title: Comparison of in-house and commercial 16S rRNA sequencing with high-performance liquid chromatography and genotype AS and CM for identification of nontuberculous mycobacteria.
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.
authors.affiliation: Department of Pathology and Molecular Medicine, McMaster University, Hamilton ON L8S 4L8, Canada. daleyp@cmcvellore.ac.in
authors.forename: Peter
authors.initials: P
authors.lastname: Daley
authors.forename: Astrid
authors.initials: A
authors.lastname: Petrich
authors.forename: Kevin
authors.initials: K
authors.lastname: May
authors.forename: Kathy
authors.initials: K
authors.lastname: Luinstra
authors.forename: Candy
authors.initials: C
authors.lastname: Rutherford
authors.forename: Pamela
authors.initials: P
authors.lastname: Chedore
authors.forename: Frances
authors.initials: F
authors.lastname: Jamieson
authors.forename: Marek
authors.initials: M
authors.lastname: Smieja
mesh_terms: D001431:Bacteriological Techniques / Q000191:economics / Q000379:methods*; D002853:Chromatography, Liquid / Q000379:methods; D005838:Genotype; D006801:Humans; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D009165:Mycobacterium Infections, Nontuberculous / Q000175:diagnosis* / Q000382:microbiology; D009693:Nucleic Acid Hybridization / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000191:economics; D014376:Tuberculosis / Q000175:diagnosis* / Q000382:microbiology
chemical_list: D012336:RNA, Ribosomal, 16S