Application of single-nucleotide polymorphism and mycobacterial interspersed repetitive units-variable number of tandem repeats analyses to clinical Mycobacterium tuberculosis isolates from 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.
Department of Laboratory Medicine, Pusan National University, Busan, Korea.
Go Eun
GE
Choi
Mi Hee
MH
Jang
Hyun-Jung
HJ
Cho
Sun Min
SM
Lee
Jongyoun
J
Yi
Eun Yup
EY
Lee
Chulhun L
CL
Chang
Yeong Dae
YD
Kim
Moon-Bum
MB
Kim
D016000:Cluster Analysis; D017931:DNA Primers / Q000737:chemistry; D020071:Interspersed Repetitive Sequences; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea
D017931:DNA Primers
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