Detecting parasite associations within multi-species host and parasite communities

Molecular uncovering of important helminth species in wild ruminants in the Czech Republic

Monitoring gastrointestinal helminth infections in wild ruminants poses significant challenges for managing wildlife health, particularly regarding invasive species. Traditional coprological methods are often limited by their labor-intensive nature and potential for erroneous identification due to morphological similarities among parasite species. This study employed advanced molecular techniques to assess the prevalence and distribution of several helminth taxa, including the invasive nematode Ashworthius sidemi and the trematode Fascioloides magna, in wild ruminant populations in the Czech Republic (CR). A comprehensive and extensive survey on parasite occurrence, unique in its nationwide scope, was conducted on 983 fecal samples collected from red deer (Cervus elaphus), roe deer (Capreolus capreolus), fallow deer (Dama dama), and mouflon (Ovis musimon) across various regions of the CR. The samples were analyzed using multiplex real-time PCR assays specifically designed to detect the DNA of six helminth representatives: the nematodes A. sidemi and Haemonchus spp., as well as the trematodes F. magna, Dicrocoelium dendriticum, Fasciola hepatica, and Calicophoron daubneyi (and representatives of the family Paramphistomidae, respectively). These assays targeted regions of ribosomal DNA (rDNA) and were designed to exhibit high sensitivity and specificity, enabling accurate detection of helminth parasites directly in fecal samples. The molecular assays revealed that invasive nematode A. sidemi was the most prevalent helminth species, detected in 15.8% of all samples (155/983), with the highest infection rate observed in red deer at 30.7% (124/404). Haemonchus spp. were also frequently detected, identified in 14.9% of samples (146/983), particularly in roe deer, with a prevalence of 23.2% (86/371). Spatial analysis of these nematodes across various regions of the CR revealed the extensive distribution of both A. sidemi and Haemonchus spp. in nearly all regions. In contrast, trematode infections were less common, with F. magna and D. dendriticum each found in only 1.5% of samples (15/983). Members of the family Paramphistomidae were detected in 0.2% of the samples (2/983) and were confirmed through sequencing as C. daubneyi. The geographical distribution patterns identified in this study indicate potential hotspots for specific helminth species. These findings are critical for planning health management and conservation strategies to mitigate the impacts of helminth infections, especially in areas affected by invasive species.

Guild Dynamics and Pathogen Interactions in Hyalomma Ticks From Algerian Cattle

Ticks are pivotal in transmitting a variety of pathogens that affect both humans and animals. These pathogens often occur in guilds, groups of species that exploit similar resources in similar ways. Although the composition of tick-borne pathogen (TBP) guilds is well-documented, the interactions among pathogens within these guilds remain poorly understood. We hypothesized that abiotic and biotic factors significantly influence the patterns of occurrence and interactions among pathogens within these guilds. To investigate this, we analyzed microfluidic-based high-throughput data on microorganisms from 166 Hyalomma excavatum ticks (94 male and 72 female) collected across different seasons from cattle in the central Algerian steppe using network analysis to uncover complex pathogen-pathogen interaction patterns. We found that female ticks had a higher infection rate (63.9%) with common pathogens such as Rickettsia slovaca (26.4%), unclassified Apicomplexa (22.2%), and Borrelia afzelii (19.4%). Male ticks showed a 56.4% infection rate, with Rickettsia (31.1%) and R. slovaca (16%) being the most prevalent. Notable pathogen-pathogen interactions within guilds were identified, with positive associations such as between R. slovaca and Rickettsia conorii in males, and B. afzelii and Borrelia spielmanii in females, indicating cooperative interactions. Conversely, negative associations, such as between Anaplasma phagocytophilum and Francisella tularensis, suggested competitive exclusion. The observed variation in interaction patterns under different conditions indicates that ecological determinants, both biotic and abiotic, influence pathogen association dynamics within guilds. These findings have significant implications for understanding disease transmission and developing control strategies.

Molecular Identification of Selected Cervid Helminths in Supplementarily Fed European Bison Population

Background: Wild animals often suffer from infections with multiple species of parasites simultaneously. The exchange of parasites between different host species is common in nature and often involves intermediate hosts or sharing space such as pastures or watering holes. Supplementary feeding, leading to large aggregations of individuals, can have several adverse effects on wild ungulate populations, despite being a widespread management practice. One such effect is an increased risk of parasitic infections, particularly in social animals. We quantified the prevalence of selected helminths typically found in cervids, in samples of the European bison faeces, using molecular methods, and compared endoparasite species richness between supplementarily fed and nonfed European bison herds in the Białowieża Primeval Forest, NE Poland. Methods: Using the diagnostic PCR method, we analysed the faecal samples for molecular markers of nine parasite species which are typically found in cervids: moose, red deer, and roe deer. Results: All analysed samples tested positive for at least one parasite species, and the average number of parasite species per sample was 3.2. The most prevalent parasites were gastrointestinal nematodes: Ostertagia leptospicularis and Ostertagia antipini, found in 89.2% and 50.6% of the European bison faecal samples, respectively. We found significant differences in the prevalence of four parasite species between supplementarily fed and nonfed European bison herds. Co-occurrence analysis showed that most of the associations between parasite species pairs were random. Conclusion: Management practices, such as supplementary feeding, can influence the spread of parasite infections in social mammals. This study also promotes the application of molecular methods for noninvasive parasitological monitoring of wildlife populations of endangered ruminant species sharing resources with other ungulates.

Is the local environment more important than within-host interactions in determining coinfection?

Host populations often vary in the magnitude of coinfection they experience across environmental gradients. Furthermore, coinfection often occurs sequentially, with a second parasite infecting the host after the first has established a primary infection. Because the local environment and interactions between coinfecting parasites can both drive patterns of coinfection, it is important to disentangle the relative contributions of environmental factors and within-host interactions to patterns of coinfection. Here, we develop a conceptual framework and present an empirical case study to disentangle these facets of coinfection. Across multiple lakes, we surveyed populations of five damselfly (host) species and quantified primary parasitism by aquatic, ectoparasitic water mites and secondary parasitism by terrestrial, endoparasitic gregarines. We first asked if coinfection is predicted by abiotic and biotic factors within the local environment, finding that the probability of coinfection decreased for all host species as pH increased. We then asked if primary infection by aquatic water mites mediated the relationship between pH and secondary infection by terrestrial gregarines. Contrary to our expectations, we found no evidence for a water mite-mediated relationship between pH and gregarines. Instead, the intensity of gregarine infection correlated solely with the local environment, with the magnitude and direction of these relationships varying among environmental predictors. Our findings emphasize the role of the local environment in shaping infection dynamics that set the stage for coinfection. Although we did not detect within-host interactions, the approach herein can be applied to other systems to elucidate the nature of interactions between hosts and coinfecting parasites within complex ecological communities.

A systematic review and guide for using multi-response statistical models in co-infection research

The simultaneous infection of organisms with two or more co-occurring pathogens, otherwise known as co-infections, concomitant infections or multiple infections, plays a significant role in the dynamics and consequences of infectious diseases in both humans and animals. To understand co-infections, ecologists and epidemiologists rely on models capable of accommodating multiple response variables. However, given the diversity of available approaches, choosing a model that is suitable for drawing meaningful conclusions from observational data is not a straightforward task. To provide clearer guidance for statistical model use in co-infection research, we conducted a systematic review to (i) understand the breadth of study goals and host-pathogen systems being pursued with multi-response models and (ii) determine the degree of crossover of knowledge among disciplines. In total, we identified 69 peer-reviewed primary studies that jointly measured infection patterns with two or more pathogens of humans or animals in natural environments. We found stark divisions in research objectives and methods among different disciplines, suggesting that cross-disciplinary insights into co-infection patterns and processes for different human and animal contexts are currently limited. Citation network analysis also revealed limited knowledge exchange between ecology and epidemiology. These findings collectively highlight the need for greater interdisciplinary collaboration for improving disease management.

Large-bodied gastric spirurids (Nematoda, Spirurida) predict structure in the downstream gastrointestinal helminth community of wild spiny mice (Acomys dimidiatus)

The dominant helminths infecting spiny mice (Acomys dimidiatus) in the montane wadis of the Sinai Peninsula of Egypt are spirurid nematodes, notably Protospirura muricola and Mastophorus muris. Both are relatively large robust stomach worms that accumulate in hosts resulting in high worm burdens. To ascertain whether the presence of spirurid worms or their burdens alters the host's likelihood of infection with other helminth species, we analysed a database containing quantitative data on helminth parasites of these mice (n = 431). This comprised of worm burdens recorded during 4 surveys, conducted at 4-year intervals, in 4 wadis, during late summer of each year. The presence of spirurid worms did not significantly alter species richness with other helminth species nor the likelihood of mice carrying other nematode species. However, there was a significant association, particularly of P. muricola, with the presence of intestinal stages of cestodes, and with the acanthocephalan Moniliformis acomysi. After controlling for intrinsic and extrinsic factors, mice harbouring spirurid worms had greater worm burdens of other helminths compared with mice without spirurids. Moreover, spirurid worm burdens showed a significant positive covariation with similarly adjusted species richness of other helminths, non-spirurid helminths, non-spirurid nematodes, oxyuroid nematodes and intestinal stage cestode worm burdens. We interpret these results as an indication that the key driver for co-occurrence of spirurids with other helminths is likely to be transmission via common arthropod hosts (for cestodes and acanthocephalans), but also that mice carrying the heavier spirurid worm burdens become more susceptible to directly transmitted nematodes such as the Oxyuroidea.

Host and parasite identity interact in scale-dependent fashion to determine parasite community structure

Understanding the ecological assembly of parasite communities is critical to characterise how changing host and environmental landscapes will alter infection dynamics and outcomes. However, studies frequently assume that (a) closely related parasite species or those with identical life-history strategies are functionally equivalent, and (b) the same factors will drive infection dynamics for a single parasite across multiple host species, oversimplifying community assembly patterns. Here, we challenge these two assumptions using a naturally occurring host-parasite system, with the mussel Anodonta anatina infected by the digenean trematode Echinoparyphium recurvatum, and the snail Viviparus viviparus infected by both E. recurvatum and Echinostoma sp. By analysing the impact of temporal parasite dispersal, host species and size, and the impact of coinfection (moving from broader environmental factors to within-host dynamics), we show that neither assumption holds true, but at different ecological scales. The assumption that closely related parasites can be functionally grouped is challenged when considering dispersal to the host (i.e. larger scales), while the assumption that the same factors will drive infection dynamics for a single parasite across multiple host species is challenged when considering within-host interspecific competition (i.e. smaller scales). Our results demonstrate that host identity, parasite identity and ecological scale require simultaneous consideration in studies of parasite community composition and transmission.

Interspecific Host Variation and Biotic Interactions Drive Pathogen Community Assembly in Chinese Bumblebees

Bumblebees have been considered one of the most important pollinators on the planet. However, recent reports of bumblebee decline have raised concern about a significant threat to ecosystem stability. Infectious diseases caused by multiple pathogen infections have been increasingly recognized as an important mechanism behind this decline worldwide. Understanding the determining factors that influence the assembly and composition of pathogen communities among bumblebees can provide important implications for predicting infectious disease dynamics and making effective conservation policies. Here, we study the relative importance of biotic interactions versus interspecific host resistance in shaping the pathogen community composition of bumblebees in China. We first conducted a comprehensive survey of 13 pathogens from 22 bumblebee species across China. We then applied joint species distribution modeling to assess the determinants of pathogen community composition and examine the presence and strength of pathogen-pathogen associations. We found that host species explained most of the variations in pathogen occurrences and composition, suggesting that host specificity was the most important variable in predicting pathogen occurrences and community composition in bumblebees. Moreover, we detected both positive and negative associations among pathogens, indicating the role of competition and facilitation among pathogens in determining pathogen community assembly. Our research demonstrates the power of a pluralistic framework integrating field survey of bumblebee pathogens with community ecology frameworks to understand the underlying mechanisms of pathogen community assembly.

Schistosoma transmission: scaling-up competence from hosts to ecosystems

In a One-Health context, it is urgent to establish the links between environmental degradation, biodiversity loss, and the circulation of pathogens. Here we review and literally draw a general vision of aquatic environmental factors that interface with Schistosoma species, agents of schistosomiasis, and ultimately modulate their transmission at the ecosystem scale. From this synthesis, we introduce the concept of ecosystem competence defined as 'the propensity of an ecosystem to amplify or mitigate an incoming quantity of a given pathogen that can be ultimately transmitted to their definitive hosts'. Ecosystem competence integrates all mechanisms at the ecosystem scale underlying the transmission risk of a given pathogen and offers a promising measure for operationalizing the One-Health concept.

Is the world wormier than it used to be? We'll never know without natural history collections

Many disease ecologists and conservation biologists believe that the world is wormier than it used to be-that is, that parasites are increasing in abundance through time. This argument is intuitively appealing. Ecologists typically see parasitic infections, through their association with disease, as a negative endpoint, and are accustomed to attributing negative outcomes to human interference in the environment, so it slots neatly into our worldview that habitat destruction, biodiversity loss and climate change should have the collateral consequence of causing outbreaks of parasites. But surprisingly, the hypothesis that parasites are increasing in abundance through time remains entirely untested for the vast majority of wildlife parasite species. Historical data on parasites are nearly impossible to find, which leaves no baseline against which to compare contemporary parasite burdens. If we want to know whether the world is wormier than it used to be, there is only one major research avenue that will lead to an answer: parasitological examination of specimens preserved in natural history collections. Recent advances demonstrate that, for many specimen types, it is possible to extract reliable data on parasite presence and abundance. There are millions of suitable specimens that exist in collections around the world. When paired with contemporaneous environmental data, these parasitological data could even point to potential drivers of change in parasite abundance, including climate, pollution or host density change. We explain how to use preserved specimens to address pressing questions in parasite ecology, give a few key examples of how collections-based parasite ecology can resolve these questions, identify some pitfalls and workarounds, and suggest promising areas for research. Natural history specimens are 'parasite time capsules' that give ecologists the opportunity to test whether infectious disease is on the rise and to identify what forces might be driving these changes over time. This approach will facilitate major advances in a new sub-discipline: the historical ecology of parasitism.

Factors at multiple scales drive parasite community structure

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.

Coinfection patterns of two marine apicomplexans are not associated with genetic diversity of their polychaete host

Coinfections of two or more parasites within one host are more of a rule than an exception in nature. Interactions between coinfecting parasites can greatly affect their abundance and prevalence. Characteristics of the host, such as genetic diversity, can also affect the infection dynamics of coinfecting parasites. Here, we investigate for the first time the association of coinfection patterns of two marine apicomplexans, Rhytidocystis sp. and Selenidium pygospionis, with the genetic diversity of their host, the polychaete Pygospio elegans, from natural populations. Host genetic diversity was determined with seven microsatellite loci and summarized as allelic richness, inbreeding coefficient, and individual heterozygosity. We detected nonsignificant correlations between infection loads and both individual host heterozygosity and population genetic diversity. Prevalence and infection load of Rhytidocystis sp. were higher than those of S. pygospionis, and both varied spatially. Coinfections were common, and almost all hosts infected by S. pygospionis were also infected by Rhytidocystis sp. Rhytidocystis sp. infection load was significantly higher in dual infections. Our results suggest that factors other than host genetic diversity might be more important in marine apicomplexan infection patterns and experimental approaches would be needed to further determine how interactions between the apicomplexans and their host influence infection.

Interactions of cranial helminths in the European polecat (Mustela putorius): Implications for host body condition

Multiple helminth species commonly co-occur within mammals and their interactions may negatively affect the survival and breeding success of their hosts. However, it has been difficult to prove competition or mutualism between co-infesting helminths in field studies of wild mammals. The sinus cavities of European polecats (Mustela putorius) can be parasitised by the trematode Troglotrema acutum and the nematode Skrjabingylus nasicola and both helminths can co-occur within hosts. While both parasites can damage the host's bone structure and cause severe pathologies, their impact on host body condition is unclear. It is also unknown whether both parasites interact and how this might affect cranial damage and host body condition. We examined 515 fresh polecat skulls for the presence of both helminths and measured the hosts' amount of kidney perirenal fat as a measure of body condition. Our results demonstrated that, in addition to a host-intrinsic fixed factor (sex) and random factors accounting for spatial and temporal stochasticity, the helminths influenced each other's presence. Infestation with T. acutum increased the probability of catching S. nasicola with increasing age of the host, while males already infested with S. nasicola were more likely to become infested with T. acutum than females infested with the nematode. While we speculate that both effects resulted from parasite-induced behavioural alterations (increased foot consumption), it is not clear why, in the latter case, this effect would be stronger in males than females. We showed that the abundances of both parasites had significant positive effect on the likely presence of skull damage and a significant negative effect on the predicted presence of kidney fat. Given the evolutionary arms race that both host-parasite systems have undergone, it appears unlikely that either helminth played a significant factor in the population decline of the polecat in Europe.

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We provide evidence for interactions between co-infesting helminths in a wild mammal.

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Troglotrema acutum and Skrjabingylus nasicola can co-occur in the skulls of polecats.

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Infestation with one parasite can increase the probability of infestation with the other one.

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Heavy infestation with either helminth may have a negative effect on host body condition.

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Co-infestation does not change the severity of the parasites' clinical impact.

Changes in temperature alter competitive interactions and overall structure of fig wasp communities

Organisms exist within ecological networks, connected through interactions such as parasitism, predation and mutualism which can modify their abundance and distribution within habitat patches. Differential species responses make it hard to predict the influence of climate change at the community scale. Understanding the interplay between climate and biotic interactions can improve our predictions of how ecosystems will respond to current global warming. We aim to understand how climate affects the multi-trophic biotic interactions as well as the community structure using the enclosed communities of wasps associated with figs as study system. To examine the presence and strength of multi-trophic species interactions, we first characterized the multi-trophic community of fig wasps associated with Ficus racemosa and then applied hierarchical joint species distribution models, fitted to community monitoring data. We further evaluated the effect of climate on individual species trends as well as inter-specific interactions. We found that the competitive balance shifted to favour non-pollinating galling wasps and disadvantage the dominant pollinator in sub-optimal conditions. Further, sub-optimal conditions for galling wasps facilitated the occurrence of their specialized parasitoid, as changes cascaded across trophic levels and led to alternative community structures. Our results highlight the role of how species interactions can be modified across multiple trophic levels in a fig wasp community according to climate.

Coinfection with a virus constrains within-host infection load but increases transmission potential of a highly virulent fungal plant pathogen

The trade-off between within-host infection rate and transmission to new hosts is predicted to constrain pathogen evolution, and to maintain polymorphism in pathogen populations. Pathogen life-history stages and their correlations that underpin infection development may change under coinfection with other parasites as they compete for the same limited host resources. Cross-kingdom interactions are common among pathogens in both natural and cultivated systems, yet their impacts on disease ecology and evolution are rarely studied. The host plant Plantago lanceolata is naturally infected by both Phomopsis subordinaria, a seed killing fungus, as well as Plantago lanceolata latent virus (PlLV) in the Åland Islands, SW Finland. We performed an inoculation assay to test whether coinfection with PlLV affects performance of two P. subordinaria strains, and the correlation between within-host infection rate and transmission potential. The strains differed in the measured life-history traits and their correlations. Moreover, we found that under virus coinfection, within-host infection rate of P. subordinaria was smaller but transmission potential was higher compared to strains under single infection. The negative correlation between within-host infection rate and transmission potential detected under single infection became positive under coinfection with PlLV. To understand whether within-host and between-host dynamics are correlated in wild populations, we surveyed 260 natural populations of P. lanceolata for P. subordinaria infection occurrence. When infections were found, we estimated between-hosts dynamics by determining pathogen population size as the proportion of infected individuals, and within-host dynamics by counting the proportion of infected flower stalks in 10 infected plants. In wild populations, the proportion of infected flower stalks was positively associated with pathogen population size. Jointly, our results suggest that the trade-off between within-host infection load and transmission may be strain specific, and that the pathogen life-history that underpin epidemics may change depending on the diversity of infection, generating variation in disease dynamics.

Ectoparasitic fungi of Myrmica ants alter the success of parasitic butterflies

Exploitation of organisms by multiple parasite species is common in nature, but interactions among parasites have rarely been studied. Myrmica ants are rich in parasites. Among others, the ectoparasitic Rickia wasmannii fungus and the parasitic caterpillars of myrmecophilous Phengaris butterflies often infect the same Myrmica colonies. In this study, we examined the effects of R. wasmannii on the adoption, long-term development, and survival of P. alcon. In laboratory conditions, caterpillars introduced into nests of Myrmica scabrinodis uninfected with R. wasmannii survived significantly longer compared to caterpillars introduced into infected nests. In the field, joint infection was less common than expected if both parasites exploited M. scabrinodis colonies independently. Pre-pupal caterpillars of P. alcon were somewhat larger in nests infected with R. wasmannii than those found in uninfected nests. Based on these results it seems that R. wasmannii infection of M. scabrinodis affects the survival and development of P. alcon caterpillars, suggesting competition between these two ant parasites.

Co-occurrence in ant primary parasitoids: a Camponotus rectangularis colony as host of two eucharitid wasp genera

Different assemblages of parasitoids may attack a given host species and non-random distribution patterns in parasitoid species assemblages have been reported on various occasions, resulting in co-occurrence at the population, colony, or even individual host levels. This is the case for different closely related species of eucharitid wasps (a family of specialized ant parasitoids) sharing similar niches and co-occurring on the same host at different levels. Here we reviewed all known associations between eucharitid wasps and the ant host genus Camponotus Mayr, 1861 and reported new ant-parasitoid associations. In addition, we report a new case of co-occurrence in eucharitid wasps, at the host colony level, involving a new undescribed species of Pseudochalcura Ashmead, 1904 and an unidentified species of Obeza Heraty, 1985, which attack the common but very poorly known neotropical arboreal ant Camponotus rectangularis Emery, 1890. Most attacks were solitary, but various cocoons were parasitized by two (16%) or three (8%) parasitoids. Globally, parasitism prevalence was very low (3.7%) but showed an important variability among samples. Low parasitism prevalence along with host exposure to parasitoid attack on host plants and overlapping reproductive periods of both parasitoid species may have allowed the evolution of co-occurrence. We also provided some additional data regarding the host ant nesting habits, the colony composition and new symbiotic associations with membracids and pseudococcids. The seemingly polydomous nesting habits of C. rectangularis could play a part in the reduction of parasitism pressure at the population level and, combined with occasionally important local parasitism rates, could also contribute to some parts of the colonies escaping from parasites, polydomy possibly representing an effective parasitism avoidance trait.

Helminth communities in amphibians from Latvia, with an emphasis on their connection to host ecology

Helminth infracommunities were studied at 174 sites of Latvia in seven hosts from six amphibian taxa of different taxonomical, ontogenic and ecological groups. They were described using a standard set of parasitological parameters, compared by ecological indices and linear discriminant analysis. Their species associations were identified by Kendall's rank correlation, but relationships with host size and waterbody area were analysed by zero-inflated Poisson and zero-inflated negative binomial regressions. The richest communities (25 species) were found in post-metamorphic semi-aquatic Pelophylax spp. frogs, which were dominated by trematode species of both adult and larval stages. Both larval and terrestrial hosts yielded depauperate trematode communities with accession of aquatic and soil-transmitted nematode species, respectively. Nematode loads peaked in terrestrial Bufo bufo. Helminth infracommunities suggested some differences in host microhabitat or food object selection not detected by their ecology studies. Associations were present in 96% of helminth species (on average, 7.3 associations per species) and dominated positive ones. Species richness and abundances, in most cases, were positively correlated with host size, which could be explained by increasing parasite intake rates over host ontogeny (trematode adult stages) or parasite accumulation (larval Alaria alata). Two larval diplostomid species (Strigea strigis, Tylodelphys excavata) had a negative relationship with host size, which could be caused by parasite-induced host mortality. The adult trematode abundances were higher in larger waterbodies, most likely due to their ecosystem richness, while higher larval abundances in smaller waterbodies could be caused by elevated infection rates under high host densities.

Towards an ecosystem model of infectious disease

Increasingly intimate associations between human society and the natural environment are driving the emergence of novel pathogens, with devastating consequences for humans and animals alike. Prior to emergence, these pathogens exist within complex ecological systems that are characterized by trophic interactions between parasites, their hosts and the environment. Predicting how disturbance to these ecological systems places people and animals at risk from emerging pathogens-and the best ways to manage this-remains a significant challenge. Predictive systems ecology models are powerful tools for the reconstruction of ecosystem function but have yet to be considered for modelling infectious disease. Part of this stems from a mistaken tendency to forget about the role that pathogens play in structuring the abundance and interactions of the free-living species favoured by systems ecologists. Here, we explore how developing and applying these more complete systems ecology models at a landscape scale would greatly enhance our understanding of the reciprocal interactions between parasites, pathogens and the environment, placing zoonoses in an ecological context, while identifying key variables and simplifying assumptions that underly pathogen host switching and animal-to-human spillover risk. As well as transforming our understanding of disease ecology, this would also allow us to better direct resources in preparation for future pandemics.

Parasite counts or parasite incidences? Testing differences with four analyses of infracommunity modelling for seven parasite-host associations

One of the challenges in studies of parasite community ecology is whether the input data for analyses should be parasite abundances/counts, i.e. count data (CD), or parasite incidences (presences/absences), i.e. incidence data (ID). We analysed species responses to environmental factors and species associations in the infracommunities of helminths and ectoparasites in four hosts from Europe (Sorex araneus and Myodes glareolus) and South Africa (Rhabdomys pumilio and Rhabdomys dilectus) and compared the results of four analyses [redundancy analysis (RD), RLQ analysis, joint species distribution modelling (JSDM) and Markov random fields (MRF)] that used either CD or ID as an input. In addition, we compared the differences between the CD and ID results of two analyses (JSDM and MRF) across parasite species between (a) host species within helminths and ectoparasites; (b) helminths and ectoparasites within a host species; and (c) parasite species with contrasting levels of intensity. The results of most analyses for the majority of parasite-host associations were qualitatively similar. However, models based on the ID input performed better than models based on the CD input in three out of four types of analyses (RDA, JSDM and MRF). The differences between the CD and ID models varied between host species (being the lowest in R. pumilio for JSDM and in S. araneus for MRF). However, they were not affected by the level of parasite intensity.

Infestation risk of the intermediate snail host of Schistosoma japonicum in the Yangtze River Basin: improved results by spatial reassessment and a random forest approach

BACKGROUND

Oncomelania hupensis is only intermediate snail host of Schistosoma japonicum, and distribution of O. hupensis is an important indicator for the surveillance of schistosomiasis. This study explored the feasibility of a random forest algorithm weighted by spatial distance for risk prediction of schistosomiasis distribution in the Yangtze River Basin in China, with the aim to produce an improved precision reference for the national schistosomiasis control programme by reducing the number of snail survey sites without losing predictive accuracy.

METHODS

The snail presence and absence records were collected from Anhui, Hunan, Hubei, Jiangxi and Jiangsu provinces in 2018. A machine learning of random forest algorithm based on a set of environmental and climatic variables was developed to predict the breeding sites of the O. hupensis intermediated snail host of S. japonicum. Different spatial sizes of a hexagonal grid system were compared to estimate the need for required snail sampling sites. The predictive accuracy related to geographic distances between snail sampling sites was estimated by calculating Kappa and the area under the curve (AUC).

RESULTS

The highest accuracy (AUC = 0.889 and Kappa = 0.618) was achieved at the 5 km distance weight. The five factors with the strongest correlation to O. hupensis infestation probability were: (1) distance to lake (48.9%), (2) distance to river (36.6%), (3) isothermality (29.5%), (4) mean daily difference in temperature (28.1%), and (5) altitude (26.0%). The risk map showed that areas characterized by snail infestation were mainly located along the Yangtze River, with the highest probability in the dividing, slow-flowing river arms in the middle and lower reaches of the Yangtze River in Anhui, followed by areas near the shores of China's two main lakes, the Dongting Lake in Hunan and Hubei and the Poyang Lake in Jiangxi.

CONCLUSIONS

Applying the machine learning of random forest algorithm made it feasible to precisely predict snail infestation probability, an approach that could improve the sensitivity of the Chinese schistosome surveillance system. Redesign of the snail surveillance system by spatial bias correction of O. hupensis infestation in the Yangtze River Basin to reduce the number of sites required to investigate from 2369 to 1747.

QSAR Modeling for Multi-Target Drug Discovery: Designing Simultaneous Inhibitors of Proteins in Diverse Pathogenic Parasites

Parasitic diseases remain as unresolved health issues worldwide. While for some parasites the treatments involve drug combinations with serious side effects, for others, chemical therapies are inefficient due to the emergence of drug resistance. This urges the search for novel antiparasitic agents able to act through multiple mechanisms of action. Here, we report the first multi-target model based on quantitative structure-activity relationships and a multilayer perceptron neural network (mt-QSAR-MLP) to virtually design and predict versatile inhibitors of proteins involved in the survival and/or infectivity of different pathogenic parasites. The mt-QSAR-MLP model exhibited high accuracy (>80%) in both training and test sets for the classification/prediction of protein inhibitors. Several fragments were directly extracted from the physicochemical and structural interpretations of the molecular descriptors in the mt-QSAR-MLP model. Such interpretations enabled the generation of four molecules that were predicted as multi-target inhibitors against at least three of the five parasitic proteins reported here with two of the molecules being predicted to inhibit all the proteins. Docking calculations converged with the mt-QSAR-MLP model regarding the multi-target profile of the designed molecules. The designed molecules exhibited drug-like properties, complying with Lipinski’s rule of five, as well as Ghose’s filter and Veber’s guidelines.

Abundance data applied to a novel model invertebrate host shed new light on parasite community assembly in nature

Understanding how environmental drivers influence the assembly of parasite communities, in addition to how parasites may interact at an infracommunity level, are fundamental requirements for the study of parasite ecology. Knowledge of how parasite communities are assembled will help to predict the risk of parasitism for hosts, and model how parasite communities may change under variable conditions. However, studies frequently rely on presence-absence data and examine multiple host species or sites, metrics which may be too coarse to characterise nuanced within-host patterns. We utilised a novel host system, the freshwater mussel Anodonta anatina, to investigate the drivers of community structure and explore parasite interactions. In addition, we aimed to highlight consistencies and inconsistencies between PA and abundance data. Our analysis incorporated 14 parasite taxa and 720 replicate infracommunities. Using Redundancy Analysis, a joint species distribution model and a Markov random field approach, we modelled the impact of both host-level and environment-level characteristics on parasite structure, as well as parasite-parasite correlations after accounting for all other factors. This approach was repeated for both the presence and abundance of all parasites. We demonstrated that the regional species pool, individual host characteristics (mussel length and gravidity) and predicted parasite-parasite interactions are all important but to varying degrees across parasite species, suggesting that applying generalities to parasite community construction is too simplistic. Furthermore, we showed that PA data fail to capture important density-dependent effects of parasite load for parasites with high abundance, and in general performs poorly for high-intensity parasites. Host and parasite traits, as well as broader environmental factors, all contribute to parasite community structure, emphasising that an integrated approach is required to study community assembly. However, care must be taken with the data used to infer patterns, as presence-absence data may lead to incorrect ecological inference.

Biodiversity of the Coccidia (Apicomplexa: Conoidasida) in vertebrates: what we know, what we do not know, and what needs to be done

Over the last two decades my colleagues and I have assembled the literature on a good percentage of most of the coccidians (Conoidasida) known, to date, to parasitise: Amphibia, four major lineages of Reptilia (Amphisbaenia, Chelonia, Crocodylia, Serpentes), and seven major orders in the Mammalia (Carnivora, Chiroptera, Lagomorpha, Insectivora, Marsupialia, Primates, Scandentia). These vertebrates, combined, comprise about 15,225 species; only about 899 (5.8%) of them have been surveyed for coccidia and 1,946 apicomplexan valid species names or other forms are recorded in the literature. Based on these compilations and other factors, I extrapolated that there yet may be an additional 31,381 new apicomplexans still to be discovered in just these 12 vertebrate groups. Extending the concept to all of the other extant vertebrates on Earth; i.e. lizards (6,300 spp.), rodents plus 12 minor orders of mammals (3,180 spp.), birds (10,000 spp.), and fishes (33,000 spp.) and, conservatively assuming only two unique apicomplexan species per each vertebrate host species, I extrapolate and extend my prediction that we may eventually find 135,000 new apicomplexans that still need discovery and to be described in and from those vertebrates that have not yet been examined for them! Even doubling that number is a significant underestimation in my opinion.

Habitat type and interannual variation shape unique fungal pathogen communities on a California native bunchgrass

The role of infectious disease in regulating host populations is increasingly recognized, but how environmental conditions affect pathogen communities and infection levels remains poorly understood. Over 3 y, we compared foliar disease burden, fungal pathogen community composition, and foliar chemistry in the perennial bunchgrass Stipa pulchra occurring in adjacent serpentine and nonserpentine grassland habitats with distinct soil types and plant communities. We found that serpentine and nonserpentine S. pulchra experienced consistent, low disease pressure associated with distinct fungal pathogen communities with high interannual species turnover. Additionally, plant chemistry differed with habitat type. The results indicate that this species experiences minimal foliar disease associated with diverse fungal communities that are structured across landscapes by spatially and temporally variable conditions. Distinct fungal communities associated with different growing conditions may shield S. pulchra from large disease outbreaks, contributing to the low disease burden observed on this and other Mediterranean grassland species.

Sex-biased polyparasitism in moose (Alces alces) based on molecular analysis of faecal samples

Simultaneous infection with multiple parasite species in an individual host is often observed in wild populations. The understanding of parasite species distribution across populations of wild animals is of basic and applied importance, because parasites can have pronounced effects on the dynamics of host population. Here, we quantified prevalence and endoparasite species richness in moose and explored sex-biased polyparasitism using diagnostic PCR method coupled with DNA sequencing of moose faecal samples from the Biebrza River valley, North-Eastern Poland. This is the largest moose population in Central Europe that has not been harvested for almost 20 years. We also evaluated the appropriate quantity of faeces for detecting DNA of parasite species. Faecal samples were screened for molecular markers of 10 different species of endoparasites. Endoparasite prevalence was high in the studied population. Almost all of the samples (98%) tested positive for at least one parasite species, and we found polyparasitism in the majority of the tested individuals. The number of different parasite species found in a single individual ranged from 0 to 9. The parasite species richness was significantly higher in male than in female individuals. The most prevalent were liver fluke Parafasciolopsis fasciolaemorpha and gastrointestinal nematodes Ostertargia sp. Of the ten endoparasite species detected, only the prevalence of the tapeworm Moniezia benedeni was significantly higher in males than in females. Additionally, we identified co-occurrence associations of parasite species, which tended to be random, but we noted some evidence of both positive and negative associations. Our findings promote applications of molecular methods for parasite species identification from non-invasively collected faecal samples in management and scientific study of moose population, which should include investigation of parasite status, and in health monitoring programs for other wild cervids.

What would it take to describe the global diversity of parasites?

How many parasites are there on Earth? Here, we use helminth parasites to highlight how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host-parasite associations and one of the world's largest parasite collections, we estimate a global total of roughly 100 000-350 000 species of helminth endoparasites of vertebrates, of which 85-95% are unknown to science. The parasites of amphibians and reptiles remain the most poorly described, but the majority of undescribed species are probably parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries. At current rates, it would take centuries to comprehensively sample, collect and name vertebrate helminths. While some have suggested that macroecology can work around existing data limitations, we argue that patterns described from a small, biased sample of diversity aren't necessarily reliable, especially as host-parasite networks are increasingly altered by global change. In the spirit of moonshots like the Human Genome Project and the Global Virome Project, we consider the idea of a Global Parasite Project: a global effort to transform parasitology and inventory parasite diversity at an unprecedented pace.

Microhabitat distributions and species interactions of ectoparasites on the gills of cichlid fish in Lake Victoria, Tanzania

Heterogeneous exposure to parasites may contribute to host species differentiation. Hosts often harbour multiple parasite species which may interact and thus modify each other's effects on host fitness. Antagonistic or synergistic interactions between parasites may be detectable as niche segregation within hosts. Consequently, the within-host distribution of different parasite taxa may constitute an important axis of infection variation among host populations and species. We investigated the microhabitat distributions and species interactions of gill parasites (four genera) infecting 14 sympatric cichlid species in Lake Victoria, Tanzania. We found that the two most abundant ectoparasite genera (the monogenean Cichlidogyrus spp. and the copepod Lamproglena monodi) were non-randomly distributed across the host gills and their spatial distribution differed between host species. This may indicate microhabitat selection by the parasites and cryptic differences in the host-parasite interaction among host species. Relationships among ectoparasite genera were synergistic: the abundances of Cichlidogyrus spp. and the copepods L. monodi and Ergasilus lamellifer tended to be positively correlated. In contrast, relationships among morphospecies of Cichlidogyrus were antagonistic: the abundances of morphospecies were negatively correlated. Together with niche overlap, this suggests competition among morphospecies of Cichlidogyrus. We also assessed the reproductive activity of the copepod species (the proportion of individuals carrying egg clutches), as it may be affected by the presence of other parasites and provide another indicator of the species specificity of the host-parasite relationship. Copepod reproductive activity did not differ between host species and was not associated with the presence or abundance of other parasites, suggesting that these are generalist parasites, thriving in all cichlid species examined from Lake Victoria.

Intraspecific host variation plays a key role in virus community assembly

Infection by multiple pathogens of the same host is ubiquitous in both natural and managed habitats. While intraspecific variation in disease resistance is known to affect pathogen occurrence, how differences among host genotypes affect the assembly of pathogen communities remains untested. In our experiment using cloned replicates of naive Plantago lanceolata plants as sentinels during a seasonal virus epidemic, we find non-random co-occurrence patterns of five focal viruses. Using joint species distribution modelling, we attribute the non-random virus occurrence patterns primarily to differences among host genotypes and local population context. Our results show that intraspecific variation among host genotypes may play a large, previously unquantified role in pathogen community structure.

Eutrophication, biodiversity loss, and species invasions modify the relationship between host and parasite richness during host community assembly

Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post-assembly host species richness, richness-independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance-communities dominated by exotic species exhibited a stronger positive relationship between post-assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship-the positive relationship between host and parasite richness.

Temporal dynamics of species associations in the parasite community of European eels, Anguilla anguilla, from a coastal lagoon

The resilience of biological communities is of central importance in ecology, but is difficult to investigate in nature. Parasite communities in individual hosts provide good model systems, as they allow a level of replication usually not possible with free-living communities. Here, using temporal data (2005-2017) on the communities of endohelminth parasites in European eels, Anguilla anguilla, from brackish-water lagoons in Italy, we test the resilience of interspecific associations to changes in the abundance of some parasite species and the disappearance of others. While most parasite species displayed changes in abundance over time, three trematodes that were present in the early years, two of which at high abundance, completely disappeared from the parasite community by the end of the study period. Possibly other host species required for the completion of their life cycles have declined in abundance, perhaps due to environmental changes. However, despite these marked changes to the overall community, pairwise correlations in abundance among the three most common parasite species (all trematodes) were stable over time and remained mostly unaffected by what happened to other species. We explore possible reasons for these resilient species associations within a temporally unstable parasite community inhabiting a mostly stable host population.

Parasite species co-occurrence patterns on Peromyscus: Joint species distribution modelling

Hosts are often infested by multiple parasite species, but it is often unclear whether patterns of parasite co-occurrence are driven by parasite habitat requirements or parasite species interactions. Using data on infestation patterns of ectoparasitic arthropods (fleas, trombiculid mites, cuterebrid botflies) from deer mice (Peromyscus maniculatus), we analyzed species associations using joint species distribution modelling. We also experimentally removed a flea (Orchopeas leucopus) from a subset of deer mice to examine the effect on other common ectoparasite species. We found that the mite (Neotrombicula microti) and botfly (Cuterebra sp.) had a negative relationship that is likely a true biotic species interaction. The flea had a negative association with the mite and a positive association with the botfly species, both of which appeared to be influenced by host traits or parasite life-history traits. Furthermore, experimental removal of the flea did not have a significant effect on ectoparasite prevalence of another species. Overall, these findings suggest that complex parasite species associations can be present among multiple parasite taxa, and that aggregation is not always the rule for ectoparasite communities of small mammals.

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A negative species interaction was identified between a mite and botfly species.

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Additional parasite associations appear to be influenced by host traits or parasite life-history traits.

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Removal of the flea species did not have an effect on prevalence of another species.

Coinfections by noninteracting pathogens are not independent and require new tests of interaction

If pathogen species, strains, or clones do not interact, intuition suggests the proportion of coinfected hosts should be the product of the individual prevalences. Independence consequently underpins the wide range of methods for detecting pathogen interactions from cross-sectional survey data. However, the very simplest of epidemiological models challenge the underlying assumption of statistical independence. Even if pathogens do not interact, death of coinfected hosts causes net prevalences of individual pathogens to decrease simultaneously. The induced positive correlation between prevalences means the proportion of coinfected hosts is expected to be higher than multiplication would suggest. By modelling the dynamics of multiple noninteracting pathogens causing chronic infections, we develop a pair of novel tests of interaction that properly account for nonindependence between pathogens causing lifelong infection. Our tests allow us to reinterpret data from previous studies including pathogens of humans, plants, and animals. Our work demonstrates how methods to identify interactions between pathogens can be updated using simple epidemic models.

If pathogen species, strains, or clones do not interact, intuition suggests the proportion of coinfected hosts can be obtained by simply multiplying the individual prevalences. However, even simple epidemiological models show this to be untrue. This study develops new tests for interaction between pathogens that account for this surprising lack of statistical independence.