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 G...

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Bibliographic Details
Published in:Diagnostic microbiology and infectious disease 2008-07, Vol.61 (3), p.284-293
Main Authors: Daley, Peter, Petrich, Astrid, May, Kevin, Luinstra, Kathy, Rutherford, Candy, Chedore, Pamela, Jamieson, Frances, Smieja, Marek
Format: Article
Language:English
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
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Summary: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.
ISSN:0732-8893
1879-0070
DOI:10.1016/j.diagmicrobio.2008.02.018