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

The present study was designed to evaluate the use of variable number tande m repeat (VNTR) and IS6110-restriction fragment length polymorphism (RFLP) analyses in combination as a two-step strategy for discrimination (as measu red by the Hunter-Gaston Discrimination Index [HGDI]) of both high- and low -copy-number IS6110 Mycobacterium tuberculosis isolates compared to IS611O- 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 clu stered (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 iso lates to 29% (HGDI = 0.988) and discriminated a further 27% of low-copy-num ber isolates that would have been clustered by IS6110-RFLP alone. The use o f 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.