Antibiotic breakdown by susceptible bacteria enhances the establishment of β-lactam resistant mutants

For a better understanding of the evolution of antibiotic resistance, it is imperative to study the factors that determine the initial establishment of mutant resistance alleles. In addition to the antibiotic concentration, the establishment of resistance alleles may be affected by interactions with the surrounding susceptible cells from which they derive, for instance via the release of nutrients or removal of the antibiotic. Here, we investigate the effects of social interactions with surrounding susceptible cells on the establishment of Escherichia coli mutants with increasing β-lactamase activity (i.e. the capacity to hydrolyze β-lactam antibiotics) from single cells under the exposure of the antibiotic cefotaxime on agar plates. We find that mutant establishment probability is increased in the presence of susceptible cells due to the active breakdown of the antibiotic, but the rate of breakdown by the susceptible strain is much higher than expected based on its low enzymatic activity. A detailed theoretical model suggests that this observation can be explained by cell filamentation causing delayed lysis. While susceptible cells may hamper the spread of higher-resistant β-lactamase mutants at relatively high frequencies, our findings show that they could promote establishment during their emergence.

Mutability of demographic noise in microbial range expansions

Demographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from the E. coli Keio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude (compared to in the wild type). Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable trait of a population.

Stochastic effects on the establishment of mutants resistant to β-lactam antibiotics

For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Understanding the stochastic factors influencing mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four Escherichia coli strains expressing β-lactamase alleles with different activity against the antibiotic cefotaxime, as a function of concentration. Using a simple branching model, we show that concentrations well below the minimal inhibitory concentration (MIC) can substantially hamper establishment, particularly for highly resistant mutants, suggesting cooperative effects due to antibiotic breakdown at high cell densities. We further show that variation among cell lineages may explain the more gradual influence of increased antibiotic concentrations on agar. Finally, we use the single-cell establishment probability to predict a strain’s MIC in the absence of social interactions, as a general reference to detect cooperative resistance effects.

The mutability of demographic noise in microbial range expansions

Demographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from the E. coli Keio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude higher than the wild type. Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable phenotype of a population.

Influence of nutrient enrichment on the growth, recruitment and trophic ecology of a highly invasive freshwater fish

The establishment probability of introduced alien fish can be context dependent, varying according to factors including propagule pressure and biotic resistance. The influence of nutrient enrichment on establishment outcomes of alien fishes is uncertain, yet this is a common anthropogenic stressor of many freshwaters. Here, the small-bodied alien topmouth gudgeon Pseudorasbora parva was used in mesocosms to experimentally test how a gradient of nutrient enrichment affected their growth rates, recruitment and trophic ecology. A ‘Control’ represented ambient, mesotrophic conditions, while treatments covered three levels of nutrient enrichment: low (eutrophic), medium (hypertrophic) and high (very hypertrophic). Each mesocosm was seeded with 6 mature P. parva (equal sex ratio) at the start of their reproductive season. After 100 days, length increments of the adult fish were significantly elevated in the low treatment, and these fish had also produced significantly higher numbers of 0+ fish compared to all other treatments. The trophic niche width of the mature fish was substantially higher in the control than the treatments, but this did not appear to confer any advantages to them in somatic growth rate or reproductive output. These results suggest that the nutrient status of receiving waters can have substantial impacts on the outcomes of fish introductions, where eutrophic conditions can assist the rapid population establishment of some alien species.

Evolutionary Rescue and Drug Resistance on Multicopy Plasmids

Bacteria often carry “extra DNA” in the form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant homozygous cells over the course of several generations. To model this process, we use the theory of multitype branching processes, where a type is defined by the genetic composition of the cell. Both factors—the availability of advantageous alleles and their establishment probability—depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

Evolutionary rescue and drug resistance on multicopy plasmids

Bacteria often carry “extra DNA” in form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant-homozygous cells over the course of several generations. To model this process, we use the theory of multi-type branching processes, where a type is defined by the genetic composition of the cell. Both factors – the number of adaptive alleles and their establishment probability – depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

When exotic introductions fail: updating invasion beliefs

Decisions regarding invasive risk of exotic species are often based on species distribution models projected onto the recipient region of interest. Such projections are essentially a measure of prior belief in the ability of an organism to invade. Whilst many decisions are made on the basis of such projections, it is less clear how such prior belief may be empirically modified on the basis of data, in particular introduction events that haven’t led to establishment. Here, using the Asian green mussel (Perna viridis) as an example, we illustrate how information on failed introduction attempts may be used to continually update our beliefs in the ability of an organism to invade per introduction, and the underlying habitat suitability for establishment. Our results show that the establishment probability of P. viridis per fouled ship visit in the supposedly favourable northern Australian waters are much lower than initially though, and are continuing to decline. A Bayesian interpretation of our results notes the dramatic reduction in our belief of the ability of P. viridis to invade in the light of what we estimate to be 100’s of fouled vessels per year visiting ports without any persistent populations establishing. Under a hypothetico-deductive approach we would reject the null (prior) species distribution model as being useful, and seek to find a better one that can withstand the challenge of data.

Adaptational lags during periods of environmental change

Effects of climate change can be handled by means of mitigation and adaptation. In the biological sciences, adaptations are evolved solutions of engineering problems where organisms need to match an ecological challenge. Based on Adaptive Dynamics theory, a definition is proposed of adapted states and adaptational lags which is applicable during periods with environmental change of any speed and to any character. Adaptation can thus be studied even when it emerges from complex eco-evolutionary processes and targets for adaptation are not defined or known a priori. The approach is exemplified with a model for delayed germination (germination probability) in an annual plant, which is the classic life history example for adaptation to uncertain environments. Plasticity and maternal effects are added to the model to investigate lags in these modes of trait determination which are often presumed to be adaptive. In the example, adaptational lags are not converging to an equilibrium and change sign. For the model version with plasticity and maternal effect weights, the presence of a lag in these trait components can temporarily change the direction of selection on the genotypic weight. Adaptational lag is related to the establishment probability of mutants in the model example. It could therefore have practical relevance. A first general classification is proposed of model structures that include both adaptive control and evolutionary adaptation.