The community ecology of pathogens: coinfection,coexistence and community composition

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host–pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two‐pathogen susceptible‐infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species‐diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.     

Movement can mediate temporal mismatches between resource availability and biological events in host–pathogen interactions

Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species’ populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host–pathogen systems. We adapted an established individual‐based model of host–pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host''s explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life‐history events affect host–pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts’ biological events. However, a temporal mismatch reduced host–pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat‐dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host–pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.     

The effect of landscape heterogeneity and host movement on a tick-borne pathogen

Landscape heterogeneity can be instrumental in determining local disease risk, pathogen persistence and spread. This is because different landscape features such as habitat type determine the abundance and spatial distributions of hosts and pathogen vectors. Therefore, disease prevalence and distribution are intrinsically linked to the hosts and vectors that utilise the different habitats. Here, we develop a simplified reaction diffusion model of the louping-ill virus and red grouse (Lagopus lagopus scoticus) system to investigate the occurrence of a tick-borne pathogen and the effect of host movement and landscape structure. Ticks (Ixodes ricinus), the virus-vector, are dispersed by a virally incompetent tick host, red deer (Cervus elephus), between different habitats, whilst the virus infects only red grouse. We investigated how deer movement between different habitats (forest and moorland) affected tick distribution and hence prevalence of infected ticks and grouse and hence, the effect of habitat size ratio and fragmentation on infection. When habitat type has a role in the survival of the pathogen vector, we demonstrated that habitat fragmentation can have a considerable effect on infection. These results highlight the importance of landscape heterogeneity and the proximity and size of adjacent habitats when predicting disease risk in a particular location. In addition, this model could be useful for other pathogen systems with generalist vectors and may inform policy on possible disease management strategies that incorporate host movements.     

Impact of biodiversity and seasonality on Lyme-pathogen transmission

Lyme disease imposes increasing global public health challenges. To better understand the joint effects of seasonal temperature variation and host community composition on the pathogen transmission, a stage-structured periodic model is proposed by integrating seasonal tick development and activity, multiple host species and complex pathogen transmission routes between ticks and reservoirs. Two thresholds, one for tick population dynamics and the other for Lyme-pathogen transmission dynamics, are identified and shown to fully classify the long-term outcomes of the tick invasion and disease persistence. Seeding with the realistic parameters, the tick reproduction threshold and Lyme disease spread threshold are estimated to illustrate the joint effects of the climate change and host community diversity on the pattern of Lyme disease risk. It is shown that climate warming can amplify the disease risk and slightly change the seasonality of disease risk. Both the “dilution effect” and “amplification effect” are observed by feeding the model with different possible alternative hosts. Therefore, the relationship between the host community biodiversity and disease risk varies, calling for more accurate measurements on the local environment, both biotic and abiotic such as the temperature and the host community composition.     

Spatial Simulation of Epizootics Caused by Beauveria bassiana in Russian Wheat Aphid Populations

Models of disease dynamics commonly make the assumption of spatial homogeneity in the underlying host population. However, insect behavior may result in spatially heterogeneous populations with which pathogens interact. We modified a simulation model of temporal and spatial population dynamics of the Russian wheat aphid, Diuraphis noxia, on preferred or nonpreferred host plants, by incorporating effects of the entomopathogenic fungus, Beauveria bassiana. Epizootic parameters included time from inoculation of aphids until death, duration of sporulation, and estimated exposure probability. Simulations first predicted results of previously described experiments in which D. noxia adults were inoculated with conidial suspensions or water and placed on wheat or oat seedlings in 81-plant grids in cages. Subsequently, large-scale simulations were run for hypothetical field situations on 50 × 50-plant grids of wheat or oat. With B. bassiana present for both cage and larger scale simulations, results indicated that, on oat, an expanding infection front lagged behind the expanding aphid population front. Continual aphid movement from hosts resulted in many escapes, and the aphid population persisted at slightly reduced levels. On the preferred wheat host, patterns developed with pockets of infected aphids and other pockets of healthy aphids. Localized aphid populations that escaped initial infestation were able to proliferate, whereas other local populations were greatly reduced or became extinct due to lack of movement from the hosts, resulting in increased exposure to pathogen inoculum. Thus, proliferation and fluctuation of the pathogen were strongly influenced by the plant hosts' effects on aphid movement behavior. Incorporating spatial dynamics into disease models should prove useful in other efforts to predict biological control efficacy by entomopathogenic fungi in heterogeneous habitats.     

Towards an eco‐phylogenetic framework for infectious disease ecology

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi‐host and/or multi‐parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco‐phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi‐host multi‐parasite systems, yet the incorporation of eco‐phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco‐phylogenetics is a transformative approach that uses evolutionary history to infer present‐day dynamics. Here, we present an eco‐phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco‐phylogenetic methods can help untangle the mechanisms of host–parasite dynamics from individual (e.g. co‐infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi‐host and multi‐pathogen dynamics across scales will increase our ability to predict disease threats.     

Vector preference for hosts differing in infection status: sharpshooter movement and Xylella fastidiosa transmission

1. Epidemiological theory predicts that vector preference for hosts differing in infection status (i.e. healthy or infected) affects disease dynamics. 2. Numerous studies have documented strong vector preference for or discrimination against infected hosts. However, the significance of these behaviours for pathogen transmission and spread has been poorly described. 3. We conducted a series of choice assays to evaluate orientation preference, feeding preference, and movement rates of an important group of vectors, the sharpshooter leafhoppers, based on host infection status for the generalist plant pathogen, Xylella fastidiosa Wells et al. 4. Sharpshooters did not discriminate between healthy versus infected‐but‐asymptomatic grapevines, but they oriented preferentially to healthy grapevines more frequently than either symptomatic vines or those artificially coloured to mimic disease symptoms. 5. In a field trial three sharpshooter species showed different movement rates and preferences for feeding site, but all species exhibited similar and significant preference for healthy hosts. 6. Although there was no significant difference in acquisition efficiency among vector species, those individuals that spent more time on healthy hosts tended to be less likely to acquire the pathogen. 7. These results suggest that sharpshooters discriminate against infected grapevines, which are likely to be of poorer quality, with visual cues playing a role in host selection. Preference by these vectors may affect pathogen acquisition, which could affect disease spread in the field.     

The Role of Human Transportation Networks in Mediating the Genetic Structure of Seasonal Influenza in the United States

Recent studies have demonstrated the importance of accounting for human mobility networks when modeling epidemics in order to accurately predict spatial dynamics. However, little is known about the impact these movement networks have on the genetic structure of pathogen populations and whether these effects are scale-dependent. We investigated how human movement along the aviation and commuter networks contributed to intra-seasonal genetic structure of influenza A epidemics in the continental United States using spatially-referenced hemagglutinin nucleotide sequences collected from 2003–2013 for both the H3N2 and H1N1 subtypes. Comparative analysis of these transportation networks revealed that the commuter network is highly spatially-organized and more heavily traveled than the aviation network, which instead is characterized by high connectivity between all state pairs. We found that genetic distance between sequences often correlated with distance based on interstate commuter network connectivity for the H1N1 subtype, and that this correlation was not as prevalent when geographic distance or aviation network connectivity distance was assessed against genetic distance. However, these patterns were not as apparent for the H3N2 subtype at the scale of the continental United States. Finally, although sequences were spatially referenced at the level of the US state of collection, a community analysis based on county to county commuter connections revealed that commuting communities did not consistently align with state geographic boundaries, emphasizing the need for the greater availability of more specific sequence location data. Our results highlight the importance of utilizing host movement data in characterizing the underlying genetic structure of pathogen populations and demonstrate a need for a greater understanding of the differential effects of host movement networks on pathogen transmission at various spatial scales.     

The interaction between plant competition and disease

It is well documented that pathogens can affect the survival, reproduction, and growth of individual plants. Drawing together insights from diverse studies in ecology and agriculture, we evaluate the evidence for pathogens affecting competitive interactions between plants of both the same and different species. Our objective is to explore the potential ecological and evolutionary consequences of such interactions. First, we address how disease interacts with intraspecific competition and present a simple graphical model suggesting that diverse outcomes should be expected. We conclude that the presence of pathogens may have either large or minimal effects on population dynamics depending on many factors including the density-dependent compensatory ability of healthy plants and spatial patterns of infection. Second, we consider how disease can alter competitive abilities of genotypes, and thus may affect the genetic composition of populations. These genetic processes feed back on population dynamics given trade-offs between disease resistance and other fitness components. Third, we examine how the effect of disease on interspecific plant interactions may have potentially far-reaching effects on community composition. A host-specific pathogen, for example, may alter a competitive hierarchy that exists between host and non-host species. Generalist pathogens can also induce indirect competitive interactions between host species. We conclude by highlighting lacunae in our current understanding and suggest that future studies should (1) examine a broader taxonomic range of pathogens since work to date has largely focused on fungal pathogens; (2) increase the use of field competition studies; (3) follow interactions for multiple generations; (4) characterize density-dependent processes; and (5) quantify pathogen, as well as plant, population and community dynamics.     

Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal

Metapopulation processes are important determinants of epidemiological and evolutionary dynamics in host-pathogen systems, and are therefore central to explaining observed patterns of disease or genetic diversity. In particular, the spatial scale of interactions between pathogens and their hosts is of primary importance because migration rates of one species can affect both spatial and temporal heterogeneity of selection on the other. In this study we developed a stochastic and discrete time simulation model to specifically examine the joint effects of host and pathogen dispersal on the evolution of pathogen specialisation in a spatially explicit metapopulation. We consider a plant-pathogen system in which the host metapopulation is composed of two plant genotypes. The pathogen is dispersed by air-borne spores on the host metapopulation. The pathogen population is characterised by a single life-history trait under selection, the infection efficacy. We found that restricted host dispersal can lead to high amount of pathogen diversity and that the extent of pathogen specialisation varied according to the spatial scale of host-pathogen dispersal. We also discuss the role of population asynchrony in determining pathogen evolutionary outcomes.     

Spatial Variation in an Avian Host Community: Implications for Disease Dynamics

Because many pathogens can infect multiple host species within a community, disease dynamics in a focal host species can be affected by the composition of the host community. We examine the extent to which spatial variation in species’ abundances in an avian host community may contribute to geographically varying prevalence of a recently emerged wildlife pathogen. Mycoplasma gallisepticum is a pathogen novel to songbirds that has caused substantial mortality in house finches (Carpodacus mexicanus) in eastern North America. Though the house finch is the primary host species for M. gallisepticum, the American goldfinch (Spinus tristis) and northern cardinal (Cardinalis cardinalis) are alternate hosts, and laboratory experiments have demonstrated M. gallisepticum transmission between house finches and goldfinches. Still unknown is the real world impact on disease dynamics of variation in abundances of the three hosts. We analyzed data from winter-long bird and disease surveys in the northeastern United States. We found that higher disease prevalence in house finches was associated with higher numbers of northern cardinals and American goldfinches, although only the effect of cardinal abundance was statistically significant. Nevertheless, our results indicate that spatial variation in bird communities has the potential to cause geographic variation in disease prevalence in house finches.     

Specificity and seasonal prevalence of anther smut disease Microbotryum on sympatric Himalayan Silene species

Host sympatry provides opportunities for cross‐species disease transmission and compounded disease effects on host population and community structure. Using the Silene–Microbotryum interaction (the castrating anther smut disease), eleven Himalayan Silene species were assessed in regions of high host diversity to ascertain levels of pathogen specificity. We also investigated disease prevalence, seasonal dynamics of infection and flowering patterns in five co‐blooming Silene species. We identified several new Microbotryum lineages with varying degrees of specialization that is likely influenced by degrees of host divergence and ecological similarities (i.e. shared pollinator guilds). Affected species had 15%–40% of plants infected by anther smut. Flowering was seasonally overlapping among host species (except for the species pair S. asclepiadea and S. atrocastanea), but diseased flowering onset was earlier than healthy plants, leading to dramatic seasonal shifts in observed disease prevalence. Overlapping distributions and flowering provides opportunities for floral pathogen movement between host species, but host specialization may be constrained by the plant phylogenetic relatedness, adaptation to micro‐habitats and difference in pollinator/vector guilds.     

Among population variation in specialist and generalist seed predation – the importance of host plant distribution, alternative hosts and environmental variation

Pre-dispersal seed predators can have important effects on population dynamics and trait selection in their host plants. However, the factors determining spatial variation in predation intensity are poorly known. We assessed the relative importance of host plant distribution, alternative hosts and environmental factors for among-population variation in predation in a system with three host plants, a specialist and a generalist pre-dispersal seed predator.
Effects of host plant population size were relatively more important in the specialist than in the generalist seed predator. The specialist seed predator Apion opeticum , utilizing only Lathyrus vernus occurred in less than half of the patches, and specialist seed predation was influenced only by host plant population size. The generalist Bruchus atomarius was present in nearly all patches, and generalist predation was influenced by environmental factors and availability of alternative hosts. Predation on alternative hosts was not affected by L. vernus presence.
The results suggest that a wide range of factors influences the strength of plant–seed–predator interactions, and that the relative importance of different factors depend on the degree of specialization. This will result in highly complex selection mosaics and coevolutionary trajectories.     

An island paradigm on the mainland: host population fragmentation impairs the community of avian pathogens

Emergent infectious diseases represent a major threat for biodiversity in fragmented habitat networks, but their dynamics in host metapopulations remain largely unexplored. We studied a large community of pathogens (including 26 haematozoans, bacteria and viruses as determined through polymerase chain reaction assays) in a highly fragmented mainland bird metapopulation. Contrary to recent studies, which have established that the prevalence of pathogens increase with habitat fragmentation owing to crowding and habitat-edge effects, the analysed pathogen parameters were neither dependent on host densities nor related to the spatial structure of the metapopulation. We provide, to our knowledge, the first empirical evidence for a positive effect of host population size on pathogen prevalence, richness and diversity. These new insights into the interplay between habitat fragmentation and pathogens reveal properties of a host-pathogen system resembling island environments, suggesting that severe habitat loss and fragmentation could lower pathogen pressure in small populations.     

The impact of non-lethal synergists on the population and evolutionary dynamics of host-pathogen interactions

Multiple pathogenic infections can influence disease transmission and virulence, and have important consequences for understanding the community ecology and epidemiology of host-pathogen interactions. Here the population and evolutionary dynamics of a host-pathogen interaction with free-living stages are explored in the presence of a non-lethal synergist that hosts must tolerate. Through the coupled effects on pathogen transmission, host mass gain and allometry it is shown how investing in tolerance to a non-lethal synergist can lead to a broad range of different population dynamics. The effects of the synergist on pathogen fitness are explored through a series of life-history trait trade-offs. Coupling trade-offs between pathogen yield and pathogen speed of kill and the presence of a synergist favour parasites that have faster speeds of kill. This evolutionary change in pathogen characteristics is predicted to lead to stable population dynamics. Evolutionary analysis of tolerance of the synergist (strength of synergy) and lethal pathogen yield show that decreasing tolerance allows alternative pathogen strategies to invade and replace extant strategies. This evolutionary change is likely to destabilise the host-pathogen interaction leading to population cycles. Correlated trait effects between speed of kill and tolerance (strength of synergy) show how these traits can interact to affect the potential for the coexistence of multiple pathogen strategies. Understanding the consequences of these evolutionary relationships is important for the both the evolutionary and population dynamics of host-pathogen interactions.     

Ecosystem dynamics, biological diversity and emerging infectious diseases

In this article, we summarize the major scientific developments of the last decade on the transmission of infectious agents in multi-host systems. Almost sixty percent of the pathogens that have emerged in humans during the last 30-40 years are of animal origin and about sixty percent of them show an important variety of host species besides humans (3 or more possible host species). In this review, we focus on zoonotic infections with vector-borne transmission and dissect the contrasting effects that a multiplicity of host reservoirs and vectors can have on their disease dynamics. We discuss the effects exerted by host and vector species richness and composition on pathogen prevalence (i.e., reduction, including the dilution effect, or amplification). We emphasize that, in multiple host systems and for vector-borne zoonotic pathogens, host reservoir species and vector species can exert contrasting effect locally. The outcome on disease dynamics (reduced pathogen prevalence in vectors when the host reservoir species is rich and increased pathogen prevalence when the vector species richness increases) may be highly heterogeneous in both space and time. We then ask briefly how a shift towards a more systemic perspective in the study of emerging infectious diseases, which are driven by a multiplicity of hosts, may stimulate further research developments. Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective.     

Characteristics and drivers of plant virus community spatial patterns in US west coast grasslands

The spatial distribution of disease risk caused by multi‐pathogen infections is not frequently characterized, limiting understanding of the drivers of infection and thwarting prediction of future risk in a changing environment. Further complicating this predictive understanding is that interactions among multiple pathogens within a host commonly alter transmission success, infection risk, and disease dynamics. By characterizing spatial patterns of Barley and Cereal Yellow Dwarf Virus (B/CYDV) infections that range from the scale of an individual plant to thousands of neighboring plants, we examined the contributions of spatial processes to the distribution of disease risk. In a two‐year field experiment, we planted grass hosts of B/CYDVs into fertilized plots of US west coast grasslands. We determined how vector‐sharing, environmental conditions and spatial variation in host quality affected spatial patterns of single viruses, pairs of viruses and the whole virus community across out‐planted grass hosts. We found that single viruses and virus communities were spatially random, indicating that infection does not solely spread through the community in a wave‐like manner. On the other hand, we found that pairs of viruses, especially those that share a vector species, were aggregated spatially. This suggests that if within‐host competition exists, it is not strong. Aggregation in one pair of viruses was more frequent due to environmental conditions and spatial variation in out‐planted host quality, measured as vector preference. These results highlight the importance of insect vectors for predicting the spatial distribution of coinfection risk by B/CYDVs.     

Abundance,origin, and phylogeny of plants do not predict community‐level patterns of pathogen diversity and infection

Pathogens have the potential to shape plant community structure, and thus, it is important to understand the factors that determine pathogen diversity and infection in communities. The abundance, origin, and evolutionary relationships of plant hosts are all known to influence pathogen patterns and are typically studied separately. We present an observational study that examined the influence of all three factors and their interactions on the diversity of and infection of several broad taxonomic groups of foliar, floral, and stem pathogens across three sites in a temperate grassland in the central United States. Despite that pathogens are known to respond positively to increases in their host abundances in other systems, we found no relationship between host abundance and either pathogen diversity or infection. Native and exotic plants did not differ in their infection levels, but exotic plants hosted a more generalist pathogen community compared to native plants. There was no phylogenetic signal across plants in pathogen diversity or infection. The lack of evidence for a role of abundance, origin, and evolutionary relationships in shaping patterns of pathogens in our study might be explained by the high generalization and global distributions of our focal pathogen community, as well as the high diversity of our plant host community. In general, the community‐level patterns of aboveground pathogen infections have received less attention than belowground pathogens, and our results suggest that their patterns might not be explained by the same drivers.     

Forest species diversity reduces disease risk in a generalist plant pathogen invasion

Empirical evidence suggests that biodiversity loss can increase disease transmission, yet our understanding of the 'diversity-disease hypothesis' for generalist pathogens in natural ecosystems is limited. We used a landscape epidemiological approach to examine two scenarios regarding diversity effects on the emerging plant pathogen Phytophthora ramorum across a broad, heterogeneous ecoregion: (1) an amplification effect exists where disease risk is greater in areas with higher plant diversity due to the pathogen's wide host range, or (2) a dilution effect where risk is reduced with increasing diversity due to lower competency of alternative hosts. We found evidence for pathogen dilution, whereby disease risk was lower in sites with higher species diversity, after accounting for potentially confounding effects of host density and landscape heterogeneity. Our results suggest that although nearly all plants in the ecosystem are hosts, alternative hosts may dilute disease transmission by competent hosts, thereby buffering forest health from infectious disease.     

Social immunity modulates competition between coinfecting pathogens

Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.