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.

在抗生素治疗期间，细菌病原体的进化从根本上受到药物施加的瓶颈和不同选择水平的影响。瓶颈——即细菌种群规模的减少——导致细菌进化过程中随机效应（遗传漂移）的影响增加，并且治疗过程中不同的抗生素浓度可能有利于不同的耐药性变异。这两个方面都会影响抗生素治疗期间细菌进化的过程，从而影响治疗结果。令人惊讶的是，这些相互关联的因素对抗生素耐药性演变的共同影响在很大程度上仍未得到探索。铜绿假单胞菌，最有问题的机会性人类病原体之一。在高抗生素选择和弱瓶颈的情况下，耐药性受到青睐，但出乎意料的是，在低抗生素选择和严重瓶颈的情况下，耐药性也会受到青睐。后者可能是由于在弱选择下通过漂移而失去有利变体的可能性降低。此外，在低选择和弱瓶颈下没有高抗性是由于在这些条件下具有高竞争适应性的低抗性变体的传播造成的。我们得出结论，瓶颈与药物诱导选择相结合，是目前被忽视的病原体进化和抗生素治疗结果的关键决定因素。