Miller Ruth R, Hird Trevor J, Tang Patrick, Zlosnik James E A
School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.
British Columbia Centre for Disease Control, University of British Columbia, Canada, Vancouver, British Columbia, Canada.
PLoS One. 2015 Nov 24;10(11):e0143472. doi: 10.1371/journal.pone.0143472. eCollection 2015.
Burkholderia cepacia complex bacteria are amongst the most feared of pathogens in cystic fibrosis (CF). The BCC comprises at least 20 distinct species that can cause chronic and unpredictable lung infections in CF. Historically the species B. cenocepacia has been the most prevalent in CF infections and has been associated in some centers with high rates of mortality. Modeling chronic infection by B. cenocepacia in the laboratory is challenging and no models exist which effectively recapitulate CF disease caused by BCC bacteria. Therefore our understanding of factors that contribute towards the morbidity and mortality caused by this organism is limited. In this study we used whole-genome sequencing to examine the evolution of 3 clonal clinical isolates of B. cenocepacia from a patient with cystic fibrosis. The first isolate was from the beginning of infection, and the second two almost 10 years later during the final year of the patients' life. These isolates also demonstrated phenotypic heterogeneity, with the first isolate displaying the mucoid phenotype (conferred by the overproduction of exopolysaccharide), while one of the later two was nonmucoid. In addition we also sequenced a nonmucoid derivative of the initial mucoid isolate, acquired in the laboratory by antibiotic pressure. Examination of sequence data revealed that the two late stage isolates shared 20 variant nucleotides in common compared to the early isolate. However, despite their isolation within 10 months of one another, there was also considerable variation between the late stage isolates, including 42 single nucleotide variants and three deletions. Additionally, no sequence differences were identified between the initial mucoid isolate and its laboratory acquired nonmucoid derivative, however transcript analysis indicated at least partial down regulation of genes involved in exopolysaccharide production. Our study examines the progression of B. cenocepacia throughout chronic infection, including establishment of sub-populations likely evolved from the original isolate, suggestive of parallel evolution. Additionally, the lack of sequence differences between two of the isolates with differing mucoid phenotypes suggests that other factors, such as gene regulation, come into play in establishing the mucoid phenotype.
洋葱伯克霍尔德菌复合体细菌是囊性纤维化（CF）中最令人恐惧的病原体之一。该复合体至少包含20个不同的物种，可在CF患者中引起慢性且不可预测的肺部感染。从历史上看，洋葱伯克霍尔德菌在CF感染中最为常见，在一些中心与高死亡率相关。在实验室中模拟洋葱伯克霍尔德菌的慢性感染具有挑战性，并且不存在能够有效重现由该复合体细菌引起的CF疾病的模型。因此，我们对导致该病原体发病和死亡的因素的理解有限。在本研究中，我们使用全基因组测序来研究来自一名囊性纤维化患者的3株洋葱伯克霍尔德菌克隆临床分离株的进化情况。第一株分离株来自感染初期，后两株分离株则来自近10年后患者生命的最后一年。这些分离株还表现出表型异质性，第一株分离株呈现黏液样表型（由胞外多糖过度产生所致），而后两株中的一株则为非黏液样表型。此外，我们还对最初黏液样分离株在实验室通过抗生素压力获得的非黏液样衍生物进行了测序。对序列数据的检查显示，与早期分离株相比，两株晚期分离株共有20个变异核苷酸。然而，尽管它们在彼此10个月内被分离，但晚期分离株之间也存在相当大的差异，包括42个单核苷酸变异和3个缺失。此外，在最初的黏液样分离株与其实验室获得的非黏液样衍生物之间未发现序列差异，然而转录分析表明参与胞外多糖产生的基因至少部分下调。我们的研究考察了洋葱伯克霍尔德菌在慢性感染过程中的进展，包括可能从原始分离株进化而来的亚群的形成，提示平行进化。此外，具有不同黏液样表型的两株分离株之间缺乏序列差异表明，其他因素，如基因调控，在黏液样表型的形成中起作用。
