Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium.

Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, coinfections between bacterial strains and metazoan parasites (fluke Diplostomum pseudospathaceum) and antibiotic exposure. We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to spread and long-term persistence of resistance.

Host Developmental Stage Effects on Parasite Resistance and Tolerance.

AbstractHosts can defend themselves against parasites either by preventing or limiting infections (resistance) or by limiting parasite-induced damage (tolerance). However, it remains underexplored how these defense types vary over host development with shifting patterns of resource allocation priorities. Here, we studied the role played by developmental stage in resistance and tolerance in Atlantic salmon (Salmo salar). This anadromous fish has distinct life stages related to living in freshwater and seawater. We experimentally exposed 1-year-old salmon, either at the freshwater stage or at the stage transitioning to the marine phase, to the trematode Diplostomum pseudospathaceum. Using 56 pedigreed families and multivariate animal models, we show that developmental transition is associated with reduced resistance but does not affect tolerance. Furthermore, by comparing tolerance slopes (host fitness against parasite load) based on additive genetic effects among infected and unexposed control relatives, we observed that the slopes can be largely independent of the infection, that is, they may not reflect tolerance. Together, our results suggest that the relative importance of different defense types may vary with host development and emphasize the importance of including control treatments for more confident interpretations of tolerance estimates.

Life-history genotype explains variation in migration activity in Atlantic salmon (Salmo salar).

One of the most well-known life-history continuums is the fast-slow axis, where 'fast' individuals mature earlier than 'slow' individuals. 'Fast' individuals are predicted to be more active than 'slow' individuals because high activity is required to maintain a fast life-history strategy. Recent meta-analyses revealed mixed evidence for such integration. Here, we test whether known life-history genotypes differ in activity expression by using Atlantic salmon (Salmo salar) as a model. In salmon, variation in Vgll3, a transcription cofactor, explains approximately 40% of variation in maturation timing. We predicted that the allele related to early maturation (vgll3*E) would be associated with higher activity. We used an automated surveillance system to follow approximately 1900 juveniles including both migrants and non-migrants (i.e. smolt and parr fish, respectively) in semi-natural conditions over 31 days (approx. 580 000 activity measurements). In migrants, but not in non-migrants, vgll3 explained variation in activity according to our prediction in a sex-dependent manner. Specifically, in females the vgll3*E allele was related to increasing activity, whereas in males the vgll3*L allele (later maturation allele) was related to increasing activity. These sex-dependent effects might be a mechanism maintaining within-population genetic life-history variation.

Cold water reduces the severity of parasite-inflicted damage: support for wintertime recuperation in aquatic hosts.

The reduction in host fitness caused by parasite infections (virulence) depends on infection intensity and the degree of damage caused per parasite. Environmental conditions can shape both virulence components, but in contrast to infection intensity, environmental impacts on per-parasite damage are poorly understood. Here, we studied the effect of ambient temperature on per-parasite damage, which is jointly determined by the ability of parasites to induce harm (per-parasite pathogenicity) and the ability of hosts to limit damage (tolerance). We experimentally exposed two salmonid species, Atlantic salmon (Salmo salar) and sea trout (Salmo trutta), to replicated genotypes of the eye fluke Diplostomum pseudospathaceum. After development of health damage (eye cataracts) in warm water (16 °C) during the first 12 weeks post exposure, we maintained the fish at either 5 °C (cold water) or 16 °C for another 8 weeks and quantified changes in cataracts as a function of parasite load. We found that per-parasite damage was reduced in cold compared to warm water, suggesting that cold temperatures improved host health. Per-parasite damage was also affected by parasite genotype and host species, but these effects did not change with temperature. Our findings suggest that cold-water seasons, which are often neglected in host-parasite studies due to low infection risk, could allow hosts to recuperate and thus, may have important implications for the ecology and epidemiology of parasite infections.

Negative associations between parasite avoidance, resistance and tolerance predict host health in salmonid fish populations.

Genetic variation in defence against parasite infections is fundamental for host-parasite evolution. The overall level of defence of a host individual or population includes mechanisms that reduce parasite exposure (avoidance), establishment (resistance) or pathogenicity (tolerance). However, how these traits operate and evolve in concert is not well understood. Here, we investigated genetic variation in and associations between avoidance, resistance and tolerance in a natural host-parasite system. Replicated populations of Atlantic salmon (Salmo salar) and sea trout (an anadromous form of brown trout, Salmo trutta) were raised under common garden conditions and infected with the eye fluke Diplostomum pseudospathaceum. We demonstrate significant genetic variation in the defence traits across host populations and negative associations between the traits, with the most resistant populations showing the weakest avoidance and the lowest infection tolerance. These results are suggestive of trade-offs between different components of defence and possibly underlie the genetic variation in defence traits observed in the wild. Because the three defence mechanisms affect host-parasite evolution in profoundly different ways, we emphasize the importance of studying these traits in concert.

Within-host interactions shape virulence-related traits of trematode genotypes.

Within-host interactions between co-infecting parasites can significantly influence the evolution of key parasite traits, such as virulence (pathogenicity of infection). The type of interaction is expected to predict the direction of selection, with antagonistic interactions favouring more virulent genotypes and synergistic interactions less virulent genotypes. Recently, it has been suggested that virulence can further be affected by the genetic identity of co-infecting partners (G × G interactions), complicating predictions on disease dynamics. Here, we used a natural host-parasite system including a fish host and a trematode parasite to study the effects of G × G interactions on infection virulence. We exposed rainbow trout (Oncorhynchus mykiss) either to single genotypes or to mixtures of two genotypes of the eye fluke Diplostomum pseudospathaceum and estimated parasite infectivity (linearly related to pathogenicity of infection, measured as coverage of eye cataracts) and relative cataract coverage (controlled for infectivity). We found that both traits were associated with complex G × G interactions, including both increases and decreases from single infection to co-infection, depending on the genotype combination. In particular, combinations where both genotypes had low average infectivity and relative cataract coverage in single infections benefited from co-infection, while the pattern was opposite for genotypes with higher performance. Together, our results show that infection outcomes vary considerably between single and co-infections and with the genetic identity of the co-infecting parasites. This can result in variation in parasite fitness and consequently impact evolutionary dynamics of host-parasite interactions.

Divergent parasite infections in sympatric cichlid species in Lake Victoria.

Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species-rich communities and as a driver of post-speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species at Makobe Island in Lake Victoria, a model system of vertebrate adaptive radiation. We asked whether host niche, host abundance or host genetic differentiation explains variation in infection patterns. We found significant differences in infections, the magnitude of which was weakly correlated with the extent of genomic divergence between the host species, but more strongly with the main ecological gradient, water depth. These effects were most evident with infections of Cichlidogyrus monogeneans, whereas the only host species with a strictly crevice-dwelling niche, Pundamilia pundamilia, deviated from the general negative relationship between depth and parasitism. In accordance with the Janzen-Connell hypothesis, we also found that host abundance tended to be positively associated with infections in some parasite taxa. Data on the Pundamilia sister species pairs from three other islands with variable degrees of habitat (crevice) specialization suggested that the lower parasite abundance of P. pundamilia at Makobe could result from both habitat specialization and the evolution of specific resistance. Our results support influences of host genetic differentiation and host ecology in determining infections in this diverse community of sympatric cichlid species.

Minor environmental concentrations of antibiotics can modify bacterial virulence in co-infection with a non-targeted parasite.

Leakage of medical residues into the environment can significantly impact natural communities. For example, antibiotic contamination from agriculture and aquaculture can directly influence targeted pathogens, but also other non-targeted taxa of commensals and parasites that regularly co-occur and co-infect the same host. Consequently, antibiotics could significantly alter interspecific interactions and epidemiology of the co-infecting parasite community. We studied how minor environmental concentrations of antibiotic affects the co-infection of two parasites, the bacterium Flavobacterium columnare and the fluke Diplostomum pseudospathaceum, in their fish host. We found that antibiotic in feed, and particularly the minute concentration in water, significantly decreased bacterial virulence and changed the infection success of the flukes. These effects depended on the level of antibiotic resistance of the bacterial strains. Antibiotic, however, did not compensate for the higher virulence of co-infections. Our results demonstrate that even very low environmental concentrations of antibiotic can influence ecology and epidemiology of diseases in co-infection with non-targeted parasites. Leakage of antibiotics into the environment may thus have more complex effects on disease ecology than previously anticipated.

Infection, specificity and host manipulation of Australapatemon sp. (Trematoda, Strigeidae) in two sympatric species of leeches (Hirudinea).

Factors that drive parasite specificity and differences in infection dynamics among alternative host species are important for ecology and evolution of host-parasite interactions, but still often poorly known in natural systems. Here, we investigated spatiotemporal dynamics of infection, host susceptibility and parasite-induced changes in host phenotype in a rarely explored host-parasite system, the Australapatemon sp. trematode infecting two sympatric species of freshwater leeches, Erpobdella octoculata and Helobdella stagnalis. We show significant variation in infection abundance between the host species in both space and time. Using experimental infections, we also show that most of this variation likely comes from interspecific differences in exposure rather than susceptibility. Moreover, we demonstrate that the hiding behaviour of E. octoculata, but not that of H. stagnalis, was impaired by the infection irrespective of the parasite abundance. This may increase susceptibility of E. octoculata to predation by the final avian host. We conclude that differences in patterns of infection and in behavioural alterations among alternative sympatric host species may arise in narrow spatial scales, which emphasises the importance of local infection and transmission dynamics for parasite life cycles.

Learned parasite avoidance is driven by host personality and resistance to infection in a fish-trematode interaction.

Cognitive abilities related to the assessment of risk improve survival. While earlier studies have examined the ability of animals to learn to avoid predators, learned parasite avoidance has received little interest. In a series of behavioural trials with the trematode parasite Diplostomum pseudospathaceum, we asked whether sea trout (Salmo trutta trutta) hosts show associative learning in the context of parasitism and if so, whether learning capacity is related to the likelihood of infection mediated through host personality and resistance. We show that animals are capable of learning to avoid visual cues associated with the presence of parasites. However, avoidance behaviour ceased after the likely activation of host resistance following consecutive exposures during learning, suggesting that resistance to infection outweighs avoidance. Further, we found a positive relationship between learning ability and boldness, suggesting a compensation of risky lifestyles through increased investment in cognitive abilities. By contrast, an increased risk of infection due to low resistance was not balanced by learning ability. Instead, these traits were positively related, which may be explained by inherent physiological qualities controlling both traits. Overall, the results demonstrate that parasitism, in addition to other biological interactions such as predation, is an important selective factor in the evolution of animal cognition.

Host infection history modifies co-infection success of multiple parasite genotypes.

Co-infections by multiple parasite genotypes are common and have important implications for host-parasite ecology and evolution through within-host interactions. Typically, these infections take place sequentially, and therefore, the outcome of co-infection may be shaped by host immune responses triggered by previous infections. For example, in vertebrates, specific immune responses play a central role in protection against disease over the course of life, but co-infection research has mostly focused on previously uninfected individuals. Here, we investigated whether sequential exposure and activation of host resistance in rainbow trout Oncorhynchus mykiss affects infection success and interactions between co-infecting parasite genotypes of the trematode eye-fluke Diplostomum pseudospathaceum. In accordance with earlier results, we show that a simultaneous attack of two parasite genotypes facilitates parasite establishment in previously uninfected hosts. However, we find for the first time that this facilitation in co-infection is lost in hosts with prior infection. We conclude that vertebrate host infection history can affect the direction of within-host-parasite interactions. Our results may have significant implications for the evolution of co-infections and parasite transmission strategies.

Interactions among bacterial strains and fluke genotypes shape virulence of co-infection.

Most studies of virulence of infection focus on pairwise host-parasite interactions. However, hosts are almost universally co-infected by several parasite strains and/or genotypes of the same or different species. While theory predicts that co-infection favours more virulent parasite genotypes through intensified competition for host resources, knowledge of the effects of genotype by genotype (G × G) interactions between unrelated parasite species on virulence of co-infection is limited. Here, we tested such a relationship by challenging rainbow trout with replicated bacterial strains and fluke genotypes both singly and in all possible pairwise combinations. We found that virulence (host mortality) was higher in co-infections compared with single infections. Importantly, we also found that the overall virulence was dependent on the genetic identity of the co-infecting partners so that the outcome of co-infection could not be predicted from the respective virulence of single infections. Our results imply that G × G interactions among co-infecting parasites may significantly affect host health, add to variance in parasite fitness and thus influence evolutionary dynamics and ecology of disease in unexpected ways.

Prevalence of infection as a predictor of multiple genotype infection frequency in parasites with multiple-host life cycle.

In nature, parasites commonly share hosts with other conspecific parasite genotypes. While adult parasites typically show aggregated distribution in their final hosts, aggregation of clonal parasite genotypes in intermediate hosts, such as those of trematodes in molluscs, is not generally known. However, infection of a host by multiple parasite genotypes has significant implications for evolution of virulence and host-parasite coevolution. Aggregated distribution of the clonal stages can increase host mortality and reduce larval output of each infecting genotype through interclonal competition, and therefore have significant implications for parasite epidemiology. The aim of this study was (i) to find out how common multiple genotype infections (MGIs) are in aquatic snails serving as intermediate hosts for different trematode species; (ii) to find out whether the prevalence of infection could be used to predict MGI frequencies and (iii) to use the relationship to infer whether MGIs aggregate in molluscan hosts. We determined the prevalence of trematode (Diplostomum pseudospathaceum) infections and the frequency of MGIs in snail (Lymnaea stagnalis) host populations as well as compiled corresponding literature data from a range of snail-trematode systems. We used Bayesian simulations to explore the relationship between prevalence of infection and MGI frequency in these data, and tested whether genotypes aggregate in snails by comparing the simulated relations with null model (Poisson and demographic Poisson) expectations. Our results show that MGIs are common in aquatic snails with up to 90% of the infected snails carrying MGIs. Parasite prevalence is a good predictor of MGI frequencies at a range of prevailing natural prevalences of infection (0-50%). The frequency of MGIs was higher than expected by both null models, indicating parasite aggregation at genotype level. These findings are in sharp contrast with the absence of multiple infections in snails at level of trematode species, suggesting that co-infections by multiple species and multiple genotypes of one species are controlled by different biological processes. Aggregation of MGIs in snail hosts appears to be widespread across different snail-trematode systems.

Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty.

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H2 ']) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co-occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host-parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%-10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

Reciprocal interaction matrix reveals complex genetic and dose-dependent specificity among coinfecting parasites.

Understanding genetic specificity in factors determining the outcome of host-parasite interactions is especially important as it contributes to parasite epidemiology, virulence, and maintenance of genetic variation. Such specificity, however, is still generally poorly understood. We examined genetic specificity in interactions among coinfecting parasites. In natural populations, individual hosts are often simultaneously infected by multiple parasite species and genotypes that interact. Such interactions could maintain genetic variation in parasite populations if they are genetically specific so that the relative fitness of parasite genotypes varies across host individuals depending on (1) the presence/absence of coinfections and/or (2) the genetic composition of the coinfecting parasite community. We tested these predictions using clones of fish eye flukes Diplostomum pseudospathaceum and Diplostomum gasterostei. We found that interactions among parasites had a strong genetic basis and that this modified genetic variation in infection success of D. pseudospathaceum between single and multiple infections as well as across multiply infected host individuals depending on the genetic identity of the coinfecting D. gasterostei. The relative magnitude of these effects, however, depended on the exposure dose, suggesting that ecological factors can modify genetic interactions between parasites.

Synchronous attack is advantageous: mixed genotype infections lead to higher infection success in trematode parasites.

Co-infecting parasite genotypes typically compete for host resources limiting their fitness. The intensity of such competition depends on whether parasites are reproducing in a host, or using it primarily as a transmission vehicle while not multiplying in host tissues (referred to as 'competition hypothesis'). Alternatively, simultaneous attack and co-infection by several parasite genotypes might facilitate parasite infection because such a diverse attack could present an additional challenge to host immune defence (referred to as 'facilitation hypothesis'). We tested the competition hypothesis by comparing the production of transmission stages (cercariae) from snails infected with one or two genotypes of the trematode Diplostomum pseudospathaceum. We found that cercarial production did not differ between the two groups of snails, suggesting lower per genotype production in double infections, and competition for host resources. Second, we tested the facilitation hypothesis by comparing parasite infection success on fishes (proportion of parasites establishing in the host) using cercariae originating from single-infected snails, double-infected snails and artificial mixtures of the single genotypes. In both cases, we found higher infection success when fishes were challenged with two parasite genotypes instead of one, supporting the facilitation hypothesis. Our results suggest that constraints defining the success of multiple genotype infections in parasites with multiple host life cycles include both between-genotype resource competition in the host and performance of host immune defences against a diverse parasite challenge.

Variation in parasite resistance of Arctic charr, Salvelinus alpinus, between and within sympatric morphs.

Genetic variation in resistance against parasite infections is a predominant feature in host-parasite systems. However, mechanisms maintaining genetic polymorphism in resistance in natural host populations are generally poorly known. We explored whether differences in natural infection pressure between resource-based morphs of Arctic charr (Salvelinus alpinus) have resulted in differentiation in resistance profiles. We experimentally exposed offspring of two morphs from Lake Þingvallavatn (Iceland), the pelagic planktivorous charr ("murta") and the large benthivorous charr ("kuðungableikja"), to their common parasite, eye fluke Diplostomum baeri, infecting the eye humor. We found that there were no differences in resistance between the morphs, but clear differences among families within each morph. Moreover, we found suggestive evidence of resistance of offspring within families being positively correlated with the parasite load of the father, but not with that of the mother. Our results suggest that the inherited basis of parasite resistance in this system is likely to be related to variation among host individuals within each morph rather than ecological factors driving divergent resistance profiles at morph level. Overall, this may have implications for evolution of resistance through processes such as sexual selection.

Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics.

Environmental heterogeneity is a central component influencing the virulence and epidemiology of infectious diseases. The number and distribution of susceptible hosts determines disease transmission opportunities, shifting the epidemiological threshold between the spread and fadeout of a disease. Similarly, the presence and diversity of other hosts, pathogens and environmental microbes, may inhibit or accelerate an epidemic. This has important applied implications in farming environments, where high numbers of susceptible hosts are maintained in conditions of minimal environmental heterogeneity. We investigated how the quantity and quality of aquaculture enrichments (few vs. many stones; clean stones vs. stones conditioned in lake water) influenced the severity of infection of a pathogenic bacterium, Flavobacterium columnare, in salmonid fishes. We found that the conditioning of the stones significantly increased host survival in rearing tanks with few stones. A similar effect of increased host survival was also observed with a higher number of unconditioned stones. These results suggest that a simple increase in the heterogeneity of aquaculture environment can significantly reduce the impact of diseases, most likely operating through a reduction in pathogen transmission (stone quantity) and the formation of beneficial microbial communities (stone quality). This supports enriched rearing as an ecological and economic way to prevent bacterial infections with the minimal use of antimicrobials.

Interactions among co-infecting parasite species: a mechanism maintaining genetic variation in parasites?

Individuals of free-living organisms are often infected simultaneously by a community of parasites. If the co-infecting parasites interact, then this can add significantly to the diversity of host genotypexparasite genotype interactions. However, interactions between parasite species are usually not examined considering potential variation in interactions between different strain combinations of co-infecting parasites. Here, we examined the importance of interactions between strains of fish eye flukes Diplostomum spathaceum and Diplostomum gasterostei on their infectivity in naive fish hosts. We assessed the infection success of strains of both species in single-strain exposures and in co-exposures with a random strain of the other species. Parasite infection success did not consistently increase or decrease in the co-exposure treatment, but depended on the combinations of co-infecting parasite strains. This disrupted the relative infectivity of D. spathaceum strains observed in single-strain exposures. The infection success of D. gasterostei strains was independent of exposure type. These results suggest that interactions among parasite species may be strain specific and potentially promote maintenance of genetic polymorphism in parasite populations.

Host immunization shapes interspecific associations in trematode parasites.

1. Individuals of free-living organisms are commonly infected by multiple parasite species. Under such circumstances, positive or negative associations between the species are possible because of direct or indirect interactions, details in parasite transmission ecology and host-mediated factors. One possible mechanism underlying these processes is host immunity, but its role in shaping these associations has rarely been tackled experimentally. 2. In this study, we tested the effect of host immunization on associations between trematode parasites infecting eyes of fish. We first analysed the associations between three species (Diplostomum spathaceum, Diplostomum gasterostei and Tylodelphys clavata) in wild hosts, roach (Rutilus rutilus) and perch (Perca fluviatilis). Second, using rainbow trout (Oncorhynchus mykiss) as a model fish species, we experimentally investigated how sequential immunization of the host (i.e. one parasite species infects and immunizes the host first) could affect the associations between two of the species. 3. The results indicated that most of the associations were positive in wild hosts, which supports between-individual variation in host susceptibility, rather than competitive exclusion between the parasite species. However, positive associations were more common in roach than in perch, possibly reflecting differences in ecological conditions of exposure between the host species. The experimental data showed that positive associations between two of the species were eroded by host immunization against one of the parasite species. 4. We conclude that sequential immunization of hosts has a marked effect on interspecific parasite associations and basically can determine if positive associations are detected or not. This implies that correlative results suggesting non-interactive community structure in general may be obscured by the sequence of previous parasite exposure and corresponding dynamics of host immunization.