With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics. A critical step in the development of such strategies lies in understanding the critical evolutionary trajectories responsible for resistance and which proteins or biochemical pathways within those trajectories would be good candidates for co-drug discovery. We identify the most important steps in the evolution of resistance for a specific pathogen and antibiotic combination by evolving highly polymorphic populations of pathogens to resistance in a novel bioreactor that favors biofilm development. As the populations evolve to increasing drug concentrations, we use deep sequencing to elucidate the network of genetic changes responsible for resistance and subsequent in vitro biochemistry and often structure determination to determine how the adaptive mutations produce resistance. Importantly, the identification of the molecular steps, their frequency within the populations and their chronology within the evolutionary trajectory toward resistance is critical to assessing their relative importance. In this work, we discuss findings from the evolution of the ESKAPE pathogen, Pseudomonas aeruginosa to the drug of last resort, colistin to illustrate the power of this approach.

中文翻译：

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使用实验进化来确定可抑制抗药性进化的可药物化靶标。

随着多药耐药和全药耐药细菌在医院中越来越普遍，抗生素耐药性威胁着我们回到抗生素前时代，这将彻底破坏现代医学。迫切需要开发与早期药物发现工作大不相同的新抗生素和抗药性策略。一种可以补充当前和未来抗生素的策略将是一类针对耐药性进化的联合药物，从而扩展特定种类抗生素的功效。制定此类策略的关键步骤是了解引起耐药性的关键进化轨迹，以及这些轨迹中的哪些蛋白质或生化途径将是共同药物发现的良好候选者。我们通过发展有利于生物膜发展的新型生物反应器中对病原体的高度多态性种群的进化，确定了对特定病原体和抗生素组合的抗性进化中最重要的步骤。随着人群逐渐发展为增加药物浓度，我们使用深度测序来阐明造成耐药性和随后的体外生物化学的遗传变化网络，并经常通过结构确定来确定适应性突变如何产生耐药性。重要的是，鉴定分子阶跃，在种群中的频率以及在对抗性的进化轨迹内的时间顺序对于评估其相对重要性至关重要。在这项工作中，我们讨论了ESKAPE病原体进化的发现，