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

• Published in: Diagnostic microbiology and infectious disease Vol. 61; no. 3; pp. 284 - 293
• Main Authors: Daley, Peter, Petrich, Astrid, May, Kevin, Luinstra, Kathy, Rutherford, Candy, Chedore, Pamela, Jamieson, Frances, Smieja, Marek
• Format: Journal Article
• Language: English
• Published: New York, NY Elsevier Inc 01.07.2008; Elsevier
• Subjects: 16S sequencing; Bacteriological Techniques - economics; Bacteriological Techniques - methods; Bacteriology; Biological and medical sciences; Chromatography, Liquid - methods; Fundamental and applied biological sciences. Psychology; Genotype; High-performance liquid chromatography; Humans; Infectious Disease; Infectious diseases; Internal Medicine; Line probe assay; Medical sciences; Microbiology; Miscellaneous; Mycobacterium - classification; Mycobacterium - genetics; Mycobacterium - isolation & purification; Mycobacterium Infections, Nontuberculous - diagnosis; Mycobacterium Infections, Nontuberculous - microbiology; Nontuberculous mycobacteria; Nucleic Acid Hybridization - methods; RNA, Ribosomal, 16S - genetics; Sensitivity and Specificity; Sequence Analysis, DNA - economics; Tuberculosis - diagnosis; Tuberculosis - microbiology; Line probe assay; High-performance liquid chromatography; Nontuberculous mycobacteria; 16S sequencing; Mycobacterium; Microbiology; HPLC chromatography; Genotype; Identification; Infection; Mycobacteriales; Mycobacteriaceae; 16S-RNA; Bacteria; Actinomycetes
• ISSN: 0732-8893; 1879-0070
• DOI: 10.1016/j.diagmicrobio.2008.02.018

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.