Annals of Clinical Microbiology, The official Journal of the Korean Society of Clinical Microbiology


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Identification of Bacterial and Fungal Isolates by Sequence Analysis of 16S rRNA and Internal Transcribed Spacer

Original article

Annals of Clinical Microbiology (Ann Clin Microbiol) 2010 March, Volume 13, Issue 1, pages 34-39.

Identification of Bacterial and Fungal Isolates by Sequence Analysis of 16S rRNA and Internal Transcribed Spacer

Younhee Park1, Hee Bong Shin2,7, Chang Ki Kim3,7, Kyoung Ho Roh4,7, Jong Hwa Yum5,7, Dongeun Yong6,7, Seok Hoon Jeong6,7, Kyungwon Lee6,7
Department of Laboratory Medicine, 1Kwandong University College of Medicine, Goyang, 2Soonchunhyang University College of Medicine, 4Korea University College of Medicine, Seoul, 5Department of Clinical Laboratory Science, Dongeui University, Busan, 6Department of Laboratory Medicine and 7Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 3Korean Institute of Tuberculosis, Seoul, Korea


Background: Accurate and rapid identification of pathogens is one of the most important tasks of the clinical microbiology laboratory, and, in cases of rare pathogens, the identification is difficult and time-consuming upon the use of conventional methods alone. Herein, we will report our molecular work involving the identification of bacteria and fungi. 

Methods: Sixty bacterial isolates had been collected from November 2004 to May 2007, and 15 fungal isolates had been collected from September 2005 to May 2007. Species identifications were performed using sequence analyses of the 16S rRNA region of bacteria and the internal transcribed spacer (ITS) region of fungi. The data were compared with those of GenBank ( or EMBL (http:// 

Results: Sixty bacterial isolates included: 23 isolates with genus information (group 1), 17 isolates (group 2) that were too fastidious for genus or species identification, 16 isolates (group 3) with results from identification kits having low confidence, and 4 isolates (group 4) with odd antibiograms according to the species. In 58 of 60 isolates, identification of the genus or species could be obtained using molecular genetic methods. Thirty-eight isolates (63%) and 20 (33%) of 58 isolates could be identified at the species and genus levels, repectively. Among the total of 15 fungal isolates, 11 (73%) and 4 (27%) isolates were identified at the species and genus levels, respectively. 

Conclusion: 16S rRNA and ITS sequencing analyses are very useful for identifying the species or genus of a pathogenic microorganism in the clinical microbiology laboratory. (Korean J Clin Microbiol 2010;13: 34-39)


16S rRNA, Internal transcribed spacer, Nucleotide sequence, Bacterial identification