Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada.
PLoS Pathog. 2018 Dec 7;14(12):e1007453. doi: 10.1371/journal.ppat.1007453. eCollection 2018 Dec.
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions.
囊性纤维化（CF）肺部感染由伯克霍尔德氏菌复合群成员引起，如伯克霍尔德氏菌多源亚种，与高死亡率和发病率相关。我们对一名 CF 患者的 111 份伯克霍尔德氏菌多源亚种痰培养物进行了群体基因组学研究，这些培养物分属于三个感染阶段，包括早期偶发感染、慢性感染一年期间的深度采样（发生在肺移植前数周）以及移植后感染的深度采样。我们重建了该种群的进化史，并使用谱系控制的全基因组关联研究（GWAS）方法，鉴定与抗生素耐药性相关的遗传变异。我们发现偶发感染株与其余菌株的基础关系较远，对三类抗生素（β-内酰胺类、氨基糖苷类、喹诺酮类）更为敏感。慢性感染株多样化为多个不同的遗传谱系，对相同抗生素的抗菌敏感性降低。移植后再感染株源自偶发感染株，与慢性感染株在遗传上不同。它们的敏感性水平介于偶发和慢性感染株之间。我们鉴定了大量潜在平行病理适应的例子，即在同一基因座甚至密码子中发现多个突变。平行病理适应基因座集与毒力和耐药性相关的功能富集。我们的 GWAS 分析确定了 ampD 基因座中的一个多态性与β-内酰胺类耐药性之间的统计学关联，以及 araC 转录调节因子和外膜孔蛋白的多态性与氨基糖苷类和喹诺酮类耐药性之间的统计学关联。此外，这三个基因座分别独立地发生了四次、三次和两次突变，进一步支持了平行病理适应。最后，我们鉴定了至少 14 次重组事件，并观察到携带假定平行病理适应的基因座和与β-内酰胺类耐药性相关的多态性在这些重组区域中统计上占优势。
