Woo P C Y, Lau S K P, Teng J L L, Tse H, Yuen K-Y
State Key Laboratory of Emerging Infectious Diseases; and Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
Clin Microbiol Infect. 2008 Oct;14(10):908-34. doi: 10.1111/j.1469-0691.2008.02070.x.
In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7 years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However, studies on the accuracy of the software packages have given highly varied results, and interpretation of results remains difficult for most technicians, and even for clinical microbiologists. To fully utilize 16S rDNA sequencing in clinical microbiology, better guidelines are needed for interpretation of the identification results, and additional/supplementary methods are necessary for bacterial species that cannot be identified confidently by 16S rDNA sequencing alone.
在过去十年中，由于聚合酶链反应（PCR）和DNA测序的广泛应用，16S核糖体DNA（rDNA）测序在临床微生物实验室中细菌分离株的准确鉴定以及新细菌的发现方面发挥了关键作用。对于细菌鉴定而言，16S rDNA测序在具有异常表型特征的细菌、稀有细菌、生长缓慢的细菌、不可培养细菌以及培养阴性感染的情况下尤为重要。它不仅为传染病的病因提供了见解，还帮助临床医生选择抗生素、确定治疗持续时间以及制定感染控制措施。在21世纪的过去7年（2001 - 2007年）中，通过16S rDNA测序，已从人类标本中发现了215个新细菌物种，其中29个属于新属。在这215个新物种中，有100个在四个或更多个体中被发现，其中15个属于新属。发现新物种数量最多的属是分枝杆菌属（n = 12）和诺卡氏菌属（n = 6）。口腔/牙科相关标本（n = 19）和胃肠道（n = 26）是发现新物种和/或新物种储存库的最重要部位。在这100个新物种中，中华链球菌、香港利拉菌、哈氏梭菌和斯氏疏螺旋体得到了最全面的表征，记录了它们的储存库和传播途径，并且中华链球菌、香港利拉菌和哈氏梭菌在全球范围内均有发现。将1-6S rDNA测序应用于临床微生物实验室常规检测的最大障碍之一是该技术的自动化。目前唯一可以自动化的步骤是将细菌分离株的16S rDNA序列输入到其中一个软件包中，该软件包将根据其序列数据库生成分离株的鉴定结果。然而，关于这些软件包准确性的研究结果差异很大，对于大多数技术人员甚至临床微生物学家来说，结果的解读仍然很困难。为了在临床微生物学中充分利用16S rDNA测序，需要更好的指南来解读鉴定结果，对于仅通过16S rDNA测序无法可靠鉴定的细菌物种，还需要额外的/补充性方法。
