title: Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates.
abstract: The present study was designed to evaluate the use of variable number tandem repeat (VNTR) and IS6110-restriction fragment length polymorphism (RFLP) analyses in combination as a two-step strategy for discrimination (as measured by the Hunter-Gaston Discrimination Index [HGDI]) of both high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates compared to IS6110-RFLP alone with an unselected collection of isolates. Individually, IS6110-RFLP fingerprinting produced six clusters that accounted for 69% of the low-copy-number IS6110 isolates (five clusters) and 5% of the high-copy-number IS6110 isolates (one cluster). A total of 39% of all the isolates were clustered (HGDI = 0.97). VNTR analysis generated a total of 35 different VNTR allele profile sets from 93 isolates (HGDI = 0.938). Combining IS6110-RFLP analysis with VNTR analysis reduced the overall percentage of clustered isolates to 29% (HGDI = 0.988) and discriminated a further 27% of low-copy-number isolates that would have been clustered by IS6110-RFLP alone. The use of VNTR analysis as an initial typing strategy facilitates further analysis by IS6110-RFLP, and more importantly, VNTR analysis subdivides some IS6110-RFLP-defined clusters containing low- and single-copy IS6110 isolates.
authors: The Division of Microbiology, School of Biochemistry & Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors: R E
authors: RE
authors: Barlow
authors: D M
authors: DM
authors: Gascoyne-Binzi
authors: S H
authors: SH
authors: Gillespie
authors: A
authors: A
authors: Dickens
authors: S
authors: S
authors: Qamer
authors: P M
authors: PM
authors: Hawkey
mesh_terms: D016000:Cluster Analysis; D004251:DNA Transposable Elements / Q000235:genetics*; D018628:Gene Dosage; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D012150:Polymorphism, Restriction Fragment Length
chemical_list: D004251:DNA Transposable Elements