Korean J Lab Med.  2011 Jan;31(1):37-43. 10.3343/kjlm.2011.31.1.37.

Application of Single-nucleotide Polymorphism and Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats Analyses to Clinical Mycobacterium tuberculosis Isolates from Korea

• Choi GE
• Jang MH
• Cho HJ
• Lee SM
• Yi J
• Lee EY
• Chang CL
• Kim YD
• Kim MB

• KMID: 1096658
• DOI: http://doi.org/10.3343/kjlm.2011.31.1.37

Abstract

BACKGROUND
Single-nucleotide polymorphism (SNP) analysis is a powerful strategy for large-scale molecular population studies examining phylogenetic relationships among bacterial strains. Mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) can be easily digitized to share data among laboratories. This study applied SNP and MIRU-VNTR analyses for molecular strain typing of Mycobacterium tuberculosis isolates collected throughout Korea.
METHODS
We studied 102 clinical M. tuberculosis isolates, including 6 paired strains, collected from 11 university hospitals in Korea in 2008 and 2009. SNPs were detected using hairpin primer assays, and then, MIRU-VNTR analysis was performed.
RESULTS
Thirty-five SNPs contained polymorphisms that helped differentiate the 96 tested isolates. The isolates were classified into 15 clusters. The Beijing family strains were distributed within closely related clusters in the SNP dendrogram. For MIRU-VNTR analysis, the 96 isolates were divided into 12 groups. The discriminatory index in 8 of these groups (MIRU-10, -23, -26, and -31; ETR-A, -B, -C, and -F) was high (Hunter-Gaston diversity index > 0.6). Unlike the SNP method, MIRU-VNTR analysis did not identify any notable localizations of Beijing or non-Beijing family isolates in specific clusters.
CONCLUSIONS
SNP and MIRU-VNTR analyses are surrogate molecular strain-typing methods for M. tuberculosis in Korea where Beijing family isolates are predominant.

Keyword

Mycobacterium tuberculosis; Single-nucleotide polymorphism; Mycobacterial interspersed repetitive units-variable number of tandem repeats

MeSH Terms

Cluster Analysis
DNA Primers/chemistry
Interspersed Repetitive Sequences
*Minisatellite Repeats
Mycobacterium tuberculosis/*classification/genetics/isolation & purification
Phylogeny
*Polymorphism, Single Nucleotide
Republic of Korea

Figure

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  Fig. 1 Distance-based neighbor joining phylogenetic tree of 96 Mycobacterium tuberculosis isolates based on 35 single-nucleotide polymorphisms reveals 15 clusters (indicated by dotted circles). Each IS6110-restriction fragment length polymorphism type is indicated by a closed circle, quadrangle, or arrow.

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  Fig. 2 Distance-based neighbor joining phylogenetic tree of 96 Mycobacterium tuberculosis isolates based on based on mycobacterial interspersed repetitive units-variable number of tandem repeats of 16 loci reveals 12 clusters (dotted circles). Each IS6110-restriction fragment length polymorphism type is indicated by a closed circle, quadrangle, or arrow.

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