Over time bacteria can undergo a number of genetic mutations that allow them to evolve in response to changes in their surrounding environment. This process of ‘bacterial evolution’ is one of the major causes of antibiotics resistance, whereby disease-causing microorganisms become resistant to multiple drugs and can no longer be destroyed using antibiotic treatment. However, when bacteria become resistant to a drug this can result in an evolutionary trade-off known as ‘collateral sensitivity’ – when evolving resistance to one drug causes bacteria to gain increased sensitivity to another.

Now, Barbosa, Roemhild et al. have investigated whether this evolutionary trade-off could be exploited to tackle the antibiotic crisis and prevent bacteria adapting to different treatments. If this evolutionary trade-off is to be used medically, it must be stable long enough for the bacteria population to either become extinct, or less able to evolve multi-drug resistance. To test how stable collateral sensitivity is over time, Barbosa, Roemhild et al. studied the bacterium Pseudomonas aeruginosa which is known to evolve collateral sensitivity to certain drug treatments.

P. aeruginosa were subjected to two rounds of evolution: first, bacteria were evolved to resist ‘Drug A’ and at the same time became more sensitive to another drug, ‘Drug B’. The bacteria were then allowed to adapt to Drug B either alone or in the presence of Drug A. These evolutionary experiments revealed that the following factors affected the stability of the trade-off: the molecular structure of the antibiotic bacteria evolved sensitivity to, the strength of the original evolutionary trade-off (i.e. how sensitive bacteria became), the order drugs were administrated, and whether resistance came at a large fitness cost (i.e. when the genetic mutations promoting resistance affect bacteria’s ability to replicate and survive in normal conditions).

According to the World Health Organization, P. aeruginosa is the second most problematic multi-drug resistant bacteria. The data collected in this study could therefore be used to develop a new antibiotic therapeutic strategy for fighting this bacterium, as well as other microbes which are resistant to multiple drugs.

Treatment of infectious diseases and cancer often fail because of the rapid evolution of drug resistance (Bloemberg et al., 2015; Davies and Davies, 2010; Gottesman, 2002; Zaretsky et al., 2016). Optimal therapy should thus anticipate how resistance to treatment evolves and exploit this knowledge to improve therapy (Gatenby et al., 2009; Imamovic and Sommer, 2013). One promising strategy is based on evolved collateral sensitivity: the evolution of resistance against one drug A concomitantly causes hypersensitivity (i.e., collateral sensitivity) to a second drug B (Szybalski and Bryson, 1952). If evolved collateral sensitivity is reciprocal, it can – in theory – trap the bacteria in a double bind, thereby preventing the emergence of multidrug resistance during treatment (Baym et al., 2016; Pál et al., 2015; Roemhild and Schulenburg, 2019). Recent large-scale studies have demonstrated that evolved collateral sensitivity is pervasive in laboratory strains and clinical isolates of distinct bacterial species (Barbosa et al., 2017; Imamovic et al., 2018; Imamovic and Sommer, 2013; Jansen et al., 2016; Jiao et al., 2016; Lázár et al., 2014; Lázár et al., 2013; Oz et al., 2014; Podnecky et al., 2018) as well as cancer cells (Dhawan et al., 2017; Pluchino et al., 2012; Shaw et al., 2016; Zhao et al., 2016). More importantly, evolved collateral sensitivity can slow down resistance evolution during combination (Barbosa et al., 2018; Rodriguez de Evgrafov et al., 2015; Munck et al., 2014) and sequential therapy (Kim et al., 2014; Roemhild et al., 2015), and also limit the spread of plasmid-borne resistance genes (Rosenkilde et al., 2019).

Although collateral sensitivity appears to be pervasive, its utility for medical application is still dependent on several additional factors. Firstly, the evolution of collateral sensitivity should ideally be repeatable for a given set of conditions (Nichol et al., 2019). This means that independent populations selected with the same drug should produce identical collateral effects when exposed to a second one. Such high repeatability is not always observed. Recent work even identified evolution of contrasting collateral effects (i.e., some populations with evolved collateral sensitivity and others with cross-resistance) for different bacteria, including Pseudomonas aeruginosa (Barbosa et al., 2017), Escherichia coli (Nichol et al., 2019; Oz et al., 2014), Enterococcus faecalis (Maltas and Wood, 2019), and a BCR-ABL leukemeia cell line (Zhao et al., 2016). These patterns are likely due to the stochastic nature of mutations combined with alternative evolutionary paths to resistance against the first selective drug, subsequently causing distinct collateral effects against other drugs (Barbosa et al., 2017; Nichol et al., 2019). Secondly, the evolution of collateral sensitivity should ideally be repeatable across conditions, for example different population sizes. This is not always the case. For example, an antibiotic pair, which consistently produced collateral sensitivity in small Staphylococcus aureus populations (e.g., 10⁶), instead produced complete cross-resistance in large populations (e.g., 10⁹) and thus an escape from the evolutionary constraint, most likely due to the higher likelihood of advantageous rare mutations under these conditions (Jiao et al., 2016).

A third and largely unexplored factor is that evolved collateral sensitivity and, hence, the resistance trade-off should be stable across time. This implies that bacteria either cannot evolve to overcome collateral sensitivity and thus die out, or, if they achieve resistance to the new drug B, they should concomitantly be re-sensitized to the original drug A. Two recent studies, both with different main research objectives, yielded some insight into this topic. One example was focused on historical contingency during antibiotic resistance evolution of P. aeruginosa (Yen and Papin, 2017). As part of the results, the authors identified lineages with evolved resistance against ciprofloxacin that simultaneously showed increased sensitivity to piperacillin and tobramycin. The reverse pattern (i.e., evolved high resistance to either piperacillin or tobramycin and increased sensitivity to ciprofloxacin) was not observed and, thus, this case represents an example of uni-directional collateral sensitivity. The subsequent exposure of the ciprofloxacin-resistance lineages to either piperacillin or tobramycin led to the evolution of resistance against these two antibiotics and substantial (yet not complete) re-sensitization to ciprofloxacin. The second study focused on evolving E. coli populations in a morbidostat, in which the bacteria were exposed to repeated switches between two drugs (Yoshida et al., 2017). The evolution of multidrug resistance was only prevented in the two treatments with polymyxin B that were also characterized by evolved collateral sensitivity, although again only in one direction (Yoshida et al., 2017). To date, the general relevance of this third factor is still unclear, especially for conditions when collateral sensitivity is reciprocal and when the evolving populations are also allowed to go extinct (i.e., they cannot overcome the evolutionary trade-off).

Here, we specifically tested the potential of the model pathogen P. aeruginosa to escape reciprocal collateral sensitivity through de-novo evolution. We focused on the first switch between two drugs, because the evolutionary dynamics after this first switch will reveal the ability of the bacteria to adapt to the second drug, against which they evolved sensitivity, and, if so, whether this causes re-sensitization to the first drug. These two aspects are key criteria for applicability of a treatment strategy that exploits evolved collateral sensitivities. Our analysis is based on a two-step evolution experiment. Bacteria first evolved resistance against a first drug A and concomitant sensitivity against a second drug B. Thereafter, bacteria were subjected to a second evolution experiment, during which they were allowed to adapt to the second drug B, either alone or additionally in the presence of the first drug A. Phenotypic characterization of the evolved bacteria was combined with genomic and functional genetic analyses, in order to determine the exact targets of selection under these conditions. We finally validated the findings made by performing further, independent sets of similar two-step evolution experiments.

The experimental design of our two-step evolution experiment is illustrated in Figure 1a. We took advantage of previously evolved, highly resistant P. aeruginosa populations, which we obtained from serial passage experiments with increasing concentrations of clinically relevant bactericidal antibiotics (drug A, Figure 1a) (Barbosa et al., 2017). From these, we identified two cases of reciprocal collateral sensitivity, including (i) piperacillin/tazobactam (PIT) and streptomycin (STR), or (ii) carbenicillin (CAR) and gentamicin (GEN). In the current study, we now re-assessed the reciprocity of collateral effects using dose-response analysis (Figure 1b and c, Supplementary file 1–Figure 1–supplementary table 1, Figure 1—source data 1). Thereafter, we isolated resistant colonies from these populations and switched treatment to the drug, against which collateral sensitivity was observed (drug B, Figure 1a). By starting this treatment step with clonal lineages, we here tested the ability of P. aeruginosa to overcome collateral sensitivity by de-novo mutation. The evolutionary challenge was initiated at sub-inhibitory concentrations of each drug (vertical black dashed lines in Figure 1b and c, Supplementary file 1–Figure 1–supplementary table 1, Figure 1—source data 1), followed by linear concentration increases at two different rates: mild or strong (vertical orange and blue dashed lines respectively, Figure 1b and c, Supplementary file 1–Figure 1–supplementary table 1, Figure 1—source data 1). We specifically chose linear increases, because our main objective was to better understand the evolutionary dynamics occurring during the first switch of a collateral sensitivity cycling strategy. Linear increases would, in this case, facilitate evolutionary rescue and provide ample opportunity to escape the double bind, thereby yielding a conservative measure for the applicability of collateral sensitivity as a treatment strategy. We additionally considered treatments where antibiotics were also switched to collateral sensitivity, but selection by drug A was continued in combination with drug B; hereby denoted as constrained environments. Overall, four selective conditions were run in parallel: mild or strong increases of the second drug B in either the presence (constrained) or absence (unconstrained) of the first drug A (Figure 1a). We further included control experiments without antibiotics. To determine treatment success, we monitored bacterial growth with continuous absorbance measurements, quantified frequencies of population extinction, and characterized changes in antibiotic resistance of the evolved bacteria as previously evaluated for P. aeruginosa and other bacteria (Barbosa et al., 2018; Barbosa et al., 2017; Hegreness et al., 2008).

Figure 1

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Figure 1—source data 1

Mean optical density and CI95 values obtained after 12 hr of growth in minimal media and different antibiotics as reported in Figure 1.

The populations tested here include the PA14 wild type, and four resistant populations. Each value is the average of 8 technical replicates per bacterial population.

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Extinction rates were high even under mild selection regimes

The imposed antibiotic selection frequently caused population extinction (Figure 2, Figure 2—source data 1), even though sublethal drug concentrations were used. Extinction events occurred significantly more often when selection for the original resistance was maintained by the presence of both drugs (extinction in constrained treatments vs. only one drug, χ² = 12.9, df = 1, p<0.0001; Figure 2). In treatments with only the second drug B, extinction occurred significantly more often under strong, but not mild concentration increases (strong vs. mild increases in unconstrained environments, χ² = 5.5, df = 1, p=0.019). Drug switches with the antibiotic pair STR/PIT was particularly successful, with 33 extinction events (~51%, Figure 2). The results differed for the CAR/GEN pair, which produced only seven extinctions (~10%), all restricted to one drug order, GEN>CAR, suggesting asymmetry in the ability to counter collateral sensitivity. The observed differences in the extinction levels of the pairs considered here are unlikely to be the result of differences in combined synergy, since both combinations (PIT/STR and CAR/GEN) are synergistic against P. aeruginosa (Barbosa et al., 2018). From this, we conclude that strong genetic constraints against an evolutionary response to collateral sensitivity caused frequent population extinctions for STR/PIT switches, whereas evolutionary rescue was possible for the GEN/CAR pair, although influenced by drug identity and order.

Figure 2

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Figure 2—source data 1

Count data of extinction events as reported in Figure 2.

Extinct populations were determined by their inability to grow in rich media after 24 hr of incubation at 37 °C.

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Novel resistance evolved rapidly in many of the surviving populations

We subsequently focused our analysis of the evolutionary dynamics on the surviving populations of the CAR/GEN pair and identified rapid adaptive responses, especially when not constrained by the presence of the two drugs (Figure 3). We measured bacterial adaptation using relative biomass (see Materials and methods and Roemhild et al., 2018) and found it to have increased in all surviving populations (Figure 3a and b, Supplementary file 1–Figure 3–supplementary table 1, Figure 3—source data 1). For both drug orders, the increase was significantly slower in the constrained treatments, and, to a lesser extent, for the strong concentration increases (Figure 3a and b). Consistent with the asymmetry in extinction, the CAR>GEN switch (with no extinction) maintained a high relative biomass across time, while the reverse direction GEN>CAR (with extinction) produced lower relative biomass levels. These results indicate that P. aeruginosa can evolve resistance against a drug, to which it had previously shown hypersensitivity, and that such evolutionary rescue is favored for the suboptimal switch. For the STR/PIT pair, we generally obtained similar results (Figure 3—figure supplement 1a and b, Figure 3—source data 1); yet because of the few surviving populations and high variation among these rare survivors, the results remained inconclusive. We thus continued to focus on the evolved populations for the CAR/GEN pair and asked how the new adaptation influenced the original drug resistances.

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Figure 3—source data 1

Evolutionary dynamics summarized by the area under the curve (AUC) across experimental seasons relative to the reference treatment with no drugs.

Data is shown for all following experiments: CAR^R>GEN, GEN^R>CAR, PIT^R>STR and STR^R>PIT, as reported in Figure 3a and b and Figure 3—figure supplement 1a and b.

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Figure 3—source data 2

Dose-response curves data of surviving populations challenged with CAR, GEN, STR and PIT.

Data is shown in Figure 3c and d, and Figure 3—figure supplement 1c and d. Optical density values were recorded after 12 hr of incubation at 37 °C.

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Figure 3—source data 3

Growth rate estimates of the surviving population challenged with CAR or GEN, as reported in Figure 3.

Growth rate was calculated as specified in the Materials and methods section.

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Whole genome sequencing identified possible targets of antibiotic selection

We used population genomic analysis to characterize specific functional changes that were likely targeted by antibiotic selection and allowed populations to survive the second evolution experiment for the CAR/GEN pair (Figure 4, Figure 4—source data 1). In particular, we sequenced whole genomes of the resistant starting clones from the beginning and 21 surviving populations from the end of the second evolution experiment. Our results reveal that the evolution of multidrug resistance in the suboptimal switch CAR>GEN can be explained by the sequential fixation of mutations including, under unconstrained conditions, those in ptsP (Figure 4a, Figure 4—source data 1), a main component of the global regulatory system of ABC transporters and other virulence factors (Feinbaum et al., 2012). Similarly, under constrained conditions, we found mutations in the NADH-dehydrogenase genes nuoD or nuoG (Figure 4a, Figure 4—source data 1), which are known to influence proton motive force and resistance against aminoglycosides upon inactivation (El'Garch et al., 2007).

Figure 4

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Figure 4—source data 1

Genetic changes compared to Pseudomonas aeruginosa PA14 wild type strain as determined by whole-genome resequencing.

Sequencing was performed with Illumina MiSeq2 × 150 bp PE, Nextera libraries. The data is shown in Figure 4. Isolates are coded with AA-BB-CC-: AA, antibiotic to which they are originally resistant; BB, antibiotic to which the clone shows collateral sensitivity; CC, well in the plate during experimental evolution.

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Figure 4—source data 2

MIC values for several constructed mutants against CAR and GEN, as reported in Figure 4.

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For the more effective switch GEN>CAR, multidrug resistance in the constrained treatments coincided with mutations in mexR, phoQ, and cpxS, an independent regulator of MexAB-OprM (Li et al., 2016) and two-component regulators involved in aminoglycoside resistance (Gooderham and Hancock, 2009) and envelope stress response (Roemhild et al., 2018), respectively. The re-sensitization towards the first drug in the unconstrained GEN>CAR treatments was associated with two main types of mutational changes at high frequencies across several replicates, including (i) mutations in nalC and nalD that upregulate the expression of the multidrug-efflux system MexAB-OprM in P. aeruginosa (Li et al., 2016); and (ii) large deletions in pmrB, which is part of a two-component regulatory system (Figure 4b, Figure 4—source data 1). Mutations in nalC were previously shown to mediate both resistance to CAR and hypersensitivity to GEN (Barbosa et al., 2017). Thus, re-sensitization to GEN may be caused by antagonistic pleiotropy of nalC mutations that override the resistance of the original pmrB mutation (Figure 4, Figure 4—source data 1). In addition, there may be epistasis between the two functional modules. A complementary mechanism for re-sensitization against GEN is the re-mutation of pmrB (Figure 4, Figure 4—source data 1). In three cases nalC mutations coincided with mutations in pmrB, including two deletions of 17 and 225 base pairs. Whilst the original SNP in pmrB altered gene function, the latter deletions may have suppressed the expression of the original SNP by pseudogenizing the gene. We conclude that mutations in the nalC or nalD regulators of the MexAB-OprM pump, sometimes in combination with follow up mutations in pmrB are likely to account for the re-sensitization towards the first drug GEN.

Repetition of experimental evolution revealed an influence of drug type on population extinction and drug re-sensitization

To validate and generalize our findings, we repeated evolution experiments for 14 cases of collateral sensitivity, using a total of 38 distinct resistant populations (Figure 5a; Figure 5—source data 1), obtained from independent biological replicates of our previous study (Barbosa et al., 2017). We initiated experiments with the available populations (Barbosa et al., 2017), rather than clones, and applied a less severe bottleneck of 10⁷ cells. Therefore, any adaptative changes may not exclusively rely on de-novo mutations but could also result from available genetic diversity, thus reflecting a more general scenario for evolutionary adaptation to collateral sensitivity. The 14 cases of collateral sensitivity included the same four examples tested above and 10 additional cases, encompassing both reciprocal and also uni-directional collateral sensitivities. The effect size of collateral sensitivity, measured as fold-IC₇₅, differed substantially among replicates (Figure 5a, Figure 5—figure supplement 1; Figure 5—source data 1). In the current study, we now subjected the total of 38 resistant populations to either strong or strong+constrained increases of the second drug (Figure 5a) and assessed treatment outcome by measuring population extinction rates and changes in resistance profiles of the surviving populations (Supplementary file 1–Figure 5-supplementary tables 1-2, Figure 5—figure supplement 1—source data 1).

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Effect size of tested collateral sensitivities.

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Figure 5—source data 2

Extinction of experimentally evolved populations.

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Figure 5—source data 3

Evolved resistance changes of experimentally evolved populations.

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Our validation experiment now demonstrated that extinction events were frequent and occurred significantly more often when selection for the original resistance was maintained by the presence of both drugs (extinction in constrained vs. strong environments, χ² = 16.204, df = 1, p<0.0001; Figure 5b; Figure 5—source data 2). Extinction rates showed pronounced variation by drug identity and order. For example, CIP-resistant populations all survived when challenged with either of the aminoglycosides (STR, GEN), whereas more than 50% of these populations went extinct when exposed to β-lactams (CAR, PIT, Figure 5b). We specifically assessed the importance of drug target, collateral sensitivity effect size (fold-IC₇₅), and relative growth rate under drug-free conditions, using a generalized linear model (GLM; Figure 6—source data 1). We extracted data on the relative exponential growth rate of the resistant populations in drug-free media from our previous publication (Barbosa et al., 2017). Our analysis revealed that variation in extinction was significantly associated with only the molecular target of the second antibiotic (GLM, combined extinction, n = 14 drug switches, F = 11.016, p=0.011; Supplementary file 1–Figure 6–supplementary table 1, Figure 6—source data 1), but not with growth rate, extent of collateral sensitivity, or target of the first antibiotic. Extinction frequencies were on average twice as high in the six treatments that switched to β-lactam antibiotics that target the cell wall, as compared to the eight treatments that switched to aminoglycoside antibiotics that target the ribosome (Figure 6a). It thus appears that extinctions in our experiments are stochastic events that are mainly influenced by the target of the current antibiotic, but not the preceding evolutionary conditions. Taken together, we conclude that switching from one to two drugs generally increases treatment potency and that this is influenced by drug order and identity. The preferred drug order is to use a β-lactam as the second antibiotic, which is consistent with the detailed dynamics on the clonal level.

Figure 6

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Summary of total extinction in the generalized experiment in relation to average initial collateral sensitivity effects and average growth rate.

Average collateral sensitivity effects are given as fold change IC₇₅, fold change IC₉₀, and AUC relative to PA14. The data is derived from that shown in Figure 5.

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Figure 6—source data 2

Summary of average resistance changes in the generalized experiment in relation to average initial collateral sensitivity effects and average growth rate.

Average initial collateral sensitivity effects are given as fold change IC₇₅, fold change IC₉₀, and AUC relative to PA14). The data is derived from that shown in Figure 5.

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Resistance gains to drug B were frequently associated with re-sensitization to the original drug A in the unconstrained treatments, while resistance to the new drug B increased in all 14 tested cases (leading to changes of 2 up to >64 times the IC₉₀ of the starting populations; Supplementary file 1–Figure 5–supplementary tables 1 and 2). In detail, we observed significant antibiotic re-sensitization for 5 of the 14 cases (36%, Figure 5b, Figure 5—source data 3, Supplementary file 1–Figure 5–supplementary table 1, Figure 5—source data 1; Note that the single available replicate for STR>PIT showed a similar trend but could not be evaluated statistically). Within reciprocal collateral sensitivity, re-sensitization was not always observed in both directions, as illustrated by CAR/STR and STR/PIT. Re-sensitization did not occur in the constrained treatments. We noticed some differences between evolutionary outcomes of drug switches in clonal and population experiments. The resistance changes showed an overall categorical agreement of 75% (9/12 comparisons; no comparisons for STR>PIT, as this switch was tested with a single replicate). Yet, clonal evolution produced re-sensitization for only one sequential treatment direction for CAR/GEN, whereas population evolution showed re-sensitization for both directions. That re-sensitization occurred in both directions at the population level is expected if there was a residual frequency of cells lacking the collateral-sensitivity mutation in the inoculum. The population data further highlighted a lack of re-sensitization for PIT>STR, where we previously observed re-sensitization on the clonal level, albeit not at both concentration regimes. In addition, there is a mild significant increase of resistance to GEN in the strong constrained treatments in GEN>CAR, compared to no change. Overall our results indicate that re-sensitization is frequent for populations with collateral sensitivity, but not imperative (Figure 5b).

What are the drivers of the observed resistance gains and re-sensitization? Our statistical analysis revealed that the extent of re-sensitization in the unconstrained treatments was significantly associated to equal degrees with the target of drug A (GLM, resistance against drug A, n = 14, F = 15.27, p=0.0019; Supplementary file 1–Figure 6–supplementary table 2, Figure 6—source data 2), the effect size of collateral sensitivity (F = 15.91, p=0.004), and growth rate in drug-free media (F = 18.38, p=0.0027), while target of drug B did not have a significant influence. Re-sensitization was stronger in drug switches that started with an aminoglycoside, as compared to β-lactam, and fluoroquinolone (Figure 6b). This result is consistent with the drug-dependent negative epistasis (Figure 4), and validates the relative stability of collateral sensitivity switches from aminoglycosides to β -lactams. Growth rate in drug-free conditions and collateral sensitivity effect size showed small negative effects, indicating that they decelerate re-sensitization. In contrast, the extent of resistance gains in unconstrained treatments was not associated with drug targets of either drug A or B, but instead significantly associated with both the initial effect size of collateral sensitivity (GLM, resistance against drug B, n = 14, F = 6.71, p=0.0321; Supplementary file 1-Figure 6–supplementary table 2, Figure 6—source data 2), and the initial growth rate of the resistant population in drug-free media (GLM, resistance against drug B, n = 14, F = 7.90, p=0.0228). Collateral sensitivity effect size showed a negative association with the resistance gains to drug B (Figure 6c). High sensitivity thus appears to be prone to more rapid resistance gains, possibly because it opens a fitness space for rapid adaptation. The population resistance changes against drug B were generally larger than the initial collateral sensitivity (Figure 5b; Figure 5—source data 3); Supplementary file 1-Figure 5-supplementary tables 1-2; evolved lineages showed higher resistance than the PA14 wild type), indicating that they were not solely due to competition of pre-existing sub-populations, but involved new genetic adaptations. As observed above, the presence of a general adaptation trade-off (measured as reduction in growth rate relative to ancestral PA14 in drug-free environments) inhibited rapid adaptation (Figure 6d). Taken together, our results at the population level suggest that the stability of collateral sensitivity switching is shaped predominantly by drug targets, but additionally influenced by the effect size of collateral sensitivity and a general adaptation trade-off. The most stable collateral sensitivity was identified for the switch from aminoglycoside to β-lactam. Within a particular drug switch, the highest stability was achieved for low collateral sensitivity effect sizes. Large adaptation trade-offs tended to inhibit evolutionary change, that is both desirable re-sensitization, and new resistance. The conclusions are consistent with the data obtained from the clonal evolution experiments.

Collateral sensitivity is a pervasive feature of resistance evolution, but its potential for medical application is currently debated (Nichol et al., 2019; Podnecky et al., 2018; Roemhild and Schulenburg, 2019). Its promise as a treatment focus is dependent on the premise that the exploited trade-off is evolutionarily stable and cannot be easily overcome. As a consequence, it should either drive bacterial populations to extinction or minimize the emergence of multidrug resistance by re-sensitization to one of the antibiotics. We here tested the validity of these key predictions with the help of evolution experiments and the model pathogen P. aeruginosa. We found that the effective exploitation of evolved collateral sensitivity in sequential therapy is contingent on drug order and combination, collateral sensitivity effect size, general adaptation trade-offs, and also epistatic genetic interactions.

Evolved reciprocal collateral sensitivity generally limited bacterial adaptation. Adaptation was particularly constrained in treatments that switched to a β-lactam, as reflected by the elevated extinction rates. The effect was strongest when the first antibiotic was maintained and a second was added. This finding may point to a promising, yet currently unexplored treatment strategy, namely single-drug therapy followed by combination therapy (for example the addition of a β-lactam), that can maximize exploitation of the evolutionary trade-off. Yet, extinction rates were still high under unconstrained conditions, when drugs were replaced, and in spite of a relatively mild selection intensity. In the detailed analysis with the CAR/GEN drug pair, we observed higher extinction and slower growth improvements in strong, compared to mild dose increases. This finding is generally consistent with previous studies, performed in different context, in which narrowed mutation space upon fast environmental deterioration increased extinction frequencies (Bell and Gonzalez, 2011; Lindsey et al., 2013). Interestingly, extinction rates are often not reported as an evolutionary outcome in related studies, possibly because of a different main focus of the study (Yen and Papin, 2017), or because extinction could not be recorded due to the particular experimental set-up (i.e., usage of a morbidostat; Yoshida et al., 2017). Considering that antimicrobial therapy usually aims at elimination of bacterial pathogens and extinction frequencies are known from previous evolution experiments to vary among treatment types (Barbosa et al., 2018; Hansen et al., 2017; Roemhild et al., 2018; Torella et al., 2010), their consideration should help us to refine our understanding of treatment efficacy.

In the treatments that replaced drugs, evolutionary stability of the resistance trade-off was determined by drug order. In both datasets (clonal and population-level evolution), we observed high relative stability for collateral sensitivity treatments switching from an aminoglycoside to a β-lactam. Our detailed analysis for the CAR/GEN pair at the clonal level demonstrates that this stability may be caused by slower adaptation (Figure 3a), and efficient re-sensitization (Figure 3c). Also, the slow adaptation rates may be the result of selection favoring the reversal of two evolutionary trade-offs (Figures 3e and 6d) together with a relative paucity of accessible resistance mutations. The latter is highlighted by several instances of re-mutation of pmrB, where the effect of the ancestral collateral-sensitivity SNP was countered by additional larger deletions, potentially leading to a loss of function of the same gene (Figure 4b). The efficient re-sensitization that was observed during switches from an aminoglycoside to a β-lactam may be explained by pleiotropy and drug-specific negative epistasis (Figure 4c and d). On the other hand, collateral sensitivity treatments that switch to aminoglycosides, tended to show lower stability, as reflected by the lower levels of extinction (Figure 6a) and the lack of re-sensitization (Figure 6b) at the population level. For instance, the collateral sensitivity treatments CAR>STR and CIP>STR were frequently countered by the evolving bacteria. These treatments hardly resulted in extinction but allowed for rapid loss of susceptibility to both drugs (Figure 5b). While our data cannot fully explain the high instability, it appears that small values for a general adaptation trade-off (i.e., indicated by reduced growth rates in drug-free environments), which are also frequently observed for CIP resistance mutations (Huseby et al., 2017), accelerated adaptation (Figure 6d). Overall, our finding of strong variation in the stability of collateral sensitivity treatments in pathogenic P. aeruginosa indicate the importance for a careful evaluation of new treatment options.

Our detailed analyses for GEN>CAR emphasize the importance of epistasis for the stability of collateral sensitivity. A recent publication confirmed that the expression of particular collateral sensitivity mutations strongly depended on the genetic background and could even cause opposite effects in the closely related species of E. coli and Salmonella enterica due to epistasis (Apjok et al., 2019). Our work on the GEN>CAR switch now shows, that epistasis is of high importance also for the temporal stability of antibiotic sensitivity. Here, drug re-sensitization in the unconstrained treatments was likely dependent on negative epistasis among pleiotropic resistance mutations. Mutations in pmrB and the efflux regulators nalC and nalD interacted negatively with each other and caused a complete re-sensitization of bacteria that were previously resistant against GEN. While re-sensitization reliably occurred for the GEN>CAR treatment, it did not occur in the reverse case. Similar examples of antibiotic re-sensitization were previously reported for E. coli and P. aeruginosa, but these relied on different mechanisms. For E. coli, repeated alternation between two antibiotics led to re-sensitization as a consequence of clonal interference between variants in two genes, secD and/or basB (Yoshida et al., 2017). The change between drugs prevented fixation of the competing variants, thus maintaining pleiotropic alleles and thereby the allele causing resistance to one drug and hypersensitivity to the other (Yoshida et al., 2017). In the previous example for P. aeruginosa, hypersensitivity to a β-lactam depended on an expression imbalance of the MexAB-OprM and the MexEF-OprN efflux systems after exposure to a fluoroquinolone (Maseda et al., 2004; Sobel et al., 2005; Yen and Papin, 2017). Interestingly, partial re-sensitization against the aminoglycoside tobramycin was dependent on inducible resistance, a phenomenon mediated by the MexXY-OprM efflux pump, whereby expression, and consequently resistance, is induced by the presence of the drug, but then reverted after its removal (Hocquet et al., 2003; Yen and Papin, 2017). We conclude that our finding of negative epistasis between pleiotropic resistance mutations is a previously unknown mechanism underlying re-sensitization. Whilst positive epistasis can substantially amplify resistance gains (Wistrand-Yuen et al., 2018), negative epistasis can limit evolutionary trajectories (Weinreich et al., 2006), thus possibly contributing to efficacy of treatment in our case.

The mutations observed in this study are commonly associated with variants observed in clinical isolates, particularly in those obtained from cystic fibrosis patients (Hancock and Speert, 2000; Jansen et al., 2016; Marvig et al., 2015; Tueffers et al., 2019). Both efflux regulators (including nalC and nalD) and two-component regulatory systems (mainly pmrAB and phoQF) were repeatedly reported to be associated with intermediate and highly resistant isolates of P. aeruginosa, E. coli, Acinetobacter baumannii and other pathogenic species against colistin and aminoglycosides (Cao et al., 2004; Gerson et al., 2019; Sato et al., 2018). This overlap suggests that the negative epistasis between the genes involved in resistance against β-lactam and aminoglycosides observed here could also be encountered and exploited in clinical settings.

We anticipate that the findings of our study could help to guide the design of sustainable antibiotic therapy that controls the infection, whilst reducing the emergence of multidrug resistance. In principle, the refined exploitation of collateral sensitivity could represent a promising addition to new evolution-informed treatment strategies, including as alternatives specific combination treatments (Barbosa et al., 2018; Chait et al., 2007; Rodriguez de Evgrafov et al., 2015; Gonzales et al., 2015; Munck et al., 2014), fast sequential therapy (Nichol et al., 2015; Yoshida et al., 2017), or treatments utilizing negative hysteresis (Roemhild et al., 2018). The success of this treatment strategy depends on several key factors. One critical prerequisite is that collateral sensitivity does evolve in response to treatment, which may vary depending on alternative evolutionary paths to resistance against the initially used drug A (Barbosa et al., 2017; Nichol et al., 2019). Our new data additionally suggest that treatment can be further optimized by switching from an aminoglycoside to a β-lactam and/or by focusing on drugs, for which resistance is associated with large general adaptation trade-offs, and/or by using drug combinations with small collateral sensitivity effect sizes. These new insights clearly warrant further evaluation, for example by using clinical isolates of P. aeruginosa and/or patient-related test conditions.

Sequencing data have been deposited at NCBI under the BioProject number PRJNA524114. All other data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for all figures.

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Author details

1. Camilo Barbosa

   Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany

   Contribution

   Conceptualization, Investigation, Visualization, Writing—original draft, Writing—review and editing

   Contributed equally with

   Roderich Römhild

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-0433-9311

2. Roderich Römhild

   1. Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
   2. Max Planck Institute for Evolutionary Biology, Plön, Germany

   Present address

   Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

   Contribution

   Conceptualization, Investigation, Visualization, Writing—original draft, Writing—review and editing

   Contributed equally with

   Camilo Barbosa

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-9480-5261

3. Philip Rosenstiel

   Institute of Clinical Molecular Biology, UKSH, Kiel, Germany

   Contribution

   Investigation, Methodology

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-9692-8828

4. Hinrich Schulenburg

   1. Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
   2. Max Planck Institute for Evolutionary Biology, Plön, Germany

   Contribution

   Conceptualization, Supervision, Funding acquisition, Writing—original draft, Writing—review and editing

   For correspondence

   hschulenburg@zoologie.uni-kiel.de

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1413-913X

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