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Clinical Microbiology and Infection
Volume 14 Issue 10, Pages 908 - 934
Published Online: 15 Sep 2008
REVIEW
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories
16S rDNA基因测序的过去和现在:临床微生物实验室发现和鉴定新细菌的方法
REVIEW
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories
P. C. Y. Woo 1,2,3* , S. K. P. Lau 1,2,3* , J. L. L. Teng 3 , H. Tse 1,2,3 and K.-Y. Yuen 1,2,3
1 State Key Laboratory of Emerging Infectious Diseases , 2 Research Centre of Infection and Immunology and 3 Department of Microbiology, The University of Hong Kong, Hong Kong, China
Corresponding author and reprint requests: K. Y. Yuen, State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China
E-mail: hkumicro@hkucc.hku.hk
*P. C. Y. Woo and S. K. P. Lau contributed equally to the article.
Copyright Journal compilation © 2008 European Society of Clinical Microbiology and Infectious Diseases
KEYWORDS
16S rDNA gene • bacteria • discovery • identification • review • sequencing
ABSTRACT
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. |
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