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Korean J Lab Med. 2011 Jan;31(1):37-43. English. Original Article.
Choi GE , Jang MH , Cho HJ , Lee SM , Yi J , Lee EY , Chang CL , Kim YD , Kim MB .
Department of Laboratory Medicine, Pusan National University, Busan, Korea.
Department of Laboratory Medicine, Konyang University Hospital, College of Medical Science, Konyang University, Daejeon, Korea.
Department of Thoracic and Cardiovascular Surgery, School of Medicine, Pusan National University, Busan, Korea.
Department of Dermatology, School of Medicine, Pusan National University, Busan, Korea.
Medical Research Institute, Pusan National University, Busan, Korea.

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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