Variable human minisatellite‐like regions in the Mycobacterium tuberculosis genome

Abstract

Mycobacterial interspersed repetitive units (MIRUs) are 40–100 bp DNA elements often found as tandem repeats and dispersed in intergenic regions of the Mycobacterium tuberculosis complex genomes. The M. tuberculosis H37Rv chromosome contains 41 MIRU loci. After polymerase chain reaction (PCR) and sequence analyses of these loci in 31 M. tuberculosis complex strains, 12 of them were found to display variations in tandem repeat copy numbers and, in most cases, sequence variations between repeat units as well. These features are reminiscent of those of certain human variable minisatellites. Of the 12 variable loci, only one was found to vary among genealogically distant BCG substrains, suggesting that these interspersed bacterial minisatellite‐like structures evolve slowly in mycobacterial populations.

Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India

“…This deficiency is partially solved with spoligotyping as a secondary method (Cowan et al 2005). Our results also corroborate a previous proposition that it is ultimately MIRU typing that will resolve the problems stemming from low-IS6110-copy strains (Supply et al 2000); indeed, IS6110-RFLP typing in other parts of India has revealed the presence of a 2 3 3 3 2 1 82 00134 EAI3-IND 2 3 4 3 *6 3 3 3 3 2 4 83 00374 EAI3-IND 2 5 3 3 *6 2 3 3 3 2 4 84 00378 EAI3-IND 2 5 3 2 *6 3 2 3 5 2 3 85 00652 EAI3-IND 2 3 3 2 *6 2 2 3 5 2 2 86 00660 EAI3-IND 2 3 3 2 *6 2 2 3 4 3 3 87 00938 EAI3-IND 1 5 5 4 *6 2 3 3 5 3 3 88 03390 EAI3-IND 2 3 6 4 *6 3 2 4 8 3 3 89 05431 EAI3-IND 2 3 3 3 *7 2 4 3 3 2 5 90 …”

“…Though unusual for high-banded strains, similar findings have been reported by other investigators who reported isolates within IS6110-RFLP clusters that differed by two-seven loci in a 24 loci MIRU-VNTR assay (Shamputa et al 2010). We used primers for 11 loci from the original set of 12 loci used in earlier studies (Supply et al 2000). Valcheva et al (2008) compared the use of 12, 15 and 24 loci to genotype 73 strains of M. tuberculosis.…”

“…Genotyping and database comparison -The bacterial DNAs were prepared as reported previously (van Soolingen et al 1991) and were submitted to spoligotyping (Kamerbeek et al 1997), 12-loci MIRU typing (Supply et al 2000) and IS6110-RFLP (van Embden et al 1993), using published protocols. MIRU typing was performed manually using polymerase chain reaction amplification of 11 loci because the 12th locus, locus 20, was found to be poorly discriminative in a preliminary study in the North Delhi region (results not shown) and was therefore not included in the present study.…”

“…However, when used alone, these methods may underestimate the clonal diversity of M. tuberculosis (Kremer et al 1999). Molecular typing methods based on variable-number tandem repeats (VNTRs) of genetic elements called mycobacterial interspersed repetitive units (MIRUs) have also been developed by Supply et al (2000Supply et al ( , 2001. MIRU-VN-TR typing shows a discriminatory power close to that of IS6110 fingerprinting and can be used to differentiate between M. tuberculosis isolates that lack or have low copy numbers of IS6110 elements (Supply et al 2000).…”

“…Molecular typing methods based on variable-number tandem repeats (VNTRs) of genetic elements called mycobacterial interspersed repetitive units (MIRUs) have also been developed by Supply et al (2000Supply et al ( , 2001. MIRU-VN-TR typing shows a discriminatory power close to that of IS6110 fingerprinting and can be used to differentiate between M. tuberculosis isolates that lack or have low copy numbers of IS6110 elements (Supply et al 2000). Very few studies in India have reported use of MIRU-VNTRs for molecular typing of M. tuberculosis isolates , Stavrum et al 2009, Narayanan et al 2010).…”