The evolution of resistance against good and bad infections

Opportunities for genetic exchange are abundant between bacteria and foreign genetic elements (FGEs) such as conjugative plasmids, transposable elements and bacteriophages. The genetic novelty that may arise from these forms of genetic exchange is potentially beneficial to bacterial hosts, but there are also potential costs, which may be considerable in the case of phage infection. Some bacterial resistance mechanisms target both beneficial and deleterious forms of genetic exchange. Using a general epidemiological model, we explored under which conditions such resistance mechanisms may evolve. We considered a population of hosts that may be infected by FGEs that either confer a benefit or are deleterious to host fitness, and we analysed the epidemiological and evolutionary outcomes of resistance evolving under different cost/benefit scenarios. We show that the degree of co‐infection between these two types of infection is particularly important in determining the evolutionarily stable level of host resistance. We explore these results using the example of CRISPR‐Cas, a form of bacterial immunity that targets a variety of FGEs, and we show the potential role of bacteriophage infection in selecting for resistance mechanisms that in turn limit the acquisition of plasmid‐borne antibiotic resistance. Finally, beyond microbes, we discuss how endosymbiotic associations may have shaped the evolution of host immune responses to pathogens.     

Costs of resistance and infection by a generalist pathogen

Pathogen infection is typically costly to hosts, resulting in reduced fitness. However, pathogen exposure may also come at a cost even if the host does not become infected. These fitness reductions, referred to as “resistance costs”, are inducible physiological costs expressed as a result of a trade‐off between resistance to a pathogen and aspects of host fitness (e.g., reproduction). Here, we examine resistance and infection costs of a generalist fungal pathogen (Metschnikowia bicuspidata) capable of infecting a number of host species. Costs were quantified as reductions in host lifespan, total reproduction, and mean clutch size as a function of pathogen exposure (resistance cost) or infection (infection cost). We provide empirical support for infection costs and modest support for resistance costs for five Daphnia host species. Specifically, only one host species examined incurred a significant cost of resistance. This species was the least susceptible to infection, suggesting the possibility that host susceptibility to infection is associated with the detectability and size of resistance cost. Host age at the time of pathogen exposure did not influence the magnitude of resistance or infection cost. Lastly, resistant hosts had fitness values intermediate between unexposed control hosts and infected hosts. Although not statistically significant, this could suggest that pathogen exposure does come at some marginal cost. Taken together, our findings suggest that infection is costly, resistance costs may simply be difficult to detect, and the magnitude of resistance cost may vary among host species as a result of host life history or susceptibility.     

THE COEVOLUTIONARY IMPLICATIONS OF HOST TOLERANCE

Host tolerance to infectious disease, whereby hosts do not directly “fight” parasites but instead ameliorate the damage caused, is an important defense mechanism in both plants and animals. Because tolerance to parasite virulence may lead to higher prevalence of disease in a population, evolutionary theory tells us that while the spread of resistance genes will result in negative frequency dependence and the potential for diversification, the evolution of tolerance is instead likely to result in fixation. However, our understanding of the broader implications of tolerance is limited by a lack of fully coevolutionary theory. Here we examine the coevolution of tolerance across a comprehensive range of classic coevolutionary host–parasite frameworks, including equivalents of gene‐for‐gene and matching allele and evolutionary invasion models. Our models show that the coevolution of host tolerance and parasite virulence does not lead to the generation and maintenance of diversity through either static polymorphisms or through “Red‐queen” cycles. Coevolution of tolerance may however lead to multiple stable states leading to sudden shifts in parasite impacts on host health. More broadly, we emphasize that tolerance may change host–parasite interactions from antagonistic to a form of “apparent commensalism,” but may also lead to the evolution of parasites that are highly virulent in nontolerant hosts.     

THE ORIGIN OF SPECIFICITY BY MEANS OF NATURAL SELECTION: EVOLVED AND NONHOST RESISTANCE IN HOST–PATHOGEN INTERACTIONS

Most species seem to be completely resistant to most pathogens and parasites. This resistance has been called “nonhost resistance” because it is exhibited by species that are considered not to be part of the normal host range of the pathogen. A conceptual model is presented suggesting that failure of infection on nonhosts may be an incidental by‐product of pathogen evolution leading to specialization on their source hosts. This model is contrasted with resistance that results from hosts evolving to resist challenge by their pathogens, either as a result of coevolution with a persistent pathogen or as the result of one‐sided evolution by the host against pathogens that are not self‐sustaining on those hosts. Distinguishing evolved from nonevolved resistance leads to contrasting predictions regarding the relationship between resistance and genetic distance. An analysis of cross‐inoculation experiments suggests that the resistance is often the product of pathogen specialization. Understanding the contrasting evolutionary origins of resistance is critical for studies on the genetics and evolution of host–pathogen interactions in human, agricultural, and natural populations. Research on human infectious disease using animal models may often study resistances that have quite contrasting evolutionary origins, and therefore very different underlying genetic mechanisms.     

Evolution of parasite virulence against qualitative or quantitative host resistance

We analysed the effects of two different modes of host resistance on the evolution of parasite virulence. Hosts can either adopt an all-or-nothing qualitative response (i.e. resistant hosts cannot be infected) or a quantitative form of resistance (i.e. which reduces the within-host growth rate of the parasite). We show that the mode of host resistance greatly affects the evolutionary outcome. Specifically, a qualitative form of resistance reduces parasite virulence, while a quantitative form of resistance generally selects for higher virulence.     

Population genetics of Schistosoma haematobium: development of novel microsatellite markers and their application to schistosomiasis control in Mali

The recent implementation of mass drug administration (MDA) for control of uro-genital schistosomiasis has identified an urgent need for molecular markers to both directly monitor the impact of MDA, for example to distinguish re-infections from uncleared infections, as well as understand aspects of parasite reproduction and gene flow which might predict evolutionary change, such as the development and spread of drug resistance. We report the development of a novel microsatellite tool-kit allowing, for the first time, robust genetic analysis of individual S. haematobium larvae collected directly from infected human hosts. We genotyped the parasite populations of 47 children from 2 schools in the Ségou region of Mali, the first microsatellite study of this highly neglected parasite. There was only limited evidence of population subdivision between individual children or between the two schools, suggesting that few barriers to gene flow exist in this population. Complex relationships between parasite reproductive success, infection intensity and host age and gender were identified. Older children and boys harboured more diverse infections, as measured by the number of unique adult genotypes present. Individual parasite genotypes had variable reproductive success both across hosts, a pre-requisite for evolutionary selection, and, phenotypically, in hosts of different ages and genders. These data serve as a baseline against which to measure the effect of treatment on parasite population genetics in this region of Mali, and the tools developed are suitable to further investigate this important pathogen, and its close relatives, throughout their range.     

Vector preference and host defense against infection interact to determine disease dynamics

Vector preference based on host infection status has long been recognized for its importance in disease dynamics. Prior theoretical work has assumed that all hosts are uniformly susceptible to the pathogen. Here we investigated disease dynamics when this assumption is relaxed using a series of vector–host epidemiological compartment models with variable levels of host resistance or tolerance to infection – collectively termed defense. In our models, vectors cannot acquire the infection from resistant hosts but can acquire from tolerant hosts. Specifically, we investigated the interacting effects of vector preference and host defense in a series of single‐ and two‐patch models. Results indicate that resistant host types generally reduce disease prevalence and pathogen spillover, independent of vector preference. The epidemiological consequences of host tolerance, however, depended on vector preference. When vectors preferred diseased hosts, tolerance reduced incidence compared to susceptible hosts; when vectors avoided diseased hosts, tolerance enhanced disease prevalence. Finally, a variation of the model that included preference‐based vector patch leaving rates suggests that both resistance and tolerance can promote pathogen spillover if vectors prefer diseased hosts, because of increased vector dispersal into susceptible patches. Collectively, we found complex, context‐dependent effects of vector preference and host defense on disease dynamics. In the context of management programs for vector‐borne diseases, managers should consider both the precise form of host defense present in a population, breed, or cultivar, as well as vector feeding behavior.     

Genotype and diet affect resistance,survival, and fecundity but not fecundity tolerance

Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild‐type Drosophila melanogaster genotypes were kept on high‐ or low‐protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual‐level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency‐dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.     

Host life span and the evolution of resistance characteristics

There is a wide variety of resistance mechanisms that hosts may evolve in response to their parasites. These can be functionally classified as avoidance (lower probability of becoming infected), recovery (faster rate of clearance), tolerance (reduced death rate when infected), or acquired immunity. It is commonly thought that longer lived organisms should invest more in costly resistance. We show that due to epidemiological feedbacks the situation is often more complex. Using evolutionary theory we examine how the optimal investment in costly resistance varies with life span in a broad range of scenarios. In the absence of acquired immunity, longer lived populations do generally invest more in resistance. If hosts have acquired immunity, the optimal resistance may either increase or decrease with increasing life span. In addition, there may be evolutionary bistability with high and low investments in avoidance or tolerance. The optimal investment in the duration of acquired immunity always increases with life span, and due to bistability, shorter lived hosts may commonly not evolve any immunity. In contrast, the optimal investment in the probability of acquiring immunity initially increases and then decreases with life span. Our results have important implications for the evolution of invertebrate and vertebrate immunity, and for the evolution of acquired immunity itself.     

The evolution of acceptance and tolerance in hosts of avian brood parasites

Avian brood parasites lay their eggs in the nests of their hosts, which rear the parasite's progeny. The costs of parasitism have selected for the evolution of defence strategies in many host species. Most research has focused on resistance strategies, where hosts minimize the number of successful parasitism events using defences such as mobbing of adult brood parasites or rejection of parasite eggs. However, many hosts do not exhibit resistance. Here we explore why some hosts accept parasite eggs in their nests and how this is related to the virulence of the parasite. We also explore the extent to which acceptance of parasites can be explained by the evolution of tolerance; a strategy in which the host accepts the parasite but adjusts its life history or other traits to minimize the costs of parasitism. We review examples of tolerance in hosts of brood parasites (such as modifications to clutch size and multi‐broodedness), and utilize the literature on host–pathogen interactions and plant herbivory to analyse the prevalence of each type of defence (tolerance or resistance) and their evolution. We conclude that (i) the interactions between brood parasites and their hosts provide a highly tractable system for studying the evolution of tolerance, (ii) studies of host defences against brood parasites should investigate both resistance and tolerance, and (iii) tolerance and resistance can lead to contrasting evolutionary scenarios.     

The genetic architecture of defence as resistance to and tolerance of bacterial infection in Drosophila melanogaster

Defence against pathogenic infection can take two forms: resistance and tolerance. Resistance is the ability of the host to limit a pathogen burden, whereas tolerance is the ability to limit the negative consequences of infection at a given level of infection intensity. Evolutionarily, a tolerance strategy that is independent of resistance could allow the host to avoid mounting a costly immune response and, theoretically, to avoid a co‐evolutionary arms race between pathogen virulence and host resistance. Biomedically, understanding the mechanisms of tolerance and how they relate to resistance could potentially yield treatment strategies that focus on health improvement instead of pathogen elimination. To understand the impact of tolerance on host defence and identify genetic variants that determine host tolerance, we defined genetic variation in tolerance as the residual deviation from a binomial regression of fitness under infection against infection intensity. We then performed a genomewide association study to map the genetic basis of variation in resistance to and tolerance of infection by the bacterium Providencia rettgeri. We found a positive genetic correlation between resistance and tolerance, and we demonstrated that the level of resistance is highly predictive of tolerance. We identified 30 loci that predict tolerance, many of which are in genes involved in the regulation of immunity and metabolism. We used RNAi to confirm that a subset of mapped genes have a role in defence, including putative wound repair genes grainy head and debris buster. Our results indicate that tolerance is not an independent strategy from resistance, but that defence arises from a collection of physiological processes intertwined with canonical immunity and resistance.     

Transmission rates and adaptive evolution of pathogens in sympatric heterogeneous plant populations

Diversification in agricultural cropping patterns is widely practised to delay the build-up of virulent races that can overcome host resistance in pathogen populations. This can lead to balanced polymorphism, but the long-term consequences of this strategy for the evolution of crop pathogen populations are still unclear. The widespread occurrence of sibling species and reproductively isolated sub-species among fungal and oomycete plant pathogens suggests that evolutionary divergence is common. This paper develops a mathematical model of host-pathogen interactions using a simple framework of two hosts to analyse the influences of sympatric host heterogeneity on the long-term evolutionary behaviour of plant pathogens. Using adaptive dynamics, which assumes that sequential mutations induce small changes in pathogen fitness, we show that evolutionary outcomes strongly depend on the shape of the trade-off curve between pathogen transmission on sympatric hosts. In particular, we determine the conditions under which the evolutionary branching of a monomorphic into a dimorphic population occurs, as well as the conditions that lead to the evolution of specialist (single host range) or generalist (multiple host range) pathogen populations.     

Temporal patterns of genetic variation for resistance and infectivity in a Daphnia-microparasite system

Theoretical studies have indicated that the population genetics of host-parasite interactions may be highly dynamic. with parasites perpetually adapting to common host genotypes and hosts evolving resistance to common parasite genotypes. The present study examined temporal variation in resistance of hosts and infectivity of parasites within three populations of Daphnia magna infected with the sterilizing bacterium Pasteuria ramosa. Parasite isolates and host clones were collected in each of two years (1997, 1998) from one population; in two other populations, hosts were collected from both years, but parasites from only the first year. We then performed infection experiments (separately for each population) that exposed hosts to parasites from the same year or made combinations involving hosts and parasites from different years. In two populations, patterns were consistent with the evolution of host resistance: either infectivity or the speed with which parasites sterilized hosts declined from 1997 to 1998. In another population, infectivity, virulence, and parasite spore production did not vary among host-year or parasite-year. For this population, we also detected strong within-population genetic variation for resistance. Thus, in this case, genetic variability for fitness-related traits apparently did not translate into evolutionary change. We discuss a number of reasons why genetic change may not occur as expected in parasite-host systems, including negative correlations between resistance and other traits, gene flow, or that the dynamic process itself may obscure the detection of gene frequency changes.     

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.     

Species coexistence and pathogens with frequency-dependent transmission

Pathogens that infect multiple hosts are commonly transmitted by vectors, and their transmission rate is often thought to depend on the proportion of hosts or vectors infected (i.e., frequency dependence). A model of a two-host, one-pathogen system with frequency-dependent transmission is used to investigate how sharing a pathogen with an alternative host influences pathogen-mediated extinction. The results show that if there is frequency-dependent transmission, a host can be rescued from pathogen-mediated extinction by the presence of a second host with which it shares a pathogen. The study provides an important conceptual counterexample to the idea that shared pathogens necessarily result in apparent competition by showing that shared pathogens can mediate apparent mutualism. We distinguish two types of dilution effect (pathogen reduction with increasing host diversity), each resulting from different underlying pathogen transmission processes and host density effects. These results have important consequences for understanding the role of pathogens in species interactions and in maintaining host species diversity.     

Disease evolution across a range of spatio-temporal scales

Traditional explorations of infectious disease evolution have considered the competition between two cross-reactive strains within the standard framework of disease models. Such techniques predict that diseases should evolve to be highly transmissible, benign to the host and possess a long infectious period: in general, diseases do not conform to this ideal. Here we consider a more holistic approach, suggesting that evolution is a trade-off between adaptive pressures at different scales: within host, between hosts and at the population level. We present a model combining within-host pathogen dynamics and transmission between individuals governed by an explicit contact network, where transmission dynamics between hosts are a function of the interaction between the pathogen and the hosts' immune system, though ultimately constrained by the contacts each infected host possesses. Our results show how each of the scales places constraints on the evolutionary behavior, and that complex dynamics may emerge due to the feedbacks between epidemiological and evolutionary dynamics. In particular, multiple stable states can occur with switching between them stochastically driven.     

Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies

Host resistance to parasites can come in two main forms: hosts may either reduce the probability of parasite infection (anti-infection resistance) or reduce parasite growth after infection has occurred (anti-growth resistance). Both resistance mechanisms are often imperfect, meaning that they do not fully prevent or clear infections. Theoretical work has suggested that imperfect anti-growth resistance can select for higher parasite virulence by favouring faster-growing and more virulent parasites that overcome this resistance. In contrast, imperfect anti-infection resistance is thought not to select for increased parasite virulence, because it is assumed that it reduces the number of hosts that become infected, but not the fitness of parasites in successfully infected hosts. Here, we develop a theoretical model to show that anti-infection resistance can in fact select for higher virulence when such resistance reduces the effective parasite dose that enters a host. Our model is based on a monarch butterfly-parasite system in which larval food plants confer resistance to the monarch host. We carried out an experiment and showed that this environmental resistance is most likely a form of anti-infection resistance, through which toxic food plants reduce the effective dose of parasites that initiates an infection. We used these results to build a mathematical model to investigate the evolutionary consequences of food plant-induced resistance. Our model shows that when the effective infectious dose is reduced, parasites can compensate by evolving a higher per-parasite growth rate, and consequently a higher intrinsic virulence. Our results are relevant to many insect host-parasite systems, in which larval food plants often confer imperfect anti-infection resistance. Our results also suggest that - for parasites where the infectious dose affects the within-host dynamics - vaccines that reduce the effective infectious dose can select for increased parasite virulence.     

Specific resistance prevents the evolution of general resistance and facilitates disease emergence

Host-shifts, where pathogens jump from an ancestral host to a novel host, can be facilitated or impeded by standing variation in disease resistance, but only if resistance provides broad-spectrum general resistance against multiple pathogen species. Host resistance comes in many forms and includes both general resistance, as well as specific resistance, which may only be effective against a single pathogen species or even genotype. However, most evolutionary models consider only one of these forms of resistance, and we have less understanding of how these two forms of resistance evolve in tandem. Here, we develop a model that allows for the joint evolution of specific and general resistance and asks if the evolution of specific resistance drives a decrease in the evolution of general resistance. We also explore how these evolutionary outcomes affect the risk of foreign pathogen invasion and persistence. We show that in the presence of a single endemic pathogen, the two forms of resistance are strongly exclusionary. Critically, we find that specific resistance polymorphisms can prevent the evolution of general resistance, facilitating the invasion of foreign pathogens. We also show that specific resistance polymorphisms are a necessary condition for the successful establishment of foreign pathogens following invasion, as they prevent the exclusion of the foreign pathogen by the more transmissible endemic pathogen. Our results demonstrate the importance of considering the joint evolution of multiple forms of resistance when evaluating a population's susceptibility to foreign pathogens.     

Cuckoos versus hosts in insects and birds: adaptations,counter‐adaptations and outcomes

Avian parents and social insect colonies are victimized by interspecific brood parasites—cheats that procure costly care for their dependent offspring by leaving them in another species' nursery. Birds and insects defend themselves from attack by brood parasites; their defences in turn select counter‐strategies in the parasite, thus setting in motion antagonistic co‐evolution between the two parties. Despite their considerable taxonomic disparity, here we show striking parallels in the way that co‐evolution between brood parasites and their hosts proceeds in insects and birds. First, we identify five types of co‐evolutionary arms race from the empirical literature, which are common to both systems. These are: (a) directional co‐evolution of weaponry and armoury; (b) furtiveness in the parasite countered by strategies in the host to expose the parasite; (c) specialist parasites mimicking hosts who escape by diversifying their genetic signatures; (d) generalist parasites mimicking hosts who escape by favouring signatures that force specialization in the parasite; and (e) parasites using crypsis to evade recognition by hosts who then simplify their signatures to make the parasite more detectable. Arms races a and c are well characterized in the theoretical literature on co‐evolution, but the other types have received little or no formal theoretical attention. Empirical work suggests that hosts are doomed to lose arms races b and e to the parasite, in the sense that parasites typically evade host defences and successfully parasitize the nest. Nevertheless hosts may win when the co‐evolutionary trajectory follows arms race a, c or d. Next, we show that there are four common outcomes of the co‐evolutionary arms race for hosts. These are: (1) successful resistance; (2) the evolution of defence portfolios (or multiple lines of resistance); (3) acceptance of the parasite; and (4) tolerance of the parasite. The particular outcome is not determined by the type of preceding arms race but depends more on whether hosts or parasites control the co‐evolutionary trajectory: tolerance is an outcome that parasites inflict on hosts, whereas the other three outcomes are more dependent on properties intrinsic to the host species. Finally, our review highlights considerable interspecific variation in the complexity and depth of host defence portfolios. Whether this variation is adaptive or merely reflects evolutionary lag is unclear. We propose an adaptive explanation, which centres on the relative strength of two opposing processes: strategy‐facilitation, in which one line of host defence promotes the evolution of another form of resistance, and strategy‐blocking, in which one line of defence may relax selection on another so completely that it causes it to decay. We suggest that when strategy‐facilitation outweighs strategy‐blocking, hosts will possess complex defence portfolios and we identify selective conditions in which this is likely to be the case.     

Parasite spread in experimental metapopulations: resistance,tolerance and host competence

Host competence, defined as the likelihood that a host will transmit infection, may be affected by an individual's resistance to infection and its ability to withstand damage caused by infection (tolerance). Host competence may therefore be one of the most important factors to impact host–parasite dynamics, yet the relationships among resistance, tolerance and competence are poorly understood. The objective of the present study was to determine whether individual host resistance (ability to resist or minimize infection) and/or tolerance (ability to withstand or minimize reduction in fitness due to infection) contributed to the competence (ability to spread infection) of hosts using guppies infected with the ectoparasite, Gyrodactylus turnbulli. This individual-fish level analysis used data collected from a previous metapopulation experiment that had tracked host–parasite dynamics at the metapopulation scale using individually marked guppies that were moved among experimental tanks within replicate metapopulations. Fish tolerance was measured as the residual from a fish's expected survival post-infection for a given parasite burden. Fish resistance was measured as the peak parasite load (– log-transformed). Host competence was measured as the incidence (number of new infections over two days after the arrival of a fish to a tank) weighted by the density of available uninfected fish in the tank. In contrast to the assumption of a trade-off between resistance and tolerance, individual fish tolerance and resistance were both negatively associated with competence. Connectivity (the number of fish with which an individual came into contact) was not associated with competence. Our results indicate that resistance and tolerance are both important to disease spread. These findings highlight the importance of understanding how individual defence against parasites may contribute to its competence as a host, and therefore impact metapopulation-level dynamics.