Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections.
Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections.
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DOI：
10.1371/journal.pgen.1004651
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发表时间：
2014-10
期刊：
影响因子：
4.5
通讯作者：
Smania AM
中科院分区：
文献类型：
--
作者：
Feliziani S;Marvig RL;Luján AM;Moyano AJ;Di Rienzo JA;Krogh Johansen H;Molin S;Smania AM
高通量测序技术的出现使得通过比较从人类宿主中纵向采集的细菌样本来跟踪致病菌的基因组进化成为可能。在囊性纤维化（CF）患者中由铜绿假单胞菌引起的慢性气道感染的背景下进行的此类研究表明，细菌种群多样性很高。这种多样性可能是由DNA错配修复系统（MRS）缺陷引起的超易变性驱动的，这是铜绿假单胞菌在CF感染中进化出的一种共同特征。迄今为止，还没有研究利用全基因组测序来调查CF气道中宿主种群多样性或突变体的长期进化。我们分别对来自阿根廷和丹麦CF患者的13株和14株铜绿假单胞菌突变体进行了基因组测序。我们收集的分离株分别跨越6年和20年的患者感染史。我们从每位患者的单个样本中对11个分离株进行了测序，以便深入分析群体多样性。每位患者都被以突变体为主的克隆菌群感染。种群的体内突变率为每年约100个snp，比正常变异种群的突变率高约40倍。对来自同一样本的11个分离株的基因组进行比较，发现患者体内存在广泛的基因组多样化；这些种群由不同的亚谱系组成，这些亚谱系自患者最初定居以来已经共存多年。对突变的分析发现了在谱系和亚谱系中经历趋同进化的基因，这表明这些基因是通过突变来优化致病适应性的。在种群总体分解代谢能力的降低中观察到平行进化。这些发现有助于了解病原体种群的进化和确定控制慢性感染的新靶点。囊性纤维化（CF）患者通常由常见的、广泛存在的铜绿假单胞菌的单克隆定植，导致慢性气道感染。细菌的长期存在涉及多种表型变异的出现和选择。其中包括“突变”变异，其特征是由于DNA修复系统失活导致突变率增加。在慢性感染过程中，突变体的遗传进化尚不清楚，并且还没有使用基因组方法研究超突变性对细菌种群结构的影响。我们评估了从两名慢性感染CF患者的单个痰样本中获得的铜绿假单胞菌突变体群体所经历的基因组变化，发现突变体在两名患者的感染群体中完全占主导地位。这些种群显示出基于大量随机突变积累的高度基因组多样性。我们的结果与单一优势克隆组成的同质群体的概念相反；相反，它们支持由患者体内共存的不同亚群构成的群体模型。与适应有关的某些基因在两个谱系中都发生了高度和收敛的突变，这表明这些基因是有益的，并且可能对突变等位基因的共选择负责。
The advent of high-throughput sequencing techniques has made it possible to follow the genomic evolution of pathogenic bacteria by comparing longitudinally collected bacteria sampled from human hosts. Such studies in the context of chronic airway infections by Pseudomonas aeruginosa in cystic fibrosis (CF) patients have indicated high bacterial population diversity. Such diversity may be driven by hypermutability resulting from DNA mismatch repair system (MRS) deficiency, a common trait evolved by P. aeruginosa strains in CF infections. No studies to date have utilized whole-genome sequencing to investigate within-host population diversity or long-term evolution of mutators in CF airways. We sequenced the genomes of 13 and 14 isolates of P. aeruginosa mutator populations from an Argentinian and a Danish CF patient, respectively. Our collection of isolates spanned 6 and 20 years of patient infection history, respectively. We sequenced 11 isolates from a single sample from each patient to allow in-depth analysis of population diversity. Each patient was infected by clonal populations of bacteria that were dominated by mutators. The in vivo mutation rate of the populations was ∼100 SNPs/year–∼40-fold higher than rates in normo-mutable populations. Comparison of the genomes of 11 isolates from the same sample showed extensive within-patient genomic diversification; the populations were composed of different sub-lineages that had coexisted for many years since the initial colonization of the patient. Analysis of the mutations identified genes that underwent convergent evolution across lineages and sub-lineages, suggesting that the genes were targeted by mutation to optimize pathogenic fitness. Parallel evolution was observed in reduction of overall catabolic capacity of the populations. These findings are useful for understanding the evolution of pathogen populations and identifying new targets for control of chronic infections. Patients with cystic fibrosis (CF) are often colonized by a single clone of the common, widespread bacterium Pseudomonas aeruginosa, resulting in chronic airway infections. Long-term persistence of the bacteria involves the emergence and selection of multiple phenotypic variants. Among these are “mutator” variants characterized by increased mutation rates resulting from the inactivation of DNA repair systems. The genetic evolution of mutators during the course of chronic infection is poorly understood, and the effects of hypermutability on bacterial population structure have not been studied using genomic approaches. We evaluated the genomic changes undergone by mutator populations of P. aeruginosa obtained from single sputum samples from two chronically infected CF patients, and found that mutators completely dominated the infecting population in both patients. These populations displayed high genomic diversity based on vast accumulation of stochastic mutations. Our results are in contrast to the concept of a homogeneous population consisting of a single dominant clone; rather, they support a model of populations structured by diverse subpopulations that coexist within the patient. Certain genes involved in adaptation were highly and convergently mutated in both lineages, suggesting that these genes were beneficial and potentially responsible for the co-selection of mutator alleles.
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影响因子：
56.9
作者：
Giraud, A;Matic, I;Taddei, F
通讯作者：
Taddei, F
影响因子：
3.7
作者：
Feliziani, Sofia;Lujan, Adela M.;Smania, Andrea M.
通讯作者：
Smania, Andrea M.
影响因子：
64.8
作者：
Cooper, VS;Lenski, RE
通讯作者：
Lenski, RE
DOI：
10.1016/j.mrfmmm.2007.07.006
发表时间：
2008-01-01
影响因子：
2.3
作者：
Jacquelin, Daniela K.;Martina, Mariana A.;Barra, Jose L.
通讯作者：
Barra, Jose L.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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