Polymorphism of Variable-Number Tandem Repeats at Multiple Loci inMycobacterium tuberculosis

ABSTRACTGenotyping based on variable-number tandem repeats (VNTR) is currently a very promising tool for studying the molecular epidemiology and phylogeny ofMycobacterium tuberculosis. Here we investigate the polymorphisms of 48 loci of direct or tandem repeats inM. tuberculosispreviously identified by our group. Thirty-nine loci, including nine novel ones, were polymorphic. Ten VNTR loci had high allelic diversity (Nei's diversity indices ≥ 0.6) and subsequently were used as the representative VNTR typing set for comparison to IS6110-based restriction fragment length polymorphism (RFLP) typing. The 10-locus VNTR set, potentially providing >2 × 109allele combinations, obviously showed discriminating capacity over the IS6110RFLP method forM. tuberculosisisolates with fewer than six IS6110-hybridized bands, whereas it had a slightly better resolution than IS6110RFLP for the isolates having more than five IS6110-hybridized bands. Allelic diversity of many VNTR loci varied in each IS6110RFLP type. Genetic relationships inferred from the 10-VNTR set supported the notion thatM. tuberculosismay have evolved from two different lineages (high and low IS6110copy number). In addition, we found that the lengths of many VNTR loci had statistically significant relationships to each other. These relationships could cause a restriction of the VNTR typing discriminating capability to some extent. Our results suggest that VNTR-PCR typing is practically useful for application to molecular epidemiological and phylogenetic studies ofM. tuberculosis. The discriminating power of the VNTR typing system can still be enhanced by the supplementation of more VNTR loci.