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Rapid and Accurate Identification of Mycobacteria by Sequencing Hypervariable Regions of the 16S Ribosomal RNA Gene

Xiang Y. Han MD, PhD, Audrey S. Pham PhD, Jeffrey J. Tarrand MD, Pramila K. Sood MBA, Rajyalakshmi Luthra PhD
DOI: http://dx.doi.org/10.1309/HN44-XQYM-JMAQ-2EDL 796-801 First published online: 1 November 2002


We developed a method to identify mycobacteria by sequencing hypervariable regions of the polymerase chain reaction–amplified 16S ribosomal RNA gene. This method is nearly specific for mycobacteria and uses positive culture from liquid or solid medium without the need for lengthy subculture. It shortens identification time to 3 days, which is much faster than the conventional biochemical method (mean, 8 weeks). It applies to all mycobacteria (approximately 100 species), unlike current nucleic acid hybridization methods, which probe only 4 species. The identifications are the same or are species specific for the well-characterized mycobacteria (59/68 [87%]) or more accurate for recently proposed species (9/68 [13%]). The method requires a single sequencing reaction, which is efficient and cost-effective. Therefore, this method is clinically and academically useful.

Key Words:
  • Mycobacterium
  • Polymerase chain reaction
  • PCR
  • 16S rDNA sequencing