Intense genome sequencing of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) airways has shown inefficient eradication of the infecting bacteria, as well as previously undocumented patient-to-patient transmission of adapted clones. However, genome sequencing has limited potential as a predictor of chronic infection and of the adaptive state during infection, and thus there is increasing interest in linking phenotypic traits to the genome sequences. Phenotypic information ranges from genome-wide transcriptomic analysis of patient samples to determination of more specific traits associated with metabolic changes, stress responses, antibiotic resistance and tolerance, biofilm formation and slow growth. Environmental conditions in the CF lung shape both genetic and phenotypic changes of P. aeruginosa during infection. In this Review, we discuss the adaptive and evolutionary trajectories that lead to early diversification and late convergence, which enable P. aeruginosa to succeed in this niche, and we point out how knowledge of these biological features may be used to guide diagnosis and therapy.

对从囊性纤维化 (CF) 气道中分离出的铜绿假单胞菌进行的密集基因组测序显示，感染细菌的根除效率低下，以及先前未记录的适应克隆的患者间传播。然而，基因组测序作为慢性感染和感染期间适应状态的预测指标的潜力有限，因此人们越来越关注将表型特征与基因组序列联系起来。表型信息的范围从患者样本的全基因组转录组学分析到与代谢变化、应激反应、抗生素耐药性和耐受性、生物膜形成和缓慢生长相关的更具体特征的确定。CF肺中的环境条件塑造了遗传和表型的变化感染期间的铜绿假单胞菌。在这篇综述中，我们讨论了导致早期多样化和晚期趋同的适应性和进化轨迹，这使得铜绿假单胞菌能够在这一领域取得成功，并且我们指出如何利用这些生物学特征的知识来指导诊断和治疗。