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Analysis of the microbiota of sputum samples from patients with lower respiratory tract infections

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分类：S858.963[农业科学—临床兽医学;农业科学—兽医学;农业科学—畜牧兽医] TS214.2[轻工技术与工程—粮食、油脂及植物蛋白工程;轻工技术与工程—食品科学与工程]
作者机构：[1]Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, [2]Medical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China, [3]Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, [4]Departmem of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, [5]Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China
相关基金：This work was supported by grants from the National Natural Science Foundation of China （30770111, 30900051, and 30970125）, the National Key Program for Infectious Diseases of China （2008ZX10004 and 2009ZX10004）, the Program of Shanghai Subject Chief Scientist （09XD1402700）, and the Program of Shanghai Research and Development （10JC 1408200）.
相关项目：钩端螺旋体比较蛋白质组学研究

关键词：呼吸道感染, 微生物分析, 标本, 焦磷酸测序, 细菌鉴定, 细菌检测, 自动化系统, DNA片段, 16S ribosomal DNA, lower respiratoryinfection, microbiota, pyrosequence, sputum

中文摘要：

唾沫是从患更低的呼吸的道感染的病人收集的最普通的样品，它为这些感染的细菌的鉴定是关键的。在这研究，我们与更低的呼吸的道感染从 101 个病人注册了 101 件唾沫样品。开始，在唾沫包含的细菌的 16S rDNA V3 hypervariable 区域的 pyrosequencing 为 microbiota 分析作为一条文化无关的途径被利用。为比较，用一个文化依赖者的临床的实验室测试为样品也被做的唾沫的一样的队自动化了细菌的鉴定系统。由 pyrosequencing， > 70,000 DNA 碎片在被 Ribosomal 数据库工程(RDP ) 过程分析以后被发现并且分类进 129 个细菌的类。大多数序列属于几个占优势的类，例如链球菌和葡萄球菌，显示这些类起在更低的呼吸的道感染的一个重要作用。另外，属于潜在的原因的代理人的一些序列例如霉浆菌， Haemophilus，和 Moraxella，也被发现，但是这些序列没被临床的实验室测试发现。为两个方法检测的九个类，方法的敏感被比较，结果证明 pyrosequencing 是更敏感的，除了 Klebsiella 和 Mycobacterium。显著地，这个方法揭示了更复杂的细菌的社区，它为细菌的察觉显示出一个有希望的能力。

英文摘要：

Sputum is the most common sample collected from patients suffering from lower respiratory tract infections and it is crucial for the bacterial identification of these infections. In this study, we enrolled 101 sputum samples from 101 patients with lower respiratory tract infections. Initially, pyrosequencing of the 16S rDNA V3 hypervariable regions of the bacteria contained in the sputum was utilized as a culture-independent approach for microbiota analysis. For comparison, clinical laboratory tests using a culture-dependent automated bacterial identification system for the same cohort of sputum samples were also done. By pyrosequencing, 〉70,000 DNA fragments were found and classified into 129 bacterial genera after being analyzed by the Ribosomal Database Project （RDP） process. Most sequences belonged to several predominant genera, such as Streptococcus and Staphylococcus, indicating that these genera play an important role in lower res- piratory tract infections. In addition, some sequences belonging to potential causative agents, such as Mycoplasma, HaemophUus, and Moraxella, were also found, but these sequences were not found by clinical laboratory tests. For the nine genera detected by both methods, the methods＇ sensitivities were compared and the results showed that pyrosequencing was more sensitive, except for Klebsieila and Mycobacterium. Significantly, this method revealed much more complicated bacterial communities and it showed a promising ability for the detection of bacteria.

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