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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 - Korean J Lab Med (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Pusan National University, Busan, Korea.

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.

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Related in: MedlinePlus

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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Figure 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.

Mentions: The 96 isolates showed amplification products from 16 VNTR loci and contained at least 1 copy of each locus. Results of allelic diversity and HGDI testing are summarized in Table 3. Among the 16 loci, the discriminatory index in 8 (MIRU-10, -23, -26 and -31; ETR-A, -B, -C, and -F) was high (HGDI > 0.6) according to the definition of Sola et al. [23]. Six loci (MIRU-4, -16, -24, -27, -39 and -40) were dispersed and discriminated moderately well (0.3 ≤ HGDI ≤ 0.6). Two loci (MIRU-2 and -20) were poorly discriminated (HGDI < 0.3). The complete data were divided into 12 groups. The largest group was group 2, which included 15 isolates. Group 11 contained the only unique pattern (Fig. 2). Unlike the SNP method, MIRU-VNTR did not show notable localizations of Beijing or non-Beijing family isolates in specific clusters.


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 - Korean J Lab Med (2011)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3111040&req=5

Figure 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.
Mentions: The 96 isolates showed amplification products from 16 VNTR loci and contained at least 1 copy of each locus. Results of allelic diversity and HGDI testing are summarized in Table 3. Among the 16 loci, the discriminatory index in 8 (MIRU-10, -23, -26 and -31; ETR-A, -B, -C, and -F) was high (HGDI > 0.6) according to the definition of Sola et al. [23]. Six loci (MIRU-4, -16, -24, -27, -39 and -40) were dispersed and discriminated moderately well (0.3 ≤ HGDI ≤ 0.6). Two loci (MIRU-2 and -20) were poorly discriminated (HGDI < 0.3). The complete data were divided into 12 groups. The largest group was group 2, which included 15 isolates. Group 11 contained the only unique pattern (Fig. 2). Unlike the SNP method, MIRU-VNTR did not show notable localizations of Beijing or non-Beijing family isolates in specific clusters.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Pusan National University, Busan, Korea.

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.

Show MeSH
Related in: MedlinePlus