Genetic diversity of the Mycobacterium tuberculosis Beijing family based on IS6110, SNP, LSP and VNTR profiles from Thailand

Genetic Diversity and Dynamic Distribution of Mycobacterium tuberculosis Isolates Causing Pulmonary and Extrapulmonary Tuberculosis in Thailand

“…To define the SNP sequence type of each position on a DNA microarray, fluorescent signal intensities were evaluated using SNPStar software (version 0.0.0.8; Olympus, Tokyo, Japan). The SNP profiles indicating either the ST or SCG were compared with previous data (14,26,29). When necessary, the novel STs were confirmed by direct sequencing along with previous spoligotyping results (N. Smittipat, personal communication).…”

“…The next 47 SNPs were chosen for genotyping M. tuberculosis isolates, with 2 SNP positions for determina- In addition, the polymorphisms at nucleotide 4280708 are the same as the absence or presence of RD105 and were used to define the BJ genotype (13). The SNP at position 1477598 is the same as the ogt12 polymorphism and was used to classify the ancestral and modern BJ genotypes (26). The perfect concordance of the evolutionary events between either SNP 797736 or SNP 2825581 and the RD181 marker was also used to subdivide the ancestral BJ genotype into early and late genotypes (27).…”

Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

“…The Beijing strains includes several divergent sublineages which can be defined based on large sequence polymorphisms (LSPs) or single nucleotide polymorphisms (SNPs) (14,20,42,46). However, the most frequent Beijing strains in China and elsewhere, with the exception of Japan and Korea, belong to a genetically homogenous population originally characterized by one or two IS6110 insertions in the noise transfer function (NTF) region of the Mycobacterium tuberculosis genome (4,13,19,32). These strains have been referred to as the "modern" (or typical) Beijing branch (34), and Beijing strains without an IS6110 insertion in NTF region have been referred to as the "ancient" (or atypical) branch (34).…”

“…Modern Beijing strains are also characterized by SNPs in the mutT2 and ogt genes, and their population structure has been further explored by using more recently evolved LSPs (RD142 and RD150) and SNPs (11,31,42). However, the frequencies of these polymorphisms vary in different settings (13,19,24,31).…”

“…Excluding the SNP in ogt codon 12, which is redundant with the SNP in mutT2 codon 58, the other seven SNPs were included for genotyping in this study. One extra SNP at position 2532616 (according to the genome of H37Rv) which was constantly found in modern Beijing strains was also included (13,19,24). In total, eight SNPs (Table 1) were genotyped with a novel real-time PCR melting curve assay which was developed previously by us for detecting drug-resistant mutations (27).…”