Korean J Clin Microbiol.  2010 Mar;13(1):34-39. 10.5145/KJCM.2010.13.1.34.

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

• Park Y
• Shin HB
• Kim CK
• Roh KH
• Yum JH
• Yong D
• Jeong SH
• Lee K

• KMID: 1828593
• DOI: http://doi.org/10.5145/KJCM.2010.13.1.34

Abstract

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 (http://www.ncbi.nlm.nih.gov/) or EMBL (http://www.ebi.ac.uk/embl/).
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.

Keyword

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

MeSH Terms

Bacteria
Base Sequence
Databases, Nucleic Acid
Fungi
Microbial Sensitivity Tests
Molecular Biology
Sequence Analysis

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