success, with the highest establishment and success rates in late winter to early spring, which correlated with the growing period of B. pilularis. These results suggest that the seasonality of R. californica reproductive success is linked to the phenology of its host plant. When the growing conditions for the plant are less than ideal, R. californica performance is stimulated by increased stem growth. Cage presence was not a significant driver of population dynamics because it did not change the environment in an ecologically meaningful way. We therefore assert that the use of cages for experimental manipulations in this study system does not alter R. californica performance.

Emerging infectious disease as a proximate cause of amphibian mass mortality

A newly discovered infectious disease of amphibians, chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis, is implicated in population declines and possible extinctions throughout the world. The purpose of our study was to examine the effects of B. dendrobatidis on the mountain yellow-legged frog (Rana muscosa) in the Sierra Nevada of California (USA). We (1) quantified the prevalence and incidence of B. dendrobatidis through repeat surveys of several hundred R. muscosa populations in the southern Sierra Nevada; (2) described the population-level effects of B. dendrobatidis on R. muscosa population abundance; and (3) compared the mortality rates of infected and uninfected R. muscosa individuals from pre- through post-metamorphosis using both laboratory and field experiments. Mouthpart inspections conducted in 144 and 132 R. muscosa populations in 2003 and 2004, respectively, indicated that 19% of R. muscosa populations in both years showed indications of chytridiomycosis. Sixteen percent of populations that were uninfected in 2003 became infected by 2004. Rana muscosa population sizes were reduced by an average of 88% following B. dendrobatidis outbreaks at six sites, but at seven B. dendrobatidis-negative sites, R. muscosa population sizes increased by an average of 45% over the same time period. In the laboratory, all infected R. muscosa developed fatal chytridiomycosis after metamorphosis, while all uninfected individuals remained healthy. In the field experiment in which R. muscosa tadpoles were caged at infected and uninfected sites, 96% of the individuals that metamorphosed at infected sites died vs. 5% at the uninfected sites. These studies indicate that chytridiomycosis causes high mortality in post-metamorphic R. muscosa, that this emerging disease is the proximate cause of numerous observed R. muscosa population declines, and that the disease threatens this species with extirpation at numerous sites in California's Sierra Nevada.

Strategies for integrating primary health services in middle- and low-income countries at the point of delivery

BACKGROUND

Strategies to integrate primary health care aim to bring together inputs, organisation, management and delivery of particular service functions to make them more efficient, and accessible to the service user. In some middle and low income countries, services have been fragmented by separate vertical programmes established to ensure delivery of particular technologies. We examined the effectiveness of integration strategies at the point of delivery.

OBJECTIVES

To assess the effects of strategies to integrate primary health care services on producing a more coherent product and improving health care delivery and health status.

SEARCH STRATEGY

We searched the Cochrane Effective Practice and Organisation of Care Group specialised register (August 2005), MEDLINE (1966 to September 2005), EMBASE (1988 to 2005), Socio Files (1974 to September 2005), Popline (1970 to September 2005), HealthStar (1975 to September 2005), Cinahl (1982 to September 2005); Cab Health (1972 to 1999), International Bibliography of the Social Sciences (1970 to 1999), and reference lists of articles. We also searched the Internet and World Health Organization (WHO) library database, hand searched relevant WHO publications and contacted experts in the field.

SELECTION CRITERIA

Randomised trials, controlled before and after studies, and interrupted time series analyses of integration strategies in primary health care services. Health services in high-income countries were excluded. The primary outcomes were indicators of health care delivery, user views on any measure of service coherence, and health status. We also sought information on comparative costs.

DATA COLLECTION AND ANALYSIS

Two authors independently extracted data and assessed study quality.

MAIN RESULTS

Three cluster randomised trials and two controlled before and after studies were included, with three types of comparison: integration by adding on an additional component to an existing service (family planning); integrated services versus single special services (for sex workers); integrated delivery systems versus a vertical service (for family planning); and packages of enhanced primary child care services (integrated management of childhood illnesses) vs. routine child care. Interventions were complex and in some studies inputs varied substantially between comparison arms. Overall, no consistent pattern emerged. Only one study attempted to assess the user's view of the service provided.

AUTHORS' CONCLUSIONS

Few studies of good quality, large and with rigorous study design have been carried out to investigate strategies to promote service integration in low and middle income countries. All describe the service supply side, and none examine or measure aspects of the demand side. Future studies must also assess the client's view, as this will influence uptake of integration strategies and their effectiveness on community health.

Antimicrobial peptide defenses of the mountain yellow-legged frog (Rana muscosa)

The mountain yellow-legged frog (Rana muscosa) inhabits high elevation lakes in California that are largely undisturbed by human activities. In spite of this habitation in remote sites, populations continue to decline. Although predation by non-native fish is one cause for declines, some isolated populations in fishless lakes are suffering new declines. One possible cause of the current wave of declines is the introduction of the pathogenic chytrid fungus (Batrachochytrium dendrobatidis) which invades the adult skin to cause chytridiomycosis. In many amphibian species, the skin is protected by antimicrobial peptides secreted into the mucous. Here we show that R. muscosa produces three previously unknown antimicrobial peptides belonging to the ranatuerin-2 and temporin-1 families of antimicrobial peptides. These three peptides, along with bradykinin, are the most abundant peptides in the skin secretions detected by mass spectrometry. Natural mixtures of peptides and individual purified peptides strongly inhibit chytrid growth. The concentration of total peptides recovered from the skin of frogs following a mild norepinephrine induction is sufficient to inhibit chytrid growth in vitro. A comparison of the species susceptibility to chytridiomycosis and the antichytrid activity of peptides between R. muscosa and R. pipiens suggest that although R. muscosa produces more total skin peptides, it appears to be more vulnerable to B. dendrobatidis in nature. Possible differences in the antimicrobial peptide repertoires and life history traits of the two species that may account for differences in susceptibility are discussed.

Host suppression and stability in a parasitoid-host system: experimental demonstration

We elucidate the mechanisms causing stability and severe resource suppression in a consumer-resource system. The consumer, the parasitoid Aphytis, rapidly controlled an experimentally induced outbreak of the resource, California red scale, an agricultural pest, and imposed a low, stable pest equilibrium. The results are well predicted by a mechanistic, independently parameterized model. The key mechanisms are widespread in nature: an invulnerable adult stage in the resource population and rapid consumer development. Stability in this biologically nondiverse agricultural system is a property of the local interaction between these two species, not of spatial processes or of the larger ecological community.

Should we expect population thresholds for wildlife disease?

Host population thresholds for the invasion or persistence of infectious disease are core concepts of disease ecology and underlie disease control policies based on culling and vaccination. However, empirical evidence for these thresholds in wildlife populations has been sparse, although recent studies have begun to address this gap. Here, we review the theoretical bases and empirical evidence for disease thresholds in wildlife. We see that, by their nature, these thresholds are rarely abrupt and always difficult to measure, and important facets of wildlife ecology are neglected by current theories. Empirical studies seeking to identify disease thresholds in wildlife encounter recurring obstacles of small sample sizes and confounding factors. Disease control policies based solely on threshold targets are rarely warranted, but management to reduce abundance of susceptible hosts can be effective.

Stabilizing effects in spatial parasitoid-host and predator-prey models: a review

We review the literature on spatial host-parasitoid and predator-prey models. Dispersal on its own is not stabilizing and can destabilize a stable local equilibrium. We identify three mechanisms whereby limited dispersal of hosts and parasitoids combined with other features, such as spatial and temporal heterogeneity, can promote increased persistence and stability. The first mechanisms, "statistical stabilization", is simply the statistical effect that summing a number of out-of-phase population trajectories results in a relatively constant total population density. The second mechanism involves decoupling of immigration from local density, such that limited dispersal between asynchronous patches results in an effect that mimics density-dependence at the local patch level. The third mechanism involves altering spatially averaged parameter values resulting from spatial heterogeneity in density combined with non-linear responses to density. Persistence in spatially explicit models with local dispersal frequently associated with self-organized spatial patterning.