Korean J Lab Med.  2006 Jun;26(3):153-160. 10.3343/kjlm.2006.26.3.153.

Identification of Nontuberculous Mycobacteria by Sequence Analysis of the 16S Ribosomal RNA, the Heat-shock Protein 65 and the RNA Polymerase beta-Subunit Genes

• Shin S
• Kim EC
• Yoon JH

• KMID: 2238880
• DOI: http://doi.org/10.3343/kjlm.2006.26.3.153

Abstract

BACKGROUND: The diagnosis of diseases caused by nontuberculous mycobacteria (NTM) is difficult, because NTM are prevalent in the environment such as soil and water, and because they have fastidious properties. In this study we investigated clinical isolates of NTM for their distribution pattern and accurate species identification.
METHODS
We selected presumptive NTM isolates negative for probe hybridization for M. tuberculosis complex, cultured in a third referral hospital from 21 January 2003 to 20 January 2004. Ninety seven-isolates were identified to the species level by direct sequencing of fragments of 16S rRNA, hsp65 and rpoB genes. A total of 120 isolates were studied for the distribution analysis.
RESULTS
Frequently identified NTM species were M. avium (30.8%), M. intracellulare (23.3%) and M. abscessus (18.3%). Others were M. gordonae, M. senegalense, M. fortuitum, M. peregrinum, M. kansasii, M. terrae complex, M. lentiflavum, M. chelonae, and M. szulgai. Three M. tuberculosis complex (2.5%) were also identified among the presumptive NTM isolates. The identification rate by sequencing of 16S rRNA, rpoB, and hsp65 were 65%, 82% and 87%, respectively. The hsp65 or rpoB gene was more efficient than 16S rRNA for the identification of NTM by sequencing.
CONCLUSIONS
Some NTM are increasingly considered to be the causative organisms in clinical diseases. Thus, direct sequencing could be adapted to routine work of clinical laboratories for accurate identification of NTM to the species level.

Keyword

Sequence analysis; Atypical mycobacteria; rpoB; 16S rRNA; Heat-shock protein

MeSH Terms

Diagnosis
DNA-Directed RNA Polymerases*
Gordonia Bacterium
Heat-Shock Proteins*
Nontuberculous Mycobacteria*
Referral and Consultation
RNA*
RNA, Ribosomal, 16S*
Sequence Analysis*
Soil
Tuberculosis
DNA-Directed RNA Polymerases
Heat-Shock Proteins
RNA
RNA, Ribosomal, 16S
Soil

Figure

• 

  Fig. 1. Nucleotide sequences of the partial hsp65 gene from 15 M. abscessus(HSP2-HSP107) and one M. chelonae (HSP74) strains aligned with reference sequences from Genebank (AF071128 and AF071139, M. abscessus strains; AF071130, AF071141 and AF 071142, M. chelonae strains).

Reference

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