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

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 lowcopy-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.

Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage ofMycobacterium tuberculosisin Israel Originating Predominantly in Sub-Saharan Africa

“…2). Therefore, the 16-locus panel is less discriminatory than RFLP for molecular typing of PETRA lineage strains, although it still may have value for identifying epidemiological links (8,74). A 24-locus MIRU-VNTR panel has recently been reported to separate each of many different CAS spoligotypes (6).…”

Evaluation of the Selected 12-locus MIRU for Genotyping Beijing Family Mycobacterium tuberculosis in Korea

“…Some authors have found it to show a discriminatory power equivalent to that of RFLP and have considered it an alternative to IS6110-RFLP for epidemiological purposes [4][5][6][7] . However, other authors have found limitations in its discriminatory power and incomplete correlation with the RFLP analysis [8][9][10] , indicating that MIRU analysis should be combined with an additional genotyping method [10][11][12][13] . We compared the MIRU-12 version and IS6110-RFLP in independent samples in the context of molecular epi- Materials and Methods…”

Application of Mycobacterial Interspersed Repetitive Unit Typing to Manitoba Tuberculosis Cases: Can Restriction Fragment Length Polymorphism Be Forgotten?

“…VNTR typing (10), is a more rapid method, requires little culture growth, provides easy-to-compare numerical data, and can be performed by standard agarose gel electrophoresis or, alternatively, developed as a high-throughput system. Mycobacterial interspersed repetitive unit (MIRU) typing utilizes 12 VNTR loci and has been found to have similar discriminatory power to RFLP depending on the sample population, particularly in cases where isolates have zero to five copies of the IS6110 element, such as with M. bovis strains (2,7,15,18,25). It is plausible that MIRU typing may become the predominant method of choice for TB genotyping (15).…”