title: Spectrum of non-tuberculous mycobacteria identified using standard biochemical testing vs. 16S sequencing.
abstract: Non-tuberculous mycobacterial isolates from gold miners were speciated using standard biochemical testing (SBT) and 16S rDNA sequencing. Of 237 isolates tested, SBT identified 126, compared with all 237 identified using sequencing. Of 111 isolates unspeciated by SBT but identified by  sequencing, 38 (34.2%) were identified as Mycobacterium gordonae and 8 (7.2%) were new species. Of 126 isolates speciated by both methods, 37 were discordant, with 14/17 M. gordonae isolates incorrectly identified as M. scrofulaceum using SBT. The majority of these were  the potentially pathogenic strain D, M. gordonae. Sequencing is preferable where available to guide treatment.
authors.affiliation: The Aurum Institute, Parktown, South Africa. vchihota@auruminstitute.org
authors.forename: V N
authors.initials: VN
authors.lastname: Chihota
authors.forename: C L
authors.initials: CL
authors.lastname: van Halsema
authors.forename: A D
authors.initials: AD
authors.lastname: Grant
authors.forename: K L
authors.initials: KL
authors.lastname: Fielding
authors.forename: P D
authors.initials: PD
authors.lastname: van Helden
authors.forename: G J
authors.initials: GJ
authors.lastname: Churchyard
authors.forename: N C
authors.initials: NC
authors.lastname: Gey van Pittius
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis*; D006801:Humans; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D014376:Tuberculosis / Q000175:diagnosis / Q000235:genetics / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial