Abstract
During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Bottlenecks—that is, reductions in bacterial population size—lead to an increased influence of random effects (genetic drift) during bacterial evolution, and varying antibiotic concentrations during treatment may favour distinct resistance variants. Both aspects influence the process of bacterial evolution during antibiotic therapy and thereby treatment outcome. Surprisingly, the joint influence of these interconnected factors on the evolution of antibiotic resistance remains largely unexplored. Here we combine evolution experiments with genomic and genetic analyses to demonstrate that bottleneck size and antibiotic-induced selection reproducibly impact the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Resistance is favoured—expectedly—under high antibiotic selection and weak bottlenecks, but—unexpectedly—also under low antibiotic selection and severe bottlenecks. The latter is likely to result from a reduced probability of losing favourable variants through drift under weak selection. Moreover, the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks, in combination with drug-induced selection, are currently neglected key determinants of pathogen evolution and outcome of antibiotic treatment.
Highlights
During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs
The contamination of natural environments with low antibiotic concentrations from wastewater might further contribute to resistance spread[4,5]
Infections with antibiotic-resistant bacteria are predicted to be a major cause of death[6] by 2050
Summary
The evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. As higher genetic diversity is more likely to be maintained, the fittest variants tend to occur repeatedly under weak bottlenecks and steer the adaptative process[19,20,21] In this context, variation in antibiotic dose alters the degree of selection on bacterial populations, often favouring different resistance mutations[22,23]. The aim of our study is to assess to what extent bottleneck size and its likely interaction with antibiotic-induced selection affect evolution of drug resistance To address this aim, we combined evolution experiments with whole-genome sequencing (WGS) and genetic analysis using P. aeruginosa, one of the three World Health Organization priority 1 most critical multidrug-resistant pathogens[24]. Genome sequencing and genetic analyses were used to identify the targets of selection and assess competitive fitness of the identified variants
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