Application of Single-nucleotide Polymorphism and Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats Analyses to Clinical Mycobacterium tuberculosis Isolates from Korea
Application of Single-nucleotide Polymorphism and Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats Analyses to Clinical Mycobacterium tuberculosis Isolates from Korea
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DOI：
10.3343/kjlm.2011.31.1.37
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发表时间：
2011-01-01
影响因子：
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通讯作者：
Kim, Moon-Bum
中科院分区：
文献类型：
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作者：
Choi, Go Eun;Jang, Mi Hee;Kim, Moon-Bum
背景：单核苷酸多态性（SNP）分析是大规模分子群体研究检查细菌菌株之间系统发育关系的强大策略。分枝杆菌散布重复单元-可变数量串联重复序列 (MIRU-VNTR) 可以轻松数字化，以便在实验室之间共享数据。本研究应用 SNP 和 MIRU-VNTR 分析对韩国各地收集的结核分枝杆菌分离株进行分子菌株分型。方法：我们研究了 2008 年和 2009 年从韩国 11 所大学医院收集的 102 株临床结核分枝杆菌分离株，其中包括 6 个配对菌株。使用发夹引物分析检测 SNP，然后进行 MIRU-VNTR 分析。结果：包含 35 个 SNP多态性有助于区分 96 个测试分离株。分离株被分为 15 个簇。北京家族菌株分布在 SNP 树状图中密切相关的簇内。对于 MIRU-VNTR 分析，96 个分离株被分为 12 组。其中 8 个组（MIRU-10、-23、-26 和 -31；ETR-A、-B、-C 和 -F）的歧视指数很高（Hunter-Gaston 多样性指数 > 0.6）。与 SNP 方法不同，MIRU-VNTR 分析没有识别出北京科或非北京科分离株在特定簇中的任何显着定位。结论：SNP 和 MIRU-VNTR 分析是韩国结核分枝杆菌的替代分子菌株分型方法，其中北京科分离株占主导地位。
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