Table_4_Persistence and Microevolution of Pseudomonas aeruginosa in the Cystic Fibrosis Lung: A Single-Patient Longitudinal Genomic Study.pdf

Background: During its persistence in cystic fibrosis (CF) airways, P. aeruginosa develops a series of phenotypic changes by the accumulation of pathoadaptive mutations. A better understanding of the role of these mutations in the adaptive process, with particular reference to the development of multidrug resistance (MDR), is essential for future development of novel therapeutic approaches, including the identification of new drug targets and the implementation of more efficient antibiotic therapy. Although several whole-genome sequencing studies on P. aeruginosa CF lineages have been published, the evolutionary trajectories in relation to the development of antimicrobial resistance remain mostly unexplored to date. In this study, we monitored the adaptive changes of P. aeruginosa during its microevolution in the CF airways to provide an innovative, genome-wide picture of mutations and persistent phenotypes and to point out potential novel mechanisms allowing survival in CF patients under antibiotic therapy.
Results: We obtained whole genome sequences of 40 P. aeruginosa clinical CF strains isolated at Trentino Regional Support CF Centre (Rovereto, Italy) from a single CF patient over an 8-year period (2007–2014). Genotypic analysis of the P. aeruginosa isolates revealed a clonal population dominated by the Sequence Type 390 and three closely related variants, indicating that all members of the population likely belong to the same clonal lineage and evolved from a common ancestor. While the majority of early isolates were susceptible to most antibiotics tested, over time resistant phenotypes increased in the persistent population. Genomic analyses of the population indicated a correlation between the evolution of antibiotic resistance profiles and phylogenetic relationships, and a number of putative pathoadaptive variations were identified.
Conclusion: This study provides valuable insights into the within-host adaptation and microevolution of P. aeruginosa in the CF lung and revealed the emergence of an MDR phenotype over time, which could not be comprehensively explained by the variations found in known resistance genes. Further investigations on uncharacterized variations disclosed in this study should help to increase our understanding of the development of MDR phenotype and the poor outcome of antibiotic therapies in many CF patients.

研究背景：当铜绿假单胞菌（Pseudomonas aeruginosa, P. aeruginosa）在囊性纤维化（cystic fibrosis, CF）气道内持续定植时，会通过积累路径适应性突变发生一系列表型改变。深入解析这些突变在适应性进程中的作用，尤其是其与多重耐药（multidrug resistance, MDR）形成的关联，对于开发新型治疗策略至关重要，包括识别全新药物靶点以及制定更高效的抗生素治疗方案。尽管已有多项针对铜绿假单胞菌CF分离株谱系的全基因组测序研究发表，但截至目前，与抗菌耐药性发展相关的进化轨迹仍未得到充分探索。本研究对铜绿假单胞菌在CF气道内的微进化过程中的适应性变化进行监测，旨在绘制突变与持续定植表型的全基因组全景图谱，并阐明抗生素治疗压力下，铜绿假单胞菌在CF患者体内存活的潜在新型机制。
研究结果：本研究从意大利特伦托地区囊性纤维化区域支持中心（罗韦雷托，意大利）的一名CF患者体内，于2007至2014年的8年随访周期内分离得到40株铜绿假单胞菌临床CF分离株，并完成全基因组测序。对上述分离株的基因型分析显示，其克隆群体以序列型390（Sequence Type 390, ST390）及其3个紧密相关的变异株为核心类群，表明该群体的所有成员大概率属于同一克隆谱系，均由共同祖先演化而来。尽管多数早期分离株对多数受试抗生素敏感，但随着时间推移，持续定植群体的耐药表型比例逐渐升高。群体基因组分析表明，抗生素耐药谱的演化与系统发育关系存在显著相关性，同时还鉴定出多个潜在的路径适应性变异位点。
研究结论：本研究为铜绿假单胞菌在CF肺内的宿主内适应性及微进化过程提供了重要研究视角，并揭示了多重耐药表型随时间推移的出现过程——这一演化进程无法通过已知耐药基因的变异得到全面解释。本研究中发现的未表征变异位点的后续功能验证与研究，将有助于进一步阐明多重耐药表型的形成机制，以及多数CF患者抗生素治疗效果不佳的临床原因。