Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in Pseudomonas aeruginosa

The idea that interactions between mutations influence adaptation by driving populations to low and high fitness peaks on adaptive landscapes is deeply ingrained in evolutionary theory. Here, we investigate the impact of epistasis on evolvability by challenging populations of two Pseudomonas aeruginosa clones bearing different initial mutations (in rpoB conferring rifampicin resistance, and the type IV pili gene network) to adaptation to a medium containing l ‐serine as the sole carbon source. Despite being initially indistinguishable in fitness, populations founded by the two ancestral genotypes reached different fitness following 300 generations of evolution. Genome sequencing revealed that the difference could not be explained by acquiring mutations in different targets of selection; the majority of clones from both ancestors converged on one of the following two strategies: (1) acquiring mutations in either PA2449 (gcsR, an l ‐serine‐metabolism RpoN enhancer binding protein) or (2) protease genes. Additionally, populations from both ancestors converged on loss‐of‐function mutations in the type IV pili gene network, either due to ancestral or acquired mutations. No compensatory or reversion mutations were observed in RNA polymerase (RNAP) genes, in spite of the large fitness costs typically associated with mutations in rpoB. Although current theory points to sign epistasis as the dominant constraint on evolvability, these results suggest that the role of magnitude epistasis in constraining evolvability may be underappreciated. The contribution of magnitude epistasis is likely to be greatest under the biologically relevant mutation supply rates that make back mutations probabilistically unlikely.     

Epistasis buffers the fitness effects of rifampicin- resistance mutations in Pseudomonas aeruginosa

Epistatic interactions between resistance mutations in antibiotic-free environments potentially play a crucial role in the spread of resistance in pathogen populations by determining the fitness cost associated with resistance. We used an experimental evolution approach to test for epistatic interactions between 14 different pairs of rifampicin mutations in the pathogenic bacterium Pseudomonas aeruginosa in 42 different rifampicin-free environments. First, we show that epistasis between rifampicin-resistance mutations tends to be antagonistic: the fitness effect of having two mutations is generally smaller than that predicted from the effects of individual mutations on the wild-type. Second, we show that sign epistasis between resistance mutations is both common and strong; most notably, pairs of deleterious resistance mutations often partially or completely compensate for each others' costs, revealing a novel mechanism for compensatory adaptation. These results suggest that antagonistic epistasis between intragenic resistance mutations may be a key determinant of the cost of antibiotic resistance and compensatory adaptation in pathogen populations.     

AMELIORATION OF THE DELETERIOUS PLEIOTROPIC EFFECTS OF AN ADAPTIVE MUTATION IN BACILLUS SUBTILIS

The deleterious pleiotropic effects of an adaptive mutation may be ameliorated by one of two modes of evolution: (1) by replacement, in which an adaptive mutation with harmful pleiotropic effects is replaced by one that confers an equal benefit but at less cost; or (2) by compensatory evolution, in which natural selection favors modifiers at other loci that compensate for the deleterious effects of the mutant allele. In this study, we have measured the potential of these two modes of evolution to ameliorate the deleterious pleiotropic effects of resistance to the antibiotic rifampicin in the soil bacterium Bacillus subtilis. One approach was to measure the fitness cost of a series of spontaneous rifampicin-resistance mutations from each of several strains. The potential for amelioration by the replacement mode was estimated by the variation in fitness cost among the mutants of a single strain. Another approach was to introduce a series of different rifampicin-resistance alleles into a diversity of strains, and to measure the fitness cost of rifampicin resistance for each allele-by-strain combination. The potential for amelioration by the replacement mode was estimated by the variation in fitness costs among rifampicin-resistance alleles; the potential for compensatory evolution was estimated by variation in the fitness cost of rifampicin resistance among strains. This study has shown that the cost of rifampicin resistance may be ameliorated by both the compensatory and replacement modes.     

Environmental variation alters the fitness effects of rifampicin resistance mutations in Pseudomonas aeruginosa

The fitness effects of antibiotic resistance mutations in antibiotic‐free conditions play a key role in determining the long‐term maintenance of resistance. Although resistance is usually associated with a cost, the impact of environmental variation on the cost of resistance is poorly understood. Here, we test the impact of heterogeneity in temperature and resource availability on the fitness effects of antibiotic resistance using strains of the pathogenic bacterium Pseudomonas aeruginosa carrying clinically important rifampicin resistance mutations. Although the rank order of fitness was generally maintained across environments, fitness effects relative to the wild type differed significantly. Changes in temperature had a profound impact on the fitness effects of resistance, whereas changes in carbon substrate had only a weak impact. This suggests that environmental heterogeneity may influence whether the costs of resistance are likely to be ameliorated by second‐site compensatory mutations or by reversion to wild‐type rpoB. Our results highlight the need to consider environmental heterogeneity and genotype‐by‐environment interactions for fitness in models of resistance evolution.     

Fitness landscapes emerging from pharmacodynamic functions in the evolution of multidrug resistance

Adaptive evolution often involves beneficial mutations at more than one locus. In this case, the trajectory and rate of adaptation is determined by the underlying fitness landscape, that is, the fitness values and mutational connectivity of all genotypes under consideration. Drug resistance, especially resistance to multiple drugs simultaneously, is also often conferred by mutations at several loci so that the concept of fitness landscapes becomes important. However, fitness landscapes underlying drug resistance are not static but dependent on drug concentrations, which means they are influenced by the pharmacodynamics of the drugs administered. Here, I present a mathematical framework for fitness landscapes of multidrug resistance based on Hill functions describing how drug concentrations affect fitness. I demonstrate that these ‘pharmacodynamic fitness landscapes’ are characterized by pervasive epistasis that arises through (i) fitness costs of resistance (even when these costs are additive), (ii) nonspecificity of resistance mutations to drugs, in particular cross‐resistance, and (iii) drug interactions (both synergistic and antagonistic). In the latter case, reciprocal drug suppression may even lead to reciprocal sign epistasis, so that the doubly resistant genotype occupies a local fitness peak that may be difficult to access by evolution. Simulations exploring the evolutionary dynamics on some pharmacodynamic fitness landscapes with both constant and changing drug concentrations confirm the crucial role of epistasis in determining the rate of multidrug resistance evolution.     

Genotype‐by‐environment interactions due to antibiotic resistance and adaptation in Escherichia coli

Mutations that are beneficial in one environment can have different fitness effects in other environments. In the context of antibiotic resistance, the resulting genotype‐by‐environment interactions potentially make selection on resistance unpredictable in heterogeneous environments. Furthermore, resistant bacteria frequently fix additional mutations during evolution in the absence of antibiotics. How do these two types of mutations interact to determine the bacterial phenotype across different environments? To address this, I used Escherichia coli as a model system, measuring the effects of nine different rifampicin resistance mutations on bacterial growth in 31 antibiotic‐free environments. I did this both before and after approximately 200 generations of experimental evolution in antibiotic‐free conditions (LB medium), and did the same for the antibiotic‐sensitive wild type after adaptation to the same environment. The following results were observed: (i) bacteria with and without costly resistance mutations adapted to experimental conditions and reached similar levels of competitive fitness; (ii) rifampicin resistance mutations and adaptation to LB both indirectly altered growth in other environments; and (iii) resistant‐evolved genotypes were more phenotypically different from the ancestor and from each other than resistant‐nonevolved and sensitive‐evolved genotypes. This suggests genotype‐by‐environment interactions generated by antibiotic resistance mutations, observed previously in short‐term experiments, are more pronounced after adaptation to other types of environmental variation, making it difficult to predict long‐term selection on resistance mutations from fitness effects in a single environment.     

Positive Epistasis Drives the Acquisition of Multidrug Resistance

The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact—epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.     

EPISTATIC INTERACTIONS CAN LOWER THE COST OF RESISTANCE TO MULTIPLE CONSUMERS

It is widely assumed that resistance to consumers (e.g., predators or pathogens) comes at a “cost,” that is, when the consumer is absent the resistant organisms are less fit than their susceptible counterparts. It is unclear what factors determine this cost. We demonstrate that epistasis between genes that confer resistance to two different consumers can alter the cost of resistance. We used as a model system the bacterium Escherichia coli and two different viruses (bacteriophages), T4 and Λ, that prey upon E. coli. Epistasis tended to reduce the costs of multiple resistance in this system. However, the extent of cost savings and its statistical significance depended on the environment in which fitness was measured, whether the null hypothesis for gene interaction was additive or multiplicative, and subtle differences among mutations that conferred the same resistance phenotype.     

Fitness costs associated with Cry1F resistance in the European corn borer

Crops producing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely planted to manage insect pests. Bt crops can provide an effective tool for pest management; however, the evolution of Bt resistance can diminish this benefit. The European corn borer, Ostrinia nubilalis Hübner, is a significant pest of maize and is widely managed with Bt maize in the Midwest of the United States. When Bt crops are grown in conjunction with non‐Bt refuges, fitness costs of Bt resistance can delay the evolution of resistance. Importantly, fitness costs often vary with ecological factors, including host‐plant genotype and diapause. In this study, we examined fitness costs associated with Cry1F resistance in O. nubilalis when insects were reared on three maize lines. Fitness costs were tested in two experiments. One experiment assessed the fitness costs when Cry1F‐resistant and Cry1F‐susceptible insects were reared on plants as larvae and experienced diapause. The second experiment tested resistant, susceptible and F1 heterozygotes that were reared on plants but did not experience diapause. Despite some evidence of greater adult longevity for Cry1F‐resistant insects, these insects produced fewer fertile eggs than Cry1F‐susceptible insects, and this occurred independent of diapause. Reduced fecundity was not detected among heterozygous individuals, which indicated that this fitness cost was recessive. Additionally, maize lines did not affect the magnitude of this fitness cost. The lower fitness of Cry1F‐resistant O. nubilalis may contribute to the maintenance of Cry1F susceptibility in field populations more than a decade after Cry1F maize was commercialized.     

Variation in costs of parasite resistance among natural host populations

Organisms that can resist parasitic infection often have lower fitness in the absence of parasites. These costs of resistance can mediate host evolution during parasite epidemics. For example, large epidemics will select for increased host resistance. In contrast, small epidemics (or no disease) can select for increased host susceptibility when costly resistance allows more susceptible hosts to outcompete their resistant counterparts. Despite their importance for evolution in host populations, costs of resistance (which are also known as resistance trade‐offs) have mainly been examined in laboratory‐based host–parasite systems. Very few examples come from field‐collected hosts. Furthermore, little is known about how resistance trade‐offs vary across natural populations. We addressed these gaps using the freshwater crustacean Daphnia dentifera and its natural yeast parasite, Metschnikowia bicuspidata. We found a cost of resistance in two of the five populations we studied – those with the most genetic variation in resistance and the smallest epidemics in the previous year. However, yeast epidemics in the current year did not alter slopes of these trade‐offs before and after epidemics. In contrast, the no‐cost populations showed little variation in resistance, possibly because large yeast epidemics eroded that variation in the previous year. Consequently, our results demonstrate variation in costs of resistance in wild host populations. This variation has important implications for host evolution during epidemics in nature.     

Evaluating reproductive fitness and metabolic costs for insecticide resistance in Myzus persicae from Chile

The development of insecticide resistance in pest insects is an increasing problem for agriculture, forestry and public health. Aphids are ubiquitous herbivorous insects, with approximately 4700 known species, of which less than 5% exploit the agricultural environment successfully. Of these, the peach‐potato aphid Myzus persicae Sulzer is recognized as one of the most important pests worldwide because it has acquired resistance to many insecticides. Although resistance to insecticides provides important benefits for pests in agricultural fields that are treated with insecticides, it may be associated with fitness (or other) costs in environments that are insecticide free. In the present study, the fitness and energy costs that might be experienced by M. persicae in an insecticide‐free environment when carrying at least one insecticide resistance mutation (IRM), or by having an increased production of esterases, are evaluated. The study investigates whether genotypes that have an IRM also have enhanced esterase production, whether there is any metabolic cost associated with insecticide resistance, and whether there are any fitness costs associated with insecticide resistance and metabolic expenditure. The intrinsic rate of increase, standard metabolic rate (i.e. a measure of maintenance costs) and constitutive esterase activity are determined for 30 different multilocus genotypes carrying (or not carrying) at least one of the two most frequent insecticide resistance mutations (MACE and kdr/super‐kdr) that occur in Chile. The results show that genotypes carrying at least one IRM have higher levels of total esterase activity than genotypes without an IRM, that there is no evidence of an energy cost associated with total esterase activity or IRM, and no evidence for a reproductive fitness cost associated with total esterase activity, IRM or metabolic rate. The results agree with previous studies showing linkage disequilibrium between insecticide resistance mechanisms, although they contrast with those of studies that report fitness costs associated with insecticide resistance in Myzus persicae.     

The interplay between drug resistance and fitness in malaria parasites

Controlling the spread of antimalarial drug resistance, especially resistance of Plasmodium falciparum to artemisinin‐based combination therapies, is a high priority. Available data indicate that, as with other microorganisms, the spread of drug‐resistant malaria parasites is limited by fitness costs that frequently accompany resistance. Resistance‐mediating polymorphisms in malaria parasites have been identified in putative drug transporters and in target enzymes. The impacts of these polymorphisms on parasite fitness have been characterized in vitro and in animal models. Additional insights have come from analyses of samples from clinical studies, both evaluating parasites under different selective pressures and determining the clinical consequences of infection with different parasites. With some exceptions, resistance‐mediating polymorphisms lead to malaria parasites that, compared with wild type, grow less well in culture and in animals, and are replaced by wild type when drug pressure diminishes in the clinical setting. In some cases, the fitness costs of resistance may be offset by compensatory mutations that increase virulence or changes that enhance malaria transmission. However, not enough is known about effects of resistance mediators on parasite fitness. A better appreciation of the costs of fitness‐mediating mutations will facilitate the development of optimal guidelines for the treatment and prevention of malaria.     

The cost of phage resistance in a plant pathogenic bacterium is context‐dependent

Parasites are ubiquitous features of living systems and many parasites severely reduce the fecundity or longevity of their hosts. This parasite‐imposed selection on host populations should strongly favor the evolution of host resistance, but hosts typically face a trade‐off between investment in reproductive fitness and investment in defense against parasites. The magnitude of such a trade‐off is likely to be context‐dependent, and accordingly costs that are key in shaping evolution in nature may not be easily observable in an artificial environment. We set out to assess the costs of phage resistance for a plant pathogenic bacterium in its natural plant host versus in a nutrient‐rich, artificial medium. We demonstrate that mutants of Pseudomonas syringae that have evolved resistance via a single mutational step pay a substantial cost for this resistance when grown on their tomato plant hosts, but do not realize any measurable growth rate costs in nutrient‐rich media. This work demonstrates that resistance to phage can significantly alter bacterial growth within plant hosts, and therefore that phage‐mediated selection in nature is likely to be an important component of bacterial pathogenicity.     

Evolutionary trade‐offs of insecticide resistance — The fitness costs associated with target‐site mutations in the nAChR of Drosophila melanogaster

The evolution of resistance to drugs and pesticides poses a major threat to human health and food security. Neonicotinoids are highly effective insecticides used to control agricultural pests. They target the insect nicotinic acetylcholine receptor and mutations of the receptor that confer resistance have been slow to develop, with only one field‐evolved mutation being reported to date. This is an arginine‐to‐threonine substitution at position 81 of the nAChR_β1 subunit in neonicotinoid‐resistant aphids. To validate the role of R81T in neonicotinoid resistance and to test whether it may confer any significant fitness costs to insects, CRISPR/Cas9 was used to introduce an analogous mutation in the genome of Drosophila melanogaster. Flies carrying R81T showed an increased tolerance (resistance) to neonicotinoid insecticides, accompanied by a significant reduction in fitness. In comparison, flies carrying a deletion of the whole nAChR_α6 subunit, the target site of spinosyns, showed an increased tolerance to this class of insecticides but presented almost no fitness deficits.     

Effects of temperature on fitness costs in chlorpyrifos‐resistant brown planthopper,Nilaparvata lugens (Hemiptera: Delphacidae)

Insecticide resistance is inevitable if an insecticide is widely used to control insect pests. Fortunately, the resistance‐associated fitness costs often give chances to manage resistances. In most cases, the fitness cost in resistant insects is often evaluated under laboratory conditions for insect development, which limits its practical application in pest control in the field. In a laboratory population R9 with 253‐fold resistance to chlorpyrifos after nine‐generation selection with chlorpyrifos, the relative fitness was only 0.206 under laboratory conditions (25°C, humidity 70%–80% and 16 h light/8 h dark photoperiod), when compared to S9, a susceptible counterpart (resistance ratio = 2.25‐fold) from the same origin as R9 but without any selection with insecticides. Temperatures varied the resistance‐associated fitness costs, with enhanced costs at high temperatures and reduced costs at low temperatures, such as 0.174 at 32°C and 0.527 at 18°C. The copulation rate and fecundity were two key factors for the reduced costs at low temperatures. Another finding was that R9 individuals needed much more time to recover from heat shock than that of S9, but R9 and S9 individuals were similarly sensitive to cold shock. The low fitness cost at low temperatures would increase the overwintering population, which might further increase risks of rapid development and widespread distribution of chlorpyrifos resistance in Nilaparvata lugens.     

Perspective: Sign epistasis and genetic constraint on evolutionary trajectories

Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.     

Competitiveness and life‐history characteristics of Daphnia with respect to susceptibility to a bacterial pathogen

Costs of resistance, i.e. trade‐offs between resistance to parasites or pathogens and other fitness components, may prevent the fixation of resistant genotypes and therefore explain the maintenance of genetic polymorphism for resistance in the wild. Using two approaches, the cost of resistance to a sterilizing bacterial pathogen were tested for in the crustacean Daphnia magna. First, groups of susceptible and resistant hosts from each of four natural populations were compared in terms of their life‐history characteristics. Secondly, we examined the competitiveness of nine clones from one population for which more detailed information on genetic variation for resistance was known. In no case did the results show that competitiveness or life history characteristics of resistant Daphnia systematically differed from susceptible ones. These results suggest that costs of resistance are unlikely to explain the maintenance of genetic variation in D. magna populations. We discuss methods for measuring fitness and speculate on which genetic models of host‐parasite co‐evolution may apply to the Daphnia‐microparasite system.     

Mating behaviour and reproductive output in insecticide‐resistant and ‐susceptible strains of the maize weevil (Sitophilus zeamais)

Insecticide resistance is a broadly recognised and well‐studied management problem resulting from intensive insecticide use, which also provides useful evolutionary models of newly adapted phenotypes to changing environments. Two common assumptions in such models are the existence of fitness costs associated with insecticide resistance, which will place the resistant individuals at a disadvantage in insecticide‐free environments, and the prevalence of random mating among insecticide‐resistant and ‐susceptible individuals. However, cases of insecticide resistance lacking apparent fitness disadvantages do exist impacting the evolution and management of insecticide resistance. Assortative mating, although rarely considered, may also favour the evolution and spread of insecticide resistance. Thus, the possible existence of both conditions in the maize weevil (Sitophilus zeamais), a key pest of stored cereals, led to the assessment of the mating behaviour and reproductive fitness of insecticide‐resistant and ‐susceptible weevil strains and their reciprocal crosses. The patterns of female and male mating choice also were assessed. Although mating behaviour within and between weevil strains was similar without mate choice, mating within the resistant strain led to higher reproductive output than within the susceptible strain; inter‐strain matings led to even higher fertility. Thus, no apparent fitness cost associated with resistance seems to exist in these weevils, favouring the evolution of this phenotype that is further aided by the higher fertility of inter‐strain matings. Mate choice reduced latency to mate and no inter‐strain preference was detected, but female weevils were consistent in their mate selection between 1st and 2nd matings indicating existence of female mating preference among maize weevils. Therefore, if female mate selection comes to favour trait(s) associated with insecticide resistance, higher reproductive fitness will be the outcome of such matings favouring the evolution and spread of insecticide resistance among maize weevil populations reverting into a management concern.     

Insecticide resistance in the mosquito Culex pipiens: what have we learned about adaptation?

Resistance to organophosphate (OP) insecticide in the mosquito Culex pipiens has been studied for ca. 30 years. This example of micro-evolution has been thoroughly investigated as an opportunity to assess precisely both the new adapted phenotypes and the associated genetic changes. A notable feature is that OP resistance is achieved with few genes, and these genes have generally large effects. The molecular events generating such resistance genes are complex (e.g., gene amplification, gene regulation) potentially explaining their low frequency of de novo occurrence. In contrast, migration is a frequent event, including passive transportation between distant populations. This generates a complex interaction between mutations and migration, and promotes competition among resistance alleles. When the precise physiological action of each gene product is rather well known, it is possible to understand the dominance level or the type of epistasis observed. It is however difficult to predict a priori how resistance genes will interact, and it is too early to state whether or not this will be ever possible. These resistance genes are costly, and the cost is variable among them. It is usually believed that the initial fitness cost would gradually decrease due to subsequent mutations with a modifier effect. In the present example, a particular modifier occurred (a gene duplication) at one resistance locus, whereas at the other one reduction of cost is driven by allele replacement and apparently not by selection of modifiers.     

Source-sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost

Understanding the conditions that favour the evolution and maintenance of antibiotic resistance is the central goal of epidemiology. A crucial feature explaining the adaptation to harsh, or 'sink', environments is the supply of beneficial mutations via migration from a 'source' population. Given that antibiotic resistance is frequently associated with antagonistic pleiotropic fitness costs, increased migration rate is predicted not only to increase the rate of resistance evolution but also to increase the probability of fixation of resistance mutations with minimal fitness costs. Here we report in vitro experiments using the nosocomial pathogenic bacterium Pseudomonas aeruginosa that support these predictions: increasing rate of migration into environments containing antibiotics increased the rate of resistance evolution and decreased the associated costs of resistance. Consistent with previous theoretical work, we found that resistance evolution arose more rapidly in the presence of a single antibiotic than two. Evolution of resistance was also more rapid when bacteria were subjected to sequential exposure with two antibiotics (cycling therapy) compared with simultaneous exposure (bi-therapy). Furthermore, pleiotropic fitness costs of resistance to two antibiotics were higher than for one antibiotic, and were also higher under bi-therapy than cycling therapy, although the cost of resistance depended on the order of the antibiotics through time. These results may be relevant to the clinical setting where immigration is known to be important between chemotherapeutically treated patients, and demonstrate the importance of ecological and evolutionary dynamics in the control of antibiotic resistance.