Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients

Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment

Adaptive radiation and the evolution of resource specialization in experimental populations of Pseudomonas fluorescens

Understanding the origins of biological diversity is a fundamental goal of evolutionary biology. A large body of theory attributes ecological and genetic diversification to divergent natural selection for resource specialization. This thesis examines adaptive radiation in response to selection for resource specialization in microcosm populations of the asexual bacterium Pseudomonas fluorescens. The general protocol for these experiments is to introduce a clonal population of Pseudomonas into a novel environment and to allow evolution to occur through the spontaneous appearance of novel genotypes carrying beneficial mutations. Adaptation can then be quantified through direct comparisons between evolved populations and their clonal ancestors. These experiments show that resource heterogeneity generates divergent natural selection for specialization on alternative resources, irrespective of the spatial structure of the environment. Adaptive radiation is possible in sympatry because of genetic trade-offs in the ability to exploit different resources, but these trade-offs are often not the result of antagonistic pleiotropy among loci that determine fitness on alternative resources. The rate of phenotypic diversification declines during adaptive radiation, apparently because the ecological opportunities required to support specialist lineages disappear as a consequence of initial diversification. The ultimate outcome of repeated instances of adaptive radiation is the evolution of a community of ecologically equivalent specialists that share similar adaptive traits, despite differences in the underlying genetic basis of specialization in replicate radiations. Comparisons with the literature on experimental evolution in microbial populations illustrate the results of this thesis are well-supported by experiments in a wide range of microbial microcosms

The Beagle in a bottle.

Why infer evolution when you can watch it happen in real time? This is the basic premise of using populations of fast-replicating microorganisms in test tubes to study evolution. The approach, known as experimental evolution, has provided a way of testing many of the key hypotheses that arose from the modern evolutionary synthesis. However, details of the unnatural histories of microorganisms in test tubes can be extrapolated only so far. Potential future directions for the approach include studying microbial evolution for its own sake under the most natural conditions possible in the test tube, and testing some qualitative theories of genome evolution

Data from: The SOS response increases bacterial fitness, but not evolvability, under a sublethal dose of antibiotic

Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway

Fitness lex-wt time-evolvability

Fitness changes of WT and LexA populations that evolved in the presence and absence of ciprofloxacin. Fitness was measured relative to the ancestral WT strain in 10 replication populations for each treatment

MIC wt-lex time

MIC scores (ciprofloxacin concentration in ug/L) in WT and LexA populations that were allowed to evolve for 200 generations in the presence and absence of ciprofloxacin. We also present the date from the ancestor (T0) populations

5-days competition lex-wt

Short-term fitness effects of the SOS response. Frequency of the WT strain in competition with the LexA strain across multiple cycles of competition, in the presence of ciprofloxacin or not. After 16 generations, the WT strain had achieved such a high frequency that it could no longer be accurately measured

Cell density cip doses

Impacts of ciprofloxacin on bacterial population density. Mean (+/- sem; n≥3) density of viable cells in cultures of the WT strain that were grown overnight across a gradient of ciprofloxacin (ug/L)

Mutation rate wt-lex with cip

Mutation rate of WT and LexA in the absence or presence of ciprofloxacin, as calculated using a fluctuation test that measures the rate of mutation to rifampicin resistance. Estimation of mutation rate values (and 95 % confidence intervals) was done using MSS maximum likelihood method from eight independent replicates

SOS expression cip doses

Impacts of ciprofloxacin on SOS expression. Mean relative expression (+/- s.e.m; n≥3) of a bioluminescent SOS reporter construct across a gradient of ciprofloxacin (ug/L) in a WTpLex:Lux reporter strain and a WT control lacking the reporter construc