Bianconi Irene, D'Arcangelo Silvia, Esposito Alfonso, Benedet Mattia, Piffer Elena, Dinnella Grazia, Gualdi Paola, Schinella Michele, Baldo Ermanno, Donati Claudio, Jousson Olivier
Centre for Integrative Biology, University of Trento, Trento, Italy.
Trentino Cystic Fibrosis Support Centre, Rovereto Hospital, Rovereto, Italy.
Front Microbiol. 2019 Jan 11;9:3242. doi: 10.3389/fmicb.2018.03242. eCollection 2018.
During its persistence in cystic fibrosis (CF) airways, 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 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 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. We obtained whole genome sequences of 40 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 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. This study provides valuable insights into the within-host adaptation and microevolution of 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.
在其于囊性纤维化（CF）气道中持续存在期间，通过致病性适应性突变的积累发生了一系列表型变化。更好地理解这些突变在适应性过程中的作用，特别是与多药耐药性（MDR）发展的关系，对于未来新型治疗方法的开发至关重要，包括确定新的药物靶点和实施更有效的抗生素治疗。尽管已经发表了几项关于CF谱系的全基因组测序研究，但迄今为止，与抗菌药物耐药性发展相关的进化轨迹仍大多未被探索。在本研究中，我们监测了CF气道中其微观进化过程中的适应性变化，以提供关于突变和持续表型的创新全基因组图谱，并指出在抗生素治疗下CF患者体内允许其存活的潜在新机制。我们获得了在8年期间（2007 - 2014年）从意大利特伦蒂诺地区支持CF中心（罗韦雷托）的一名CF患者分离出的40株临床CF菌株的全基因组序列。对这些分离株的基因型分析显示，一个以序列型390和三个密切相关变体为主的克隆群体，表明该群体的所有成员可能属于同一克隆谱系，并从一个共同祖先进化而来。虽然大多数早期分离株对测试的大多数抗生素敏感，但随着时间的推移，持续群体中的耐药表型增加。对该群体的基因组分析表明抗生素耐药谱的进化与系统发育关系之间存在相关性，并鉴定出了一些推定的致病性适应性变异。本研究为CF肺部中其宿主内适应性和微观进化提供了有价值的见解，并揭示了随着时间的推移MDR表型的出现，这无法通过已知耐药基因中的变异得到全面解释。对本研究中发现的未表征变异的进一步研究应有助于增进我们对MDR表型发展以及许多CF患者抗生素治疗效果不佳的理解。
