Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore

Abstract

Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.

FIG. 1.

Genetic relationships of the 293 M. tuberculosis isolates. This dendrogram was generated by using the UPGMA algorithm based on the 166 distinct MIRU-VNTR patterns (Table 1) which represented the 293 isolates. M. canettii (26) was used as an outgroup. The M. tuberculosis EAI, W/Beijing, Delhi, and Haarlem families are indicated. Group I includes only the ancestral EAI strains which were TbD1⁺, and group II includes all of the modern M. tuberculosis strains which were TbD1⁻. The allele number in locus 24 is indicated as 24:n. The linkage distance is indicated at the left bottom corner.