Comparison of in-house and commercial 16S rRNA sequencing with high-performance liquid chromatography and genotype AS and CM for identification of nontuberculous mycobacteria

Diagn Microbiol Infect Dis. 2008 Jul;61(3):284-93. doi: 10.1016/j.diagmicrobio.2008.02.018. Epub 2008 May 1.

Abstract

Sequencing of the 16S gene or other targets and line probe assay are in wide use for the identification of nontuberculous mycobacteria. We compared in-house and commercial sequencing with 3 sequence databases against high-performance liquid chromatography (HPLC) and line probe assay (HAIN Genotype AS and CM) for the identification of 84 reference, clinical, and unique strains representing 41 species. Consensus of methods was used as reference standard. Sequencing identification was more specific and flexible than HPLC, but it was limited by database content and quality as well as fragment length. No one database satisfied all requirements. In-house sequencing was lower in cost than commercial sequencing or line probe assay.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriological Techniques / economics
  • Bacteriological Techniques / methods*
  • Chromatography, Liquid / methods
  • Genotype
  • Humans
  • Mycobacterium / classification*
  • Mycobacterium / genetics
  • Mycobacterium / isolation & purification*
  • Mycobacterium Infections, Nontuberculous / diagnosis*
  • Mycobacterium Infections, Nontuberculous / microbiology
  • Nucleic Acid Hybridization / methods
  • RNA, Ribosomal, 16S / genetics*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / economics
  • Tuberculosis / diagnosis*
  • Tuberculosis / microbiology

Substances

  • RNA, Ribosomal, 16S