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Comparative Study
. 2001 Jul;39(7):2453-7.
doi: 10.1128/JCM.39.7.2453-2457.2001.

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

R E Barlow  1 , D M Gascoyne-Binzi, S H Gillespie, A Dickens, S Qamer, P M Hawkey
Affiliations
Comparative Study

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

R E Barlow et al. J Clin Microbiol. 2001 Jul.

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.

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Figures

FIG. 1
FIG. 1
IS6110-RFLP patterns of VNTR profile set C (21433). Designations of isolates are shown at right. Numbers at the top indicate percent similarities of IS6110-RFLP patterns.
FIG. 2
FIG. 2
IS6110-RFLP analysis of VNTR set Ac (64466) and isolates with 90% or greater VNTR profile similarity. Designations of isolates, VNTR profile sets, and set codes are shown at right. Numbers at the top indicate percent similarities of IS6110-RFLP patterns.
See this image and copyright information in PMC

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