Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability
Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability
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DOI：
10.1513/annalsats.201903-270oc
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发表时间：
2019-12-01
影响因子：
8.3
通讯作者：
LiPuma, John J.
中科院分区：
文献类型：
--
作者：
Caverly, Lindsay J.;Lu, Junnan;LiPuma, John J.
理论基础：为了更好地了解囊性纤维化(CF)恶化的微生物触发因素，研究了临床稳定期和呼吸道症状加重之间的呼吸道微生物区系差异。以前的研究通常依赖于单个样本或有限数量的样本来代表呼吸道微生物区系。目的：确定临床稳定期呼吸道微生物群指标的时间变异性，并找出与这种变异性相关的因素。方法：对临床稳定期6例成人CF患者的痰标本(N=527)进行细菌16S核糖体RNA基因V4区序列测定。每个临床稳定期内样本间呼吸道微生物区系的变异性被计算为每个样本与同一时期内所有其他样本的Bray-Curtis相似性度量的平均值。离群值样本被定义为基线期间内相对于平均Bray-Curtis相似性超出四分位数范围1.5倍的样本。结果：同一基准期内样品间的Bray-Curtis相似性和细菌总量的差异大于技术复制对照样品的差异。总体而言，6%的样本被确定为异常值。在基准期内，细菌群落结构的变化与维持性抗生素的变化一致(P<；0.05，分子差异分析)。在受试者中，细菌群落结构在基准期之间发生了变化(P<；0.01，分子变异分析)。基准期内的样本间相似性较大，采样间隔天数较少。结论：在临床稳定期内，成人CF患者每日痰标本间的细菌群落结构和细菌载量存在差异。这种日常变化对研究设计和结果的解释有影响，特别是在依赖单个样本来代表感兴趣的时期(例如，临床稳定与肺恶化)的分析中。这些数据还强调了在研究中考虑维持抗生素使用和样本收集粒度的重要性，这些研究旨在评估与临床状态变化相关的CF呼吸道微生物区系的动态。
Rationale: Differences in cystic fibrosis (CF) airway microbiota between periods of clinical stability and exacerbation of respiratory symptoms have been investigated in efforts to better understand microbial triggers of CF exacerbations. Prior studies have often relied on a single sample or a limited number of samples to represent airway microbiota. However, the variability in airway microbiota during periods of clinical stability is not well known.Objectives: To determine the temporal variability of measures of airway microbiota during periods of clinical stability, and to identify factors associated with this variability.Methods: Sputum samples (N= 527), obtained daily from six adults with CF during 10 periods of clinical stability, underwent sequencing of the V4 region of the bacterial 16S ribosomal RNA gene. The variability in airway microbiota among samples within each period of clinical stability was calculated as the average of the Bray-Curtis similarity measures of each sample to every other sample within the same period. Outlier samples were defined as samples outside 1.5 times the interquartile range within a baseline period with respect to the average Bray-Curtis similarity. Total bacterial load was measured with droplet digital polymerase chain reaction.Results: The variation in Bray-Curtis similarity and total bacterial load among samples within the same baseline period was greater than the variation observed in technical replicate control samples. Overall, 6% of samples were identified as outliers. Within baseline periods, changes in bacterial community structure occurred coincident with changes in maintenance antibiotics (P < 0.05, analysis of molecular variance). Within subjects, bacterial community structure changed between baseline periods (P < 0.01, analysis of molecular variance). Sample-to-sample similarity within baseline periods was greater with fewer interval days between sampling.Conclusions: During periods of clinical stability, airway bacterial community structure and bacterial load vary among daily sputum samples from adults with CF. This day-to-day variation has bearing on study design and interpretation of results, particularly in analyses that rely on single samples to represent periods of interest (e.g., clinical stability vs. pulmonary exacerbation). These data also emphasize the importance of accounting for maintenance antibiotic use and granularity of sample collection in studies designed to assess the dynamics of CF airway microbiota relative to changes in clinical state.