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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 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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Figure 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.

Mentions: Among the 45 SNPs, 35 had polymorphisms that could be used to differentiate the 96 tested isolates. The other 10 SNPs did not contain polymorphisms. Based on SNP results, isolates were classified into 15 clusters (Fig. 1). Cluster 1, the most populated cluster, contained 19 isolates, followed by cluster 4 with 17 isolates. Three clusters consisted of only 1 isolate each (Table 2). As shown in Fig. 1, nearly all Beijing family strains, which are defined and identified by IS6110 RFLP data [17], were distributed within closely related clusters in the SNP dendrogram. Seventy-four of the 76 Beijing family strains were allocated to SNP clusters 1 through 12. The remaining 2 isolates were allocated to clusters 13 and 14. Nearly all 14 isolates of the K family, a subfamily of the Beijing family identified in a previous study [17], were allocated to clusters 4 and 6.


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

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

Figure 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.
Mentions: Among the 45 SNPs, 35 had polymorphisms that could be used to differentiate the 96 tested isolates. The other 10 SNPs did not contain polymorphisms. Based on SNP results, isolates were classified into 15 clusters (Fig. 1). Cluster 1, the most populated cluster, contained 19 isolates, followed by cluster 4 with 17 isolates. Three clusters consisted of only 1 isolate each (Table 2). As shown in Fig. 1, nearly all Beijing family strains, which are defined and identified by IS6110 RFLP data [17], were distributed within closely related clusters in the SNP dendrogram. Seventy-four of the 76 Beijing family strains were allocated to SNP clusters 1 through 12. The remaining 2 isolates were allocated to clusters 13 and 14. Nearly all 14 isolates of the K family, a subfamily of the Beijing family identified in a previous study [17], were allocated to clusters 4 and 6.

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