Flanagan J L, Brodie E L, Weng L, Lynch S V, Garcia O, Brown R, Hugenholtz P, DeSantis T Z, Andersen G L, Wiener-Kronish J P, Bristow J
Department of Anesthesia and Perioperative, University of California, San Francisco, CA, USA.
J Clin Microbiol. 2007 Jun;45(6):1954-62. doi: 10.1128/JCM.02187-06. Epub 2007 Apr 4.
Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.
由铜绿假单胞菌引起的气道感染的管理是一项严峻的临床挑战，但对于插管患者气道感染的微生物生态学却知之甚少。我们通过使用16S rRNA克隆文库和微阵列（系统发育芯片）分析了从被铜绿假单胞菌定植的插管患者获得的气管内吸出物中的细菌多样性，以确定抗生素治疗期间细菌群落组成的变化。从因择期手术短期插管的患者获得的吸出物中未检测到细菌16S rRNA基因，但在所有长期插管患者的样本中通过PCR检测到了该基因。16S rRNA克隆文库测序表明，在被铜绿假单胞菌定植的患者肺部存在许多与口腔、鼻腔和胃肠道相关的细菌，包括已知病原体。系统发育芯片分析检测到了相同的微生物以及许多在克隆文库中未检测到的低丰度额外细菌类群。对于每位患者，两种非培养方法均显示，抗生素给药后细菌多样性降低，且群落由一种肺部病原体主导。在七名研究患者中的六名中，铜绿假单胞菌成为优势菌种，尽管这六名患者中有五名接受了对其体外敏感的抗生素治疗。我们的数据表明，在抗生素选择下细菌多样性的丧失与被铜绿假单胞菌定植的通气患者肺炎的发生高度相关。有趣的是，系统发育芯片分析表明铜绿假单胞菌和芽孢杆菌纲之间的丰度存在相互变化，这表明这些类群可能竞争相似的生态位，并暗示了微生物多样性丧失可能直接导致病原体选择和持续存在的可能机制。
