Comparison of Variable Number Tandem Repeat and IS 6110 -Restriction Fragment Length Polymorphism Analyses for Discrimination of High- and Low-Copy-Number IS 6110 Mycobacterium tuberculosis Isolates

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Abstract
The present study was designed to evaluate the use of variable number tandem repeat (VNTR) and IS 6110 -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 IS 6110 Mycobacterium tuberculosis isolates compared to IS 6110 -RFLP alone with an unselected collection of isolates. Individually, IS 6110 -RFLP fingerprinting produced six clusters that accounted for 69% of the low-copy-number IS 6110 isolates (five clusters) and 5% of the high-copy-number IS 6110 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 IS 6110 -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 IS 6110 -RFLP alone. The use of VNTR analysis as an initial typing strategy facilitates further analysis by IS 6110 -RFLP, and more importantly, VNTR analysis subdivides some IS 6110 -RFLP-defined clusters containing low- and single-copy IS 6110 isolates.

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