Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.
Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.
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使用 16S rRNA 基因鉴定多种临床相关细菌病原体。
DOI：
10.1371/journal.pone.0117617
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Lynch SV
中科院分区：
文献类型：
--
作者：
Srinivasan R;Karaoz U;Volegova M;MacKichan J;Kato-Maeda M;Miller S;Nadarajan R;Brodie EL;Lynch SV
根据世界卫生组织2011年的统计，传染病仍然是全世界五大死亡原因之一。然而，尽管有用于微生物检测的复杂研究工具，但用于鉴定人类感染的快速和准确的分子诊断尚未被广泛采用。耗时的基于培养的方法仍然是临床微生物检测的最前沿。16S rRNA基因是一种用于鉴定细菌物种的分子标记，对该域的成员来说是普遍存在的，并且由于不断扩展的序列信息数据库，16S rRNA基因是细菌鉴定的有用工具。在这项研究中，我们组装了一个广泛的临床分离株（n = 617），代表30个医学上重要的致病物种，最初使用传统的文化为基础的或非16S分子方法确定。该菌株库用于系统地评价16S rRNA用于种水平鉴定的能力。为了基于公共数据库中积累的序列数据的缺乏实现最准确的物种水平分类，我们构建了一个朴素贝叶斯分类器，代表了医学上重要的细菌生物体的一组不同的高质量序列。我们表明，物种识别，基于模型的方法是上级对齐为基础的方法。总的来说，基于16S基因和临床身份之间，我们的研究显示属级一致率为96%，种级一致率为87.5%。我们指出，在广泛的革兰氏阴性杆菌和革兰氏阳性球菌以及常见的革兰氏阴性球菌中，基于传统培养的鉴定存在多个可能的临床错误鉴定病例。
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.
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DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
4.4
作者：
Fettweis JM;Serrano MG;Sheth NU;Mayer CM;Glascock AL;Brooks JP;Jefferson KK;Vaginal Microbiome Consortium (additional members);Buck GA
通讯作者：
Buck GA
影响因子：
9.4
作者：
Carvalho, MGS;Steigerwalt, AG;Facklam, RR
通讯作者：
Facklam, RR
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM
影响因子：
9.4
作者：
Coenye, T;Spilker, T;LiPuma, JJ
通讯作者：
LiPuma, JJ