Bottleneck size and selection level impact antibiotic resistance evolution

During antibiotic treatment, bacterial evolution is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Surprisingly, the joint influence of these interconnected factors on antibiotic resistance evolution is largely unexplored. We here 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. Resistance is favoured, expectedly, under high antibiotic selection and weak bottlenecks, but surprisingly also under low antibiotic selection and severe bottlenecks. The latter likely results from a reduced probability of losing favourable variants via 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 antibiotic treatment outcome.