Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis.

Eriko Maeda-Mitani,Akira Oishi,Nobuyuki Sera,Shuji Fujimoto,Yoshiki Etoh,Koichi Murakami

doi:10.1155/2016/5216530

Abstract

QUB11a is used as a locus for variable number of tandem repeats (VNTR) analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp) that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp) investigated contained IS6110 insertions and varied in the number of repeats (18 patterns) and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

Highlights

QUB11a, or variable number of tandem repeats (VNTR) locus 2163a, is an analytical locus that has been useful for molecular epidemiological analysis of the Beijing lineage of Mycobacterium tuberculosis [1, 2]
Wada et al [9] and Millet et al [1] showed the utility of QUB11a for discrimination of Beijing lineage in Japan, and Vlji et al recommended the use of hypervariable loci, including QUB11a, for VNTR analysis of Beijing lineage in the United Kingdom [2]
Information regarding the presence or absence of an IS6110 insertion in the locus will provide an additional way to distinguish between isolates, along with the number of repeats

Summary

Introduction

QUB11a, or variable number of tandem repeats (VNTR) locus 2163a, is an analytical locus that has been useful for molecular epidemiological analysis of the Beijing lineage of Mycobacterium tuberculosis [1, 2]. Wada et al [9] and Millet et al [1] showed the utility of QUB11a for discrimination of Beijing lineage in Japan, and Vlji et al recommended the use of hypervariable loci, including QUB11a, for VNTR analysis of Beijing lineage in the United Kingdom [2]. Based on these findings, QUB11a is not an inconsequential locus

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Conclusion