Composition and dynamics of the respiratory tract microbiome in intubated patients.
Composition and dynamics of the respiratory tract microbiome in intubated patients.
复制标题
DOI：
10.1186/s40168-016-0151-8
复制
发表时间：
2016-02-11
期刊：
影响因子：
15.5
通讯作者：
Collman RG
中科院分区：
文献类型：
--
作者：
Kelly BJ;Imai I;Bittinger K;Laughlin A;Fuchs BD;Bushman FD;Collman RG
下呼吸道感染（LRTI）是导致需要插管和机械通气的呼吸衰竭的主要原因。LRTI也发生在机械通气期间，增加了插管患者的发病率和死亡率。我们试图了解插管后呼吸道微生物群的动态以及微生物群落结构与感染之间的关系。我们在一个学术医学中心的重症监护室招募了一组15名需要插管和机械通气的呼吸衰竭受试者。在插管后24 h内和此后每48-72 h采集口咽（OP）和深部气管内（ET）分泌物。通过纯化DNA、PCR扩增16 S核糖体RNA（rRNA）基因序列、深度测序和生物信息学群落分析进行细菌群落分析。我们将入组的受试者与通过支气管镜检查进行下呼吸道采样的健康受试者队列进行比较。与健康对照中发现的上呼吸道和下呼吸道微生物群的多样性相反，重症受试者在两个地点的初始多样性较低。随着时间的推移，呼吸机上的多样性进一步减少。在几个主题中，细菌群落在多个时间点由单一分类群主导。通过图表审查确定的下呼吸道感染的临床诊断与低群落多样性和单一分类群的优势相关。优势分类群与获得培养物且呈阳性的临床细菌培养物相匹配。在一些情况下，优势类群包括培养未检测到的细菌，包括微小脲原体和粪肠球菌。对危重患者呼吸道微生物群的纵向分析可深入了解LRTI的发病机制和诊断。气管内吸出物样本的16 S rRNA基因测序有望扩大病原体鉴定。本文的在线版本（doi：10.1186/s40168-016-0151-8）包含补充材料，可供授权用户使用。
Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity and mortality of intubated patients. We sought to understand the dynamics of respiratory tract microbiota following intubation and the relationship between microbial community structure and infection. We enrolled a cohort of 15 subjects with respiratory failure requiring intubation and mechanical ventilation from the medical intensive care unit at an academic medical center. Oropharyngeal (OP) and deep endotracheal (ET) secretions were sampled within 24 h of intubation and every 48–72 h thereafter. Bacterial community profiling was carried out by purifying DNA, PCR amplification of 16S ribosomal RNA (rRNA) gene sequences, deep sequencing, and bioinformatic community analysis. We compared enrolled subjects to a cohort of healthy subjects who had lower respiratory tract sampling by bronchoscopy. In contrast to the diverse upper respiratory tract and lower respiratory tract microbiota found in healthy controls, critically ill subjects had lower initial diversity at both sites. Diversity further diminished over time on the ventilator. In several subjects, the bacterial community was dominated by a single taxon over multiple time points. The clinical diagnosis of LRTI ascertained by chart review correlated with low community diversity and dominance of a single taxon. Dominant taxa matched clinical bacterial cultures where cultures were obtained and positive. In several cases, dominant taxa included bacteria not detected by culture, including Ureaplasma parvum and Enterococcus faecalis. Longitudinal analysis of respiratory tract microbiota in critically ill patients provides insight into the pathogenesis and diagnosis of LRTI. 16S rRNA gene sequencing of endotracheal aspirate samples holds promise for expanded pathogen identification. The online version of this article (doi:10.1186/s40168-016-0151-8) contains supplementary material, which is available to authorized users.