PRIMERS, SNP MARKERS AND METHOD FOR GENOTYPING MYCOBACTERIUM TUBERCULOSIS

Abstract

The present application provides a primer set for genotyping M. tuberculosis selected from the group consisting of primer sets 1-25 (SEQ ID Nos. 1-50), and also provides an extension primer for genotyping M. tuberculosis selected from one of the group consisting of SEQ ID Nos. 51-75. The present application provides a combination of single-nucleotide polymorphism markers of M. tuberculosis. Further, the present application provides a method and a kit for genotyping M. tuberculosis.

Description

CROSS-REFERENCE TO RELATED APPLICATION(S)

[0001] This application claims priority to U.S. Provisional Patent Application No. 61/730,033, filed on Nov. 26, 2012, the disclosure of which is hereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention relates to the primers, the SNP markers and the method for detecting Mycobacterium tuberculosis, and more particularly for genotyping M. tuberculosis.

[0004] 2. Description of the Related Art

[0005] Tuberculosis (TB) is a worldwide healthcare concern. It has been characterized by the World Health Organization (WHO) as an epidemic and estimated that one-third of the world's population has been infected with Mycobacterium tuberculosis (MTB). Epidemiologic studies have revealed that various genotypes of M. tuberculosis (MTB) may be prevalent in different geographic regions and that genotype distribution is associated with population migrations. Whether MTB genomic diversity influences human disease in clinical settings remains an open question.

[0006] The complete genome of H37Rv strain MTB was published in 1988, which has a length of about 4 Mb and contains about 4000 genes. MTB can be classified as six major strains and 15 subordinate strains. Genomic variations affect the transmission, virulence, antimicrobial resistance and other attributes of the MTB, so that the development of molecular techniques for differentiating various MTB isolates is of considerable interest in epidemiological studies.

[0007] Genotyping methods aiming at generating phylogenetically informative data have been developed to investigate multiple clinical samples from different sources. Currently, there are two genotyping methods that are commonly used to study tuberculosis transmission (van Deutekom H. et al., J Clin Microbiol 2005, 43(9):4473-4479). Spoligotyping is based on polymorphisms in the direct repeat (DR) locus, which is consisted of 36-bp DR copies interspaced by non-repetitive spacer sequence. It is a PCR-based reverse hybridization technique for MTB genotyping. The portable data format facilities easy inter-laboratory comparison. To date published, freely accessible databases for strain lineage identification have been developed on the basis of spoligotype signature matching (Brudey K et al., BMC Microbiol 2006, 6:23). Another molecular technique for strain typing of MTB is based on variable number tandem repeats (VNTRs) of mycobacterial interspersed repetitive units (MIRUs) (Mazars E. et al., Proc Natl Acad Sci USA 2001, 98(4):1901-1906; Comas I. et al., PLoS One 2009, 4(11): e7815; Supply P. et al., Mol Microbiol 2000, 36(3):762-771). This method is based on the number of repeats observed at each of the 12, 15 or 24 selected MIRU loci, determined using a PCR-based method.

[0008] However, the conventional methods for genotyping MTB have disadvantages including the requirement of large amount of DNA sample, time-consumption, insufficient sensitivity and specificity, inability for genotyping particular strains. Therefore, there is a need for the improved method for genotyping MTB.

SUMMARY

[0009] The present application describes a primer set for genotyping M. tuberculosis selected from one of the group consisting of primer sets 1-25.

[0010] The present application provides an extension primer for genotyping M. tuberculosis selected from one of the group consisting of SEQ ID Nos. 51-75.

[0011] The present application provides a combination of single-nucleotide polymorphism markers of M. tuberculosis selected from the group consisting of "T" at position 301 of SEQ ID No.76, "A" at position 301 of SEQ ID No. 77, "A" at position 301 of SEQ ID No. 78, "G" at position 301 of SEQ ID No. 79, "G" at position 301 of SEQ ID No. 80, "G" at position 301 of SEQ ID No. 81, "C" at position 301 of SEQ ID No. 82, "G" at position 301 of SEQ ID No. 83, "C" at position 301 of SEQ ID No. 84, "A" at position 301 of SEQ ID No. 85, "A" at position 301 of SEQ ID No. 86, "A" at position 301 of SEQ ID No. 87, "G" at position 301 of SEQ ID No. 88, "A" at position 301 of SEQ ID No. 89, "G" at position 301 of SEQ ID No. 90, "G" at position 301 of SEQ ID No. 91, "A" at position 301 of SEQ ID No. 92, "C" at position 301 of SEQ ID No. 93, "C" at position 301 of SEQ ID No. 94, "T" at position 301 of SEQ ID No. 95, "T" at position 301 of SEQ ID No. 96, "T" at position 301 of SEQ ID No. 97, "T" at position 301 of SEQ ID No. 98, "T" at position 301 of SEQ ID No. 99, and "C" at position 301 of SEQ ID No.100.

[0012] The present application also provides a method for genotyping M. tuberculosis comprising obtaining a sample, amplifying and obtain at least one of first DNA fragment by using one or more primer sets selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), amplifying and obtain at least one of second DNA fragment by using the obtained first DNA fragment as template and using one or more extension primers selected from the group consisting of SEQ ID Nos. 51 to 75, and detecting the second DNA fragment by using mass spectrometry.

[0013] In other embodiments, the present application also provides a kit for genotyping M. tuberculosis comprising at least one primer set selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), and at least one extension primer selected from the group consisting of SEQ ID Nos. 51 to 75.

BRIEF DESCRIPTION OF THE DRAWINGS

[0014] FIG. 1 is an overall scheme for selecting lineage-specific DNA markers.

[0015] FIG. 2 illustrates linkage disequilibrium of SNP markers in the MTB genomes. The LD plot was created using Haploview software, and the color code on plot followed the standard color scheme for Haploview: blue indicates |D'|=1 and LOD<2, and bright red indicates |D'|=1 and LOD≧2.

[0016] FIG. 3 illustrates phylogenetic analysis of MTB isolates using strain-specific SNP markers. Phylip software was applied to calculate the Nei's distance using 110-SNP (A) and 25-tagSNP (B) data, and then constructed phylogenetic trees using the neighbor joining approach, and FIG. 3 also illustrates typed SNP position on MTB chromosome: 110-SNP (C) and 25-tagSNP (D).

[0017] FIG. 4 shows identification of specific markers for strain typing. The allele frequencies the 110 SNPs in 51 modern Beijing, 25 Haarlem, 11 EAI, 10 ancient Beijing, 7 T and 3 LAM isolates were characterized by combining spoligotyping and SNP genotyping data.

[0018] FIG. 5 illustrates decision tree based on four lineage-specific SNP markers. Four of 32 lineage-specific SNPs with 100% variant allele frequencies were used to classify 81 clinical isolates into ancient Beijing (Ba), modern Beijing (Bm), East African-Indian (EAI) and Latin American and Mediterranean (LAM) lineage.

[0019] FIG. 6 shows high genetic diversity within Euro American lineage. (A) Phylogenetic analysis of Euro American strains using 4,419 whole-genome SNP markers. Phylogenetic tree was constructed based on Nei's distance using the Phylip software (neighbor joining approach). (B) Principal component analysis (PCA) of Euro American strains. The genotype data of 4,419 whole-genome SNPs was transformed into numeric values, and then PCA method was applied to analyze these 14 clinical Euro American isolates and H37Rv reference strain using SAS program.

[0020] FIG. 7 shows a minimum spanning tree based on 24-MIRU-VNTR genotyping of 156 Mycobacterium tuberculosis isolates. The circles represent different types classified by 24-MIRU-VNTR genotypes and were colored according to the spoligotype classification. The sizes of circles represent the number of isolates with a particular genotype. ( : indicate misclassified by spoligotyping).

[0021] FIG. 8 shows a new hypothetic subtype definition of Euro American lineage. Phylogenetic analysis of Euro American strains using 4,419 whole-genome SNP markers. Phylogenetic tree was constructed based on Nei's distance using the Phylip software (neighbor joining approach).

[0022] FIG. 9 shows high genetic homozygosity within new hypothetic Euro American subtypes. Fourteen Euro American strains (7 Haarlem and 7 T strains) were genome-wide sequenced using 454 or HiSe2000 sequencer, and there were two major clusters (6 and 7 belong to EuAm1 and EuAm2 subtypes, respectively) of them based on phylogenetic tree (FIG. 8). There were 81 EuAm1-specific and 133 EuAm2-specific SNPs with variant allele frequency=100%.

[0023] FIG. 10 shows the PCR primers, the extension primers, the positions and the correspondent alleles for the 25 tagSNPs with the multiplex reaction well scheme.

[0024] FIG. 11 shows the comparisons of the present application and the conventional genotyping methods.

DETAILED DESCRIPTION OF THE EMBODIMENTS

[0025] In the present application, the primer set for genotyping M. tuberculosis is selected from the group consisting of primer sets 1-25, each primer set contains a forward primer and a reverse primer. The primer sets 1-25 are shown as follows:

TABLE-US-00001 Primer set 1: (SEQ ID No. 1) ACGTTGGATGTTCTGGACGACCTGTCCTAC and (SEQ ID No. 2) ACGTTGGATGAGCTGCGCCAAGGTTCGTG, Primer set 2: (SEQ ID No. 3) ACGTTGGATGTTGTAGCTGCCCAAATTGCC and (SEQ ID No. 4) ACGTTGGATGGGCTTCAATCTCGGCTTGG, Primer set 3: (SEQ ID No. 5) ACGTTGGATGTATTCAACACCGGCATCGGG and (SEQ ID No. 6) ACGTTGGATGTCGCCTGGTCGTGGAAGAAC, Primer set 4: (SEQ ID No. 7) ACGTTGGATGATCGGACAGCAGAAGGCAC and (SEQ ID No. 8) ACGTTGGATGACTCCCGCGGAACGTGGTG, Primer set 5: (SEQ ID No. 9) ACGTTGGATGCAACACCGGCAACTTCAAC and (SEQ ID No. 10) ACGTTGGATGAATTAGCGTCTCCTCCGTTG, Primer set 6: (SEQ ID No. 11) ACGTTGGATGTCGAACCCGCCGACAAATG and (SEQ ID No. 12) ACGTTGGATGTCGATTGGTCGCATGCACTG, Primer set 7: (SEQ ID No. 13) ACGTTGGATGAAACCTCGGCATAGGGATCG (SEQ ID No. 14) ACGTTGGATGTCGACAGGACTATTGGTAGC, and Primer set 8: (SEQ ID No. 15) ACGTTGGATGAAGACGACGGGCCGGATATG and (SEQ ID No. 16) ACGTTGGATGCGTCAAGAGCTTCCCAAATC, Primer set 9: (SEQ ID No. 17) ACGTTGGATGCATCCGGGAACACCGTAAAC and (SEQ ID No. 18) ACGTTGGATGATCACCTTCTTATCGGGTGG, Primer set 10: (SEQ ID No. 19) ACGTTGGATGCCTGGATTTCAGATATTGCC and (SEQ ID No. 20) ACGTTGGATGTGGCCAGCCCTAGCAAGTC, Primer set 11: (SEQ ID No. 21) ACGTTGGATGAGAACAAACGCGGGATTCAC and (SEQ ID No. 22) ACGTTGGATGTCTCCCGGAGATCACCATTC, Primer set 12: (SEQ ID No. 23) ACGTTGGATGGTTGTTTTTGGCCGGGCAG and (SEQ ID No. 24) ACGTTGGATGATCGAGCAGACTCAGCGCTT, Primer set 13: (SEQ ID No. 25) ACGTTGGATGTGCTACCGCCAATGTTCAAC and (SEQ ID No. 26) ACGTTGGATGATGGCGTTGACATAACTCGG, Primer set 14: (SEQ ID No. 27) ACGTTGGATGATAGCAAGCACGATTGCGAC and (SEQ ID No. 28) ACGTTGGATGACCCCCCGCTGAGGGCGTA, Primer set 15: (SEQ ID No. 29) ACGTTGGATGGATTCGATTGGGGAAACGGC and (SEQ ID No. 30) ACGTTGGATGTTCCACATTGGTGATCAGCG, Primer set 16: (SEQ ID No. 31) ACGTTGGATGCAAACGGCGTCACTTTGGTC and (SEQ ID No. 32) ACGTTGGATGTGAAATGTGGGCCCAAGACG, Primer set 17: (SEQ ID No. 33) ACGTTGGATGCGATTTCGATCGGGATGTTG and (SEQ ID No. 34) ACGTTGGATGCAATCACGATCCCCTCAATC, Primer set 18: (SEQ ID No. 35) ACGTTGGATGAGGCAAAGGAAAATCGACCG and (SEQ ID No. 36) ACGTTGGATGTTGACAAACTGAAACACCGC, Primer set 19: (SEQ ID No. 37) ACGTTGGATGACAACCGGCCGCAGCGTTT and (SEQ ID No. 38) ACGTTGGATGAAGAACACCGAAAGTGGCTG, Primer set 20: (SEQ ID No. 39) ACGTTGGATGTGCATTGGCCACTAAAGCTC and (SEQ ID No. 40) ACGTTGGATGTCGATGACTATCTGCGGATG, Primer set 21: (SEQ ID No. 41) ACGTTGGATGACCCATTTGCCGAACGTGTC and (SEQ ID No. 42) ACGTTGGATGTGCTTGGCGACTTTGTGCAG, Primer set 22: (SEQ ID No. 43) ACGTTGGATGAGCGTGAAGAAGACGACGA and (SEQ ID No. 44) ACGTTGGATGGTCTGTTGTCATTACGGGAG, Primer set 23: (SEQ ID No.45) ACGTTGGATGACATCAGGTGATGGTCATGC and (SEQ ID No. 46) ACGTTGGATGCGAAGGGAACAATGGATGTG, Primer set 24: (SEQ ID No.47) ACGTTGGATGTATGCCAACCGATTTGCCTG and (SEQ ID No. 48) ACGTTGGATGACATATTGTCCACCGCGTAG, and Primer set 25: (SEQ ID No. 49) ACGTTGGATGTCTTGGCAGCGGCATGGAC and (SEQ ID No. 50) ACGTTGGATGCCGAATTTCCAGTCTCACAG.

[0026] The primer set can be applied in polymerase chain reaction to amplify a DNA fragment containing a single-nucleotide polymorphism (SNP) of M. tuberculosis. The above primer sets can be used alone or in combination. In some embodiments, the combination of the primer sets can be applied simultaneously in one test tube for PCR test. In some embodiments, any combination selected from the primer sets 1-12 can be applied simultaneously. In some embodiments, any combination selected from the primer sets 13-22 can be applied simultaneously. In some embodiments, any combination selected from the primer sets 23-25 can be applied simultaneously.

[0027] In the present application, the extension primer for genotyping M. tuberculosis is selected from SEQ ID Nos. 51-75. The extension primers of the present application are listed as follows:

TABLE-US-00002 (SEQ ID No. 51) GACCTGTCCTACGAACCGGTGATGG, (SEQ ID No. 52) CGTTGCCCACGTTGTTGGCG, (SEQ ID No. 53) CACCGGCCAACGTCTCGGGCATG, (SEQ ID No. 54) CCCCCGACCGGCCGTTCTTCG, (SEQ ID No. 55) TTCAACGGCGGCATCAT, (SEQ ID No. 56) GCCGAAACAAGATTTGC, (SEQ ID No. 57) CCTTCTGCGTCTCCAAT, (SEQ ID No. 58) GATATGGGGCCGCGGAT, (SEQ ID No. 59) ACCGTAAACGGGCCTAACCCTCC, (SEQ ID No. 60) TTGGGGCTGGGAACTGGG, (SEQ ID No. 61) ATTCACGTGAAAACCCTCG,, (SEQ ID No. 62) AGCTCAGCGCGCGGCTGGTGT, (SEQ ID No. 63) CAAAATACGGCGATCATCATGGG, (SEQ ID No. 64) CCACCAGTACTTGCCGC, (SEQ ID No. 65) ATCGGGGTGACGATGAG, (SEQ ID No. 66) GCCGAGGAGCCCGCGTAACCGT, (SEQ ID No. 67) TGTTGATCGGCCCGAGGC, (SEQ ID No. 68) GCGGGCGTGGAACGCTGGTC, (SEQ ID No. 69) AGCGTTTCCAGGTCACCGCA, (SEQ ID No. 70) CCAGAGCGCAACAACAA, (SEQ ID No. 71) CACGCTGGCATCAAGTTC,, (SEQ ID No. 72) GAAGACGACGAGGACGACTGGG, (SEQ ID No. 73) GACGATTCCGGGCATGCG, (SEQ ID No. 74) TGCCTGCCTGGTATGAC, and (SEQ ID No. 75) GGCATGGACGGGATCGG.

[0028] In one embodiment, the extension primer can be applied in polymerase chain reaction to amplify a DNA fragment having a single-nucleotide polymorphism (SNP) of M. tuberculosis as a terminal nucleotide of the DNA fragment. The above primers can be used alone or in combination. In some embodiments, the combination of the above primer can applied simultaneously in one test tube for PCR test.

[0029] In the present application, the SNP markers of M. tuberculosis are selected from: "T" at position 301 of SEQ ID No. 76, "A" at position 301 of SEQ ID No. 77, "A" at position 301 of SEQ ID No. 78, "G" at position 301 of SEQ ID No. 79, "G" at position 301 of SEQ ID No. 80, "G" at position 301 of SEQ ID No. 81, "C" at position 301 of SEQ ID No. 82, "G" at position 301 of SEQ ID No. 83, "C" at position 301 of SEQ ID No. 84, "A" at position 301 of SEQ ID No. 85, "A" at position 301 of SEQ ID No. 86, "A" at position 301 of SEQ ID No. 87, "G" at position 301 of SEQ ID No. 88, "A" at position 301 of SEQ ID No. 89, "G" at position 301 of SEQ ID No. 90, "G" at position 301 of SEQ ID No. 91, "A" at position 301 of SEQ ID No. 92, "C" at position 301 of SEQ ID No. 93, "C" at position 301 of SEQ ID No. 94, "T" at position 301 of SEQ ID No. 95, "T" at position 301 of SEQ ID No. 96, "T" at position 301 of SEQ ID No. 97, "T" at position 301 of SEQ ID No. 98, "T" at position 301 of SEQ ID No. 99, and "C" at position 301 of SEQ ID No.100. The detail sequence information are shown as follows.

TABLE-US-00003 SEQ ID No. 76: TGCCGGGCCGCCTCCAGTCGACGTCGGGTAGTCGCTACCGCCGGCACCA CCACCCGGCGCACCAGCTGGTCCTGCTCGGCGAATAGCTCGGCGGCCGC CGCCTCGGCTCGCAATCGTTGTACCCCACCGGTGATCGCGTTGACCGTC ATCACGCCCGCTACCAGTAGCGCGTCGATATTGCTGCCGACAATCGCCG ATGCTGCGGCGCCCACCGCCAGGATCGGAGTCAGCGGATCGGCCAGTTC ATGGCGGGTGGCCACCGCCAGCTGCGCCAAGGTTCGTGCCGGGCCGCGC AGCGGCTCCATCACCGGTTCGTAGGACAGGTCGTCCAGAATGCGCCGCC AGGCCGGGATTCCGGGTTCGACGGCCAAGGGTCGGGAGCCGCCGGCTAG CCGCGAGTAGACGATCTCGGGGTCCAGCGCGTGCCAGGCGGTCAGCGGT TGCGGGGTGGGGTCGGGCATCCGCAGCACCTTGGCGGCCGACCACATTC CGGACACCAAAGCCGTTGCGGCAGCGGCATTGACCGGATTGAGCCAGCG ACGGAAGCTGGCTGGGTTGGTGGTTTTGTCCTGCTCACCGGTGACCAAC AACAGCCCGGCCA; SEQ ID No. 77: AGCGTTGGGACCCAGCGAGATGAGGTGCTGCATTTCCAGGGACGCGATG ACGGCGCTCTGCGAATAGCCGAACACGGTGACGTGGTTTCCGGCGTTGA TTTGCTCCCAAATCGCGCCGTCGAGAATCTGTAGGCCCAACTGCACCGA GGTTTGGAAGGGCAGGGATTTGACGCCGGTGATCGGATATAGCTCTTCG GGCGTCACCAGCGCTTTGACGACCGGATTCGAGACGACGGGGTCGATGA ACAAGGTCGTGATGGCGTTGACATAACTCGGCGTGGGTATCGGTGACCC GGTGCCACCCATGATGATCGCCGTATTTTGGTTGAACATTGGCGGTAGC ACCGGGGGTGAGGTTGGCTTAAAGAGTCCGGCCGTCGCCTCCTGCACCA GCGCGCTCGTGTTGGTGGCCTCGGCATTGACAAATGCGTTTGCGGCCGC CGCCAACCTCTGGGTGAATTCGTTGTGAAACGCCGCAACCTGTGCGCTG ATCGCCTGGAACTGCTGGCCGTACGCGCCGAACAGCGTGGCAAGGGCCG TGGACACTTCGTCCGCGGCAGCCGCCGCCAGGCCGGTTGTCGGGGCCGC GACGGCCGCCGTA; SEQ ID No. 78: CCGACAACACCGGCCCACCCGGCAGCGTGGTGCTCAGCGAGTTGGCGGC GTAGAAGGCGGCCTCCGACCGCCATTGCTTGACGTGCACCCCGGCGGAT TTCAGCAGGGTTCGCTGAATCTGGGCGAAGCTGTGCATCGAGGCGCCCG CGGCTGCCACCGCGGCCAGCAACCACCACCACTTGGCGCGATACAAGCT CACCCAGGCCTTGGCGAGCTGGTCCCAGCCCAACGCCACCTCTATAGCA AGCACGATTGCGACGATGGCCAGTACCGCCCATCGCAACCACCAGTACT TGCCGCACGGGGGTACGCCCTCAGCGGGGGGTGCCCCCACCCGCGTGCG AGGGAGTGCCCCCACGCGCTGGCGGAGGTTGCGGGCGGGGGCGTCGTGC GACACGTGCTTAAGGGTAACCGTGCAGGTGGCGCCGTAATCGCGATACA TCGCTAACCGTGTCAGCCTCGTTGGGGGGTCGTGACCGGATCGTGCCGC CTGGCAAAGTAACTATGCGGGCTCGACGCGACCCGCCGCGACCTTACGA CGCCGCCGTTCCCGTTACGCTTGCCGGATGTCGGCGAGCCTGGATGACG CTTCGGTCGCACC; SEQ ID No. 79: CGAGGCCAGGTTCCAAAAGCCCGAAGCGCCGCCGCCGAAGTTGCCGAAG CCCGAGGCGGTGCCGGCGCCAGCGTTGAAGAAGCCCGACGACGGGCTGG TGGTCGAGTTCCCGAAGCCCGGGGCCGCCGGAATCTTGATGAGCGGGAT GCTGACGCCCCCCACCATGCCGGTGAGGTTGCCGTCGATCGTGGTGGTT GGTCCGCCCACGGTGATCGTCACCGTGGGAAGGGTGAGCGTGGATTGCG GGAGCTCGACCGGGCCGTAGTAAACAACGAAGGGAACAATGGATGTGAA GGGCAAGCGCATGCCCGGAATCGTCATCACGCTTCCGGGCATGACCATC ACCTGATGTATCGGCATGCTGAATAGCTGCGCGTTTATCGGAATGGCGG GAATCTCGAGGGCGATATCGGCACCGATCAGGCCTTGGTAGTCGCCCCG CCACAAGACGCCGTTGCTGTAGTTGCCGGCGATGAAGGCGCCGGTGTTG ACGTTGCCGGTGTTGGCCACTCCAGTGTTGTAGTCGCCGGTGTTGAAGT AGCCGGTGTTGTAGTTACCTGCGTTGAAGCTGCCGGTGTTGTAGTTGCC GGTGTTGAAGTTC; SEQ ID No. 80: TTGAACAACCCGACGTTTCCGCTGCCGGAGTTGAACAGGCCGATGTTGT GGCTGCCCGAGTTGAAGCTGCCGAACCCGATCTGTCCGTTGCCGGTGAG CCCGATGCCGACATTGTTGCTGCCCGTATTCCCAAAGCCGACATTGTTG CTGCCGGTGTTCGCAAAGCCGATGTTGTGGCCGCCCAGGTTGGCCAAAC CCAGGTTGTCGCTGCCCAGGTTTGCAAAGCCGAGGTTGTAGCTGCCCAA ATTGCCGAAGCCGACGTTGAACACGCCGACGTTTCCGTTGCCCACGTTG TTGGCGGCGACGTTTGCCAAGCCGAGATTGAAGCCCGCCGCGCTCGGGG GGCCGGCAGCGGCTGCCGCGGCGCTGGTCAGCCGCTCCGATAGGCCCGC CAGCTTCTTCAGCTGCTGGGTGAACGGCATCAACGCGGAGACGGCCGCC GACGCTCCAGCGTGATAGCCAACCATCGCGGCCACATCCTGGGCCCACA TCCGCTCATAGGCGGCCTCGGTGGCCGCGATCGCCGGAGCGTTGAATCC CAGCAGATTCGAGCTCACCAGCGACACCAGCACGGCGCGGTTGGCCGCG ACGATCGCCGGAT; SEQ ID No. 81: AGTCGCCGGCGTTGCCGAATCCGAAGTTGTAGCTGCCCAGGTTGCCTAG GCCGATGTTGTAGTTACCCAGGTTCGCCGGGCCGATGTTGTATGAGCCC TGGTTTCCGCCGAAGACGTTGAAGCTGCCGAGGTTGCCGCTGCCGAGGT TGAAGCTGCCGATGTTCGCCAAGCCGGCGTTGCTGTCGCCTACGTTGGA GAAGCCGACGTTGAATTGGCCGATGTTTCCCAGGCCGAGGTTGAACATC GACATCCCGGTCGCCTGGTCGTGGAAGAACCCCGCGAGGTTGCTGCCGA TGTTGAGCATGCCCGAGACGTTGGCCGGTGCCCCGATGCCGGTGTTGAA TACGCCCGAGACGGTATCGCCCAGGTTCGCCAGTCCCGATTGCAGCGAG CCGTAGTTGTTGAAGCCCGAGGTCGCGGAGTTCGCGACGTTCTGGAAGC CGGAAATGTTGGCGCCGATGTTGGCGATGCCCGATACGGTTCCGGGGCC GCCGTTGAAGAAGCCCGAGGACGGATCGGTGGTGGCGTTGAAAAAGCCC GTGGTAGCCGCAATGTTGACGAACGTGACATCGAAGGGACCGACGCTTG CGGTGGCCGGGAT; SEQ ID No. 82: TAAAGCTCAACGGCTACAACACCGCCCAGTTCGGCAAGTGCCACGAAGT CCCGGTCTGGCAGACCAGCCCGGTCGGGCCGTTCGACGCGTGGCCCAGC GGCGGCGGTGGTTTCGAATACTTCTACGGGTTTATCGGTGGCGAGGCTA ACCAGTGGTATCCGAGTCTGTACGAGGGCACCACGCCGGTCGAGGTGAA CCGCACGCCCGAGGAGGGTTACCATTTCATGGCGGACATGACCGACAAG GCCCTCGGCTGGATCGGACAGCAGAAGGCACTGGCCCCCGACCGGCCGT TCTTCGCGTACTTCGCCCCGGGCGCCACCCACGCGCCCCACCACGTTCC GCGGGAGTGGGCCGACAAGTACCGGGGCCGCTTCGATGTGGGCTGGGAC GCACTGCGAGAGGAAACCTTCGCCCGGCAAAAGGAACTCGGGGTGATCC CGGCGGACTGCCAGCTGACCGCGCGGCACGCCGAAATCCCGGCGTGGGA CGACATGCCGGAGGACCTCAAACCCGTGCTATGCCGGCAGATGGAGGTC TACGCGGGCTTTCTGGAATACACCGACCACCACGTCGGCCGGCTCGTCG ACGGCCTGCAGCG; SEQ ID No. 83: GTTGGCGAAGCCCGAGATTTGTAAATTACCAACGTTTTGGGCGCCGGAG TTTCCCCTACCAGAATTATTGAAACCCGAATTTCCACTGCCGGCGTTTC CGAATCCCGAGTTTTCGCCCAGCCCATCGGTAGTATTGCCGAAACCGGT GTTCAGGTTGCCCGCGTTAAAGCCGCCCGTGTTGATATTGCCAGAATTT GCGAAGCCGGTGTTCGTCAGGCCAGAGTTCAAGAAACCAGAATTAGCGT CTCCTCCGTTGAAGCTGCCTGAGTTGAATGCACCCGAGTTGAAGCTACC GGTGTTGATGATGCCGCCGTTGAAGTTGCCGGTGTTGAAATCGCCCGCG TTCCCTATGCCGGTATTGGCCTGACCTGAGTTGCCAAAGCCAGTGTTGA CGCTTAACGCGTTCCCGAAGCCGGTGTTGATAAAGCCGGAGTTTCCGAA GCCGGTGTTGATGTTGCCTGAGTTGGCTACGCCCGTGTTGGTGACGCCC GAGTTGCCCACGCCGAAGTTGCCGCTGCCCGAGTTGAAGAAGCCGATGT TCCCGGTGCCCGAGTTACCAAATCCTATATTACCGCTACCGGAATTCAG TCCGCCAAAGCCG; SEQ ID No. 84: TTGTCCGCAGGAGTGTTGAGTGAGGCGGCCAGCGCCGTGTAGTAGTCAC GGTGACGTGCGTGCACATCGGCCTCGCCGGAGTCGCCCAGTTTTTCCAG CGCGTACCGACGCACCGTTTCCAGCAGCCGGTACCGCGTGCGGCCCTGG CAGTCGTCGGCCACCACCAGCGACTTGTCTACCAGCAGGGTCAGCTGAT CAAGCACCGAAAACGGATCCAGGTCGCTACCGGCGGCGACCGCCCGCAC CGCGGCGAGGTCGAACCCGCCGACAAATGGCGCCAGTCGCCGAAACAAG ATTTGCCCGGTCTCGGTCAGCAGTGCATGCGACCAATCGATCGAGGCGC GAAGTGTCTGCTGGCGCTGCACCGCGCCCCGCACACCGCCGGCCAACAG CCGGAAACAGTCGTCCAGACCGTCGGCAATCTCGAGCGGTGACATCGAC CGCACCCGTGCGGCAGCGAACTCGATCGCCAGCGGTATGCCGTCTAGCC GCCGGCAGATCTCGCCGACGGCCGCGGCGTTGTGATTGGCGATGGTGAA CCCGGGCTGAACTCGGCTGGCTCGGTCAGCAAACAATTCGACTGCTTCG TCGGTTATCGACA; SEQ ID No. 85: TCCAACTCGAAGATTGTTGTCCCGATTGGCCATTGCAATCGGAATGCAC GGGAATCCAATCCTGCAGCCAAGATGACCACCTGCTTCATGCCGGCGGC CGTTGCCCGGGAGAAATACTCGTCGAAATACCTGGTGCGGGCACCTTGG

AAGTTGACGAAATGCTCACCGAAGTCCCCGGTTGTCAGATAGTGATCGG GCAGCTTGCCGTCCAATACGTCGGCCCATTCACCACCTGCGGCACGGCA GAAAACCTCGGCATAGGGATCGATGGCCAGCGGATCGGCCTTCTGCGTC TCCAATACTCTTGCGGCGGCTACCAATAGTCCTGTCGAACCAACACTCG TGGTGACATCCCAGCTATCGTCCTCGGTCCGCATTCATCGAACTCTAGT TGCTCCAGTCCGCCCACCGCTGTCGGTATCCCAGCGCAGTCGGCCGTGC ACACATATCTGCGCGGTGGACTTGGTACTTCTACGCGCATTCGCCGATG TTTTGCGATCCGCGGCGGGTCTATGGTGCCATTTATGTGCCAGGATCGG TCTTCAATAACAACGTCGCGAAGCGAGGGGTCGTGACGTGAGAGGGCTC GCTTATGCCGGCG; SEQ ID No. 86: GAGCGCTACCTTGGATGTTGAGGGAGTTGAACTCCGGCGGAAAAATTGT GAAATCCATTGTCGCTCAACCGCTGTCTAGGTGGAGGTGCCCGCGCGGT TGGCTAATTCGGTGAGCCAATACGAAGTCTTGCTGGTCTGAAGTGTTTG GACAAATGACTCGTGGATCACATGGGCCTGGCGCGCGATCGCCTTGTAC AGCTCGCCGTGCATGGAAAACAGCATCGACGTCACGATGGACACAAGAT CGTGGGCGGGGGATTCCACATTGGTGATCAGCGGCGTGACCCCGTCATC ATGGGCACTCATCGTCACCCCGATCTCGTGGAGGTTGGCGGCCGTTTCC CCAATCGAATCGGGCCGTGTGGTGACAAAAGACACGCGTGCATCTCCTT CCACTGACGTGGTCTGATGGTGGGGGTCAGCGACGACTTGGGGTTCCGC ACGGCATTGTAGACGGAATCGTTCACTAAGGTATTTTCACCATAACGGC TTCGGTCACAAAACGGTAGCGATTCTGTTGAGGAATTTTTTCGACGCTC GCCCGGTAGGGTGCCTCCATGTCTGAGACGCCGCGGCTGCTGTTTGTTC ATGCACACCCCGA; SEQ ID No. 87: TCTGTGGGTGGTCCCGGATGTCGCGGCCCGCGGAGCCGATCTTGCCCAT GTCCCAGTGGTGACGCTGGTCGGAAGCGCCCGGCACTATTGGGGCGCGG TGGCGGCGGTGTTGGCGGCAGTGTGTGCTTTGCTCGCTGCCGTCTTCTT GATGAGTTCGGCGGCGATTCGCGGGTCGGCTGGCGAGGACATGGCGAGA TATGCGGCGCCCCGCGCCCGCCGGTCGATTGCCCGGCGCCAGCACTCGA ATGCGGCCGGCCGGGCGGCTCCGCAAGACGACGGGCCGGATATGGGGCC GCGGATATCGGAGCGAATGATTTGGGAAGCTCTTGACGAGGGCCGTGAC CCGACCGATCGGGAGCAGGAGTCTGACACCGAGGGGCGGTGACGGACCG CGCGCTGACGGTCGCTACCCTTCATGGACGTCGTCGAAATTGACGAGCG CGTGTGGGTGACAGTGGGAAGGGAACGGCAGGCATGAGTCCGGCAACCG TGCTCGACTCCATCCTCGAGGGAGTCCGGGCCGACGTTGCCGCGCGTGA AGCCTCGGTGAGCCTGTCGGAGATCAAGGCTGCCGCCGCTGCGGCGCCG CCGCCGCTCGACG; SEQ ID No. 88: AACCCACGGTGTTGTAAAACAGCTGTGATATCGGCAGATACCAGTTGAT GAACCATTCCAGCCACCCCGGGGTCGCGGCGGCGGTCAACGCGGACGAC AGGGGCGAGGTGAGGCCCAGCAGCGTGTTGGGCAAGTGGGCGATCAGCT CCGCTATTGCGCTCTGCGCCGCGCCGGCTGAGGTGCCGGCGGCTTTGGC GACTGCGGACAACTGCGTCGCCGCGGCGGATGGGCTGGTGGTGTTCGGC GGCGGGGCAAACGGCGTCACTTTGGTCGCGGTCGCCGAGGAGCCCGCGT AACCGTGCATGGCCATGGCGTCTTGGGCCCACATTTCAGCGTATTGAGC TTCGGTGGCCGCGATTGATGCGGTGTTTTGACCGAACACGTTATGCGTG ACCAGCGACGTGAGCCGCGCGCGATTGGCCGCGATCAGCGGCGGGGGCA CAATGGCGGCAAACGCGGTTTCGTAAGCGGCCGCCGCCGCACGCGCCTG ACTGGCTGCCTGCTCAGCTTGGATGGCGGTGGCTCGCATCCACGCCACA TACGGGGCGACCGCTTCGACCATCAACGTCGACGCCGGACCCAGCCATT CTTCGGTTTGCAG; SEQ ID No. 89: CCGGCCACCTGTGGCACCAGCGTCTATGTCTACCCATTCGACCTTGCCG ACGAGGTCTTTACCTGGGCCCGCGCGGTCAGCGCCGAAGTCGACCCTCG GGTCGAGCTGCAAGCCCTTGCCTCCCGCGGTGAACCGAGCATGGGCATC GACGTCCCCGTCATCTCCCTTGCCTCGCCCGCTTTCGCTGACTCGCCCG AAGAGGCCGAACAGGCCCTCGCCCTGTTCGGCACCTGCCCGGTTGTCGA GCAGGCACTGGTCAAAGTCCCTTATATGCCAACCGATTTGCCTGCCTGG TATGACATCGCGATGACCCACTACCTGTCAGACCATCACTACGCGGTGG ACAATATGTGGACGTCGGCGTCCGCTGAGGACCTGCTGCCGGGTATCCG CTCAATCCTGGACACGCTGCCCCCGCATCCGGCGCACTTCCTCTGGCTG AACTGGGGTCCATGCCCTCCCCGTCAAGACATGGCCTATAGCATCGAAG CCGACATCTACTTGGCGCTCTACGGCTCCTGGAAGGATCCGGCCGACGA GGCGAAGTACGCCGACTGGGCGCGGTCCCACATGGCCGCGATGTCGCAT CTGGCGGTCGGCA; SEQ ID No. 90: TGTTACCGACGCCGGAGTGAAAGGCCGATGTCGCTAGGCCCAGCGTGCT GGTGTTGTAGAGGCCTGAGACTGTGTTGCCGAAGTTCAAGATTCCCGAT GTCAGTGGCCCGACGTTAAGGAATCCGGAGTTGCCGAGATTCCCAGCAA TGTTCCAGAAGCCAGATCCGCCCGAACCGACGTTCCCGAAACCCGATGT GCCGCCCGTACCGCTGTTGAAGAAGCCCGATGACGGGGTGGTGGTCGAG TTTCCGAAGCCTGGGGTGCCCGCGATTTCGATCGGGATGTTGATCGGCC CGAGGCGGCCGGACACGTCGATGCCCAACGGGATTGAGGGGATCGTGAT TGGCGGGGTAGTGAGGGGGCCGATGGCGCCGCCCACATCAATACCCAAC GGGATTGCCGGAAGTGAGTAGCCATCCGGGAACACCGTAAACGGGCCTA ACCCTCCGCCCACATCAATACCCAACGGGATTGCCGGAAGTGAGTAGCC ATCCGGGAACACCGTAAACGGGCCTAACCCTCCGCCCACATCAATACCC AACGGGATTGCCGGAAGTGAGTAGCCATCCGGGAACACCGTAAACGGGC CTAACCCTCCACC; SEQ ID No. 91: GCTGCCGGACACGTCGATGCCCAACGGGATTGAGGGGATCGTGATTGGC GGGGTAGTGAGGGGGCCGATGGCGCCGCCCACATCAATACCCAACGGGA TTGCCGGAAGTGAGTAGCCATCCGGGAACACCGTAAACGGGCCTAACCC TCCGCCCACATCAATACCCAACGGGATTGCCGGAAGTGAGTAGCCATCC GGGAACACCGTAAACGGGCCTAACCCTCCGCCCACATCAATACCCAACG GGATTGCCGGAAGTGAGTAGCCATCCGGGAACACCGTAAACGGGCCTAA CCCTCCGCCCACATCAATACCCAACGGAATAGCCGGCAAACTATAACCA CCCGATAAGAAGGTGATGGGACCGATTTGACCACTCACTGTCACGTAAT CTGGAGGGAATCCGGGGAAAAATGGCGGAATCGCGGGAATCTCAGGAGT GCCTAGCTGTATCGATATGCTACCCGGGCCTATGCTGCCAACGGTGGGA TTTACGCCGAATAAGCCGATCGCAAGCGGAGACGCGGGGATCGAAATCG ATCCCACGTTAATGACCTGGAACGCCGATAGCTCTAGGCCAATAGAATT TAGAGTGATCGGC; SEQ ID No. 92: CCATGCGGTGCCGCGGTGGTCCAGCCAGCGCCCTGCAGTGTGCTGGTGC TCGATACCAGGTTGGCCTGTCCCGCCCAGCTGGGCGGCACCGACAATGC GCCGATTGACGACGCCCGACTAAGGCCGGCGGCTAGCGGAGCCGCACCC AGACCGGCCGCGATCGGCGCCTCGCCGACGGCCGCCTCCGCCGCCCCCA GCTCCGATAGGCCCGCGCCCTCCAAGCCCTCCTCGAGGGCGGCTTCCTC GGCAGCCGGAAGAAGACCACCGCTGGCCAGCCCTAGCAAGTCCGACGCG GCGGAGACCCAGTTCCCAGCCCCAATGTTGAAGATATTGGCAATATCTG AAATCCAGGAGGGCACCTTCCCGGGCGTGGAACCCAAGATGCTCGCGAT ACCCGACAACGGCGAAGCGGCCGCGGATGAGTTGGCGGCCTCGGTGGCC GCATAGGTGCCAGCGCTGACCCCCAGGGTCTTCACAAACAGGTCGTATA CCGCAGCTGCTTCAGCACTGACCTGCTGGTAGAGAGTGCCGTACGCGGT GAACAACGGCGCCTGTAGCACTGATATCTCATCAGCGGCGGCGGGAATC ACGCCCGTGGTGG; SEQ ID No. 93: ACGTCGAGCCAACCCCACTTCAGTGGGTAGGTGAACTCGTCCAGCAGAT AGAAGTCGTGACGTTGCGTGGCCAGCCGGAGCGCGATCTCGGCCCAACC GTCCGCCGCCGCGGCCGCACGATCGACGTCGGTGCCGGCCTTGCGAGAC GTACGTGTCCAGGACCAGCCCGCACCCATCTTGTGCCACTCCACCGCTC CGCCGATCCCGTGCTGGTCGTGCAGCCGGCCCAGTTGACGAAACGCCGC CTCCTCACCCACTTTCCACTTAGCGCTCTTGACAAACTGAAACACCGCG ATGTCCCGACCAGCGTTCCACGCCCGCAACGCCATTCCGAACGCCGCGG CTCGATTTTCCTTTGCCTTCACCGGTGTGTACGCCAGTATCGGCATGTT GCGCCGGGCCCGGGTGGTCAGGCCATCGTTGGGCACTGCGAGCGGATTG CCCTGCGGCATGTGTGGTTACCTATCCATCGTCAAGCCACGCCACGCAC GGCATGCACTAGATAATCCGCGTGCAACTGCTCCAACCGAACCACCGGC GCACCCAGCTGACGAGCCAGTTGCGCTGCCAAACCCAGCCGTACATACG ACGTTTCGCAGTC; SEQ ID No. 94: CTGCGAGTGGGCCGACCGATAGGCCCGATGCTGGCACAGACCGCGACCA GCGTCCATGATGCACTCGAACGTCACGGCGGCACAACCATTTTCGAGGC TAAACTAGACGGCGCGCGAGTGCAGATCCACCGGGCAAACGACCAGGTC AGGATCTACACCCGAAGCCTGGACGACGTCACTGCCCGGCTGCCCGAGG TGGTGGAGGCAACACTGGCACTGCCGGTCCGGGATCTAGTGGCCGACGG CGAGGCGATCGCGCTGTGCCCGGACAACCGGCCGCAGCGTTTCCAGGTC ACCGCACCACGGTTCGGCCGATCGGTCGATGTTGCGGCTGCCCGCGCGA

CGCAGCCACTTTCGGTGTTCTTCTTCGACATCCTGCATCGGGATGGTAC CGACTTGCTCGAAGCGCCGACCACCGAGCGGCTGGCCGCCCTGGACGCA CTGGTGCCGGCTCGGCACCGCGTGGACCGGCTGATCACGTCCGATCCAA CGGACGCGGCCAACTTCCTGGATGCGACGCTGGCCGCCGGCCACGAGGG GGTGATGGCCAAGGCACCGGCCGCTCGTTACCTTGCGGGTCGCCGCGGA GCGGGCTGGCTGA; SEQ ID No. 95: ACGGTGAGGCCGGCCGGGAACAAGGCCAAGGACGATGTGGACAGATTGA AAGTCGCGCCGAACGGGCCGGGGATCGTGCCCGGGCCGCCGTAGCTGCC GATGATGGGTCCATTGATCTGCAGGTCGCTGATGCTGAGGTAGAACGAC CCGGAGGGGAATTTCGCGCCGGGTGGGCCTAGCGGCGGGCCGTAGTGGT CGATCGTGATGAACGGGTCCGGCAAGACGACCGGGTCCGCGGTGATTTC TGCCATGGCGGTTTGCCCGAAAAGAACAAACGCGGGATTCACGTGAAAA CCCTCGTGGCCGACGGTTCCGGTCACGTGGATCGGGATCGCGGGAATGG TGATCTCCGGGAGAGTGAATTCGCGGATCCCGATGAATCCCCCGGTGAT TTGTATGTCGAATGCCGGAATATCGATGGGCTGGACGTGGATGGGACCG ATCCCGCCAATCACCTGCAGGTCAATGGGGATTTCGGAAATGGTGAAAA GGGTGCCGGGGGTGAAGGGGGCCAGGACGTTGATGTTGTTGCCCGTTAA GAAGAAACCGGTGTTGTGGCTTCCCGAATTGAATACGCCCAAATTCCCG GTGCCGGAGTTGA; SEQ ID No. 96: ACAAGCGCGGTAGCCCGCTCGACATCGCTTGCTGTCATTGCGGCAGGTG CTTGATAGAGGGCCGCCAATTCGGTCGCCGCTTCGGATCGCGAGTTCAG GGCGGCAACAACTGGCAGTGTCGCCTTACGTCGGGCAAGGTCGTTGCCG ACCGGCTTTCCCGTCACACCAGGGTCACCCCAGATGCCGATCAGATCGT CGACGCATTGAAACGCAAGACCCAACTCATGGCCAAAACGCTCCAACGC AGCAATCGTCGCGTCGTCTGCATTGGCCACTAAAGCTCCCAGAGCGCAA CAACAATCGGTCAGGGCGGCCGTCTTGCCCGCGGCCATCCGCAGATAGT CATCGACTGTAACTTCGGGCTGTCCCTCCAATAAACAATCCTCAAACTG GCCGATACACAAGTCCAGGCACGACATCTGCAATCGCCTTATCGCCCTG ACCGCCACACACTCGTCGGTCAGGCCGGTCAGTATCCGAACGGCCGTGG CGTGCAACGCATCTCCCAACAGGATCGCGACGCCCACACCCCACACACT CCATACCGTCGGCCGTCCCCTGCGAGTCGCATCCCCATCCATCACATCG TCATGCAACAACG; SEQ ID No. 97: GTCAGCCAGTCGTTGCGAACATCGTCGTCCACGTAGGGCTGTATCTGTT GGCGAACCACTTCGACGGCCGTCGGCCGATCTGCCCCCTCCGTCGTGAG CGCTTCGGCCGCAGCCAACCATGCCGGCCGCTGCGCCAGGGCACGCTCG TCGATCGCAATGGCCGTCGCGACTTTGGAGTCCACCAGCTGCCAGAGGT TGTCGCGCAGCGATTCGCAGCGTTGGGCCGCGGCACGGACTTCGGTGAC CACCGAATTTCCAGTCTCACAGTGACGCTGCACAAAGTGCACCGCCGCG TCGGCCTCCGATCCCGTCCATGCCGCTGCCAAGACGGCGACCTGGCTAC GCTCCATCCGCAGCGCCTCCATGAGCACACTGGCGGCAGCCCGCAGCTG CGCGCAGTCAGCGTCGAGCGCGTGCAGGTCAAGTCCGTCTTCGCTGCCG TACCAGTCGTGGATCTGGGCAGGGTAGGCGGTCAGGTCGGGATGTTGGT AGCCCACCAGGTGGCAAGCCCGCACGTAGCTTTGCGTGTGCTCGGCTGC GGGCCTGCCCTCGGCGAGACGCTCAGCGACGTTCAACCGGTCAGCCACC CTCACCCGATCCG; SEQ ID No. 98: CGCCAGCACCGCGGGGCTCGCCGCCGGGGTCGTGGCGGTCCAAACGGCC GGAACCTTCAATCCCCCGACCGACGCCGCCTGACCGACGGCGCCCGCAA CGCCGCTCAGGCCAGCACTCGGAATGGCCGGAACGGCGGCCGGCAACGC CTTGGCGGCCTCACCGGCGGCTTTGGCGCCTTCACTCGCCCACTTCGGC AGGTCGTGCGCCAGGCCAAAGTAGTCCTTGAATTGGGTGACCATGAGCC GAGCGGGCGAGACCCATTTGCCGAACGTGTCCATGGCCACGCTGGCATC AAGTTCTGCCGACCCGGTCACACCCTGCACAAAGTCGCCAAGCACTCCG CCCACGATGAGCCCGCTACCGTCCGAGGACCAGGTGTGCCCGGTCAAAC CGAGCGCCTTGCCAAGGTCGGTGAGCCAAGGCGGTTCATTGGTGAAGAT TCCGCTAAGCCCAAACAACGCTTTAGGAATGTCGGTGAGTGCTTGCGCA TTTGCGGCCCCGCTGACAGCTTGTCCGACAGATGCGGCCTGGCTGGCCA GCCCGGCCGGGTTGATGGTCTGCGCCGCCGGATTGAATGGCGACAACTG CGTCGCCGCCGCC; SEQ ID No. 99: TGCGCGATGCCGACGATGCCGCGCTGCTTGCCGCAATCGAGGACTGCGC GCGTGCCGAGGTGGCCGCCGGCGCCCGCCGCCTGTCAGCGATCGCCGAA CTCACCAGCCGGCGCACCGGCAATGACCAGCGGGCCGACTGGGCGTGCG ACGGCTGGGACTGCGCGGCCGCCGAGGTGGCCGCCGCACTGACCGTAAG CCACCGTAAGGCCTCCGGGCAGATGCATCTGAGCCTCACCCTAAACCGA GCTGCCCCAGGTGGCGGCGTTTTTTTGGCCGGGCAGCTCAGCGCGCGGC TGGTGTTGATCATCGCCTGGCGCACCTACCTGGTTCGCGACCCCGAAGC GCTGAGTCTGCTCGATGCCGCCCTCGCCAAACACGCCACAGCGTGGGGT CCGCTGTCGGCCCCCAAACTGGAAAAGGCTATCGACTCCTGGATTGATC GGTACGATCCCGCCGCACTGCGACGCACCCGTATCTCGGCCCGCAGCCG CGACCTGTGCATCGGTGATCCCGACGAAGATGCCGGCACCGCCGCACTA TGGGGCCGGTTGTTTGCCACCGACGCCGCCATGCTGGATAAGCGCCTCA CCCAGCTGGCCCA; and SEQ ID No. 100: ATCCGCTGGCTGGTGGATCAGGCCCCAGCGCGGGCGCGGGCCTGCTGCG CGCGGAGTCGCTACCTGGCGCAGGTGGGTCGTTGACCCGCACGCCGCTG ATGTCTCAGCTGATCGAAAAGCCGGTTGCCCCCTCGGTGATGCCGGCGG CTGCTGCCGGATCGTCGGCGACGGGTGGCGCCGCTCCGGTGGGTGCGGG AGCGATGGGCCAGGGTGCGCAATCCGGCGGCTCCACCAGGCCGGGTCTG GTCGCGCCGGCACCGCTCGCGCAGGAGCGTGAAGAAGACGACGAGGACG ACTGGGCCGAAGAGGACGACTGGTGAGCTCCCGTAATGACAACAGACTT CCCGGCCACCCGGGCCGGAAGACTTGCCAACATTTTGGCGAGGAAGGTA AAGAGAGAAAGTAGTCCAGCATGGCAGAGATGAAGACCGATGCCGCTAC CCTCGCGCAGGAGGCAGGTAATTTCGAGCGGATCTCCGGCGACCTGAAA ACCCAGATCGACCAGGTGGAGTCGACGGCAGGTTCGTTGCAGGGCCAGT GGCGCGGCGCGGCGGGGACGGCCGCCCAGGCCGCGGTGGTGCGCTTCCA AGAAGCAGCCAAT.

[0030] The above SNP markers of M. tuberculosis are correspondent to "T" at position 128290 of genome of the reference strain, "A" at position 178812 of genome of the reference strain, "A" at position 243118 of genome of the reference strain, "G" at position 374353 of genome of the reference strain, "G" at position 375095 of genome of the reference strain, "G" at position 430332 of genome of the reference strain, "C" at position 756840 of genome of the reference strain, "G" at position 848652 of genome of the reference strain, "C" at position 991896 of genome of the reference strain, "A" at position 996219 of genome of the reference strain, "A" at position 1300047 of genome of the reference strain, "A" at position 1810066 of genome of the reference strain, "G" at position 1932201 of genome of the reference strain, "A" at position 2008738 of genome of the reference strain, "G" at position 2165256 of genome of the reference strain, "G" at position 2165554 of genome of the reference strain, "A" at position 3078579 of genome of the reference strain, "C" at position 3157993 of genome of the reference strain, "C" at position 3426415 of genome of the reference strain, "T" at position 3734189 of genome of the reference strain, "T" at position 3797876 of genome of the reference strain, "T" at position 3859376 of genome of the reference strain, "T" at position 4061113 of genome of the reference strain, "T" at position 4221423 of genome of the reference strain, and "C" at position 4352162 of genome of the reference strain, respectively.

[0031] In the present application, the reference strain is M. tuberculosis H37Rv having a complete genome sequence NC_--000962.2. Said genome sequence is public information, which is published in the database of National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/nuccore/57116681?report=fasta) entitled "gi57116681/ref. NC_--000962.2/ Mycobacterium tuberculosis H37Rv chromosome, complete genome".

[0032] Table 1 shows the detail information of the SNP markers of the present application. In Table 1, the H37Rv genome position indicates the position of each SNP marker in the reference chromosome, the reference allele indicates the nucleotide exist in M. tuberculosis H37Rv strain, and the variant allele is the SNP marker of the present application.

TABLE-US-00004 TABLE 1 SNP markers of M. tuberculosis Correspondent H37Rv SEQ ID genome position reference variant No. varID (NC_000962.2) allele allele 76 94 128290 G T 77 128 178812 G A 78 164 243118 G A 79 246 374353 A G 80 247 375095 C G 81 270 430332 A G 82 450 756840 T C 83 503 848652 A G 84 570 991896 T C 85 573 996219 G A 86 732 1300047 G A 87 998 1810066 G A 88 1060 1932201 A G 89 1093 2008738 G A 90 1181 2165256 T G 91 1182 2165554 A G 92 1626 3078579 G A 93 1673 3157993 A C 94 1799 3426415 T C 95 1943 3734189 A T 96 2000 3797876 C T 97 2035 3859376 C T 98 2137 4061113 G T 99 2236 4221423 C T 100 2329 4352162 A C

[0033] In some embodiments, various genotypes of M. tuberculosis possess various combinations of the SNP markers. Preferably, the combination of the SNP markers contains at least two markers, such as 3, 5, 7, 10, 15, 20, or 25 markers. However, in some embodiments, the above SNP markers may used alone.

[0034] The present application also provides a method for genotyping M. tuberculosis comprising obtaining a sample, amplifying and obtain at least one of first DNA fragment by using one or more primer sets selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), amplifying and obtain at least one of second DNA fragment by using the obtained first DNA fragment as template and using one or more extension primers selected from the group consisting of SEQ ID Nos. 51 to 75, and detecting the second DNA fragment by using mass spectrometry.

[0035] In some embodiments, the method can further comprises analyzing the mass spectrometry data based on the single-nucleotide polymorphism markers selected from Table 1.

[0036] In one preferred embodiment, the mass spectrometry is matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

[0037] Examples of the suitable sample applied for the method can include, without limitation, bacterial culture, nasal mucus, phlegm saliva, blood, section of tissues or organ, biopsy and the like.

[0038] The present application further provides a kit for genotyping M. tuberculosis comprising at least one primer set selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), and at least one extension primer selected from the group consisting of SEQ ID Nos. 51 to 75. In some embodiments, the kit may further comprises a database of genotypes of M. tuberculosis based on single-nucleotide polymorphism markers, preferably, based on the SNP markers shown in Table 1.

EXAMPLES

[0039] To investigate the transmission, virulence, antimicrobial resistance and other attributes of the MTB, the inventors sequenced the genome of six strains isolated in Taiwanese population using next-generation DNA sequencers (Roche 454/Illumina GAIIx). Based on the comparative genome analysis, there were 60 and 141 strain-specific single nucleotide polymorphisms (SNPs) found in PE/PPE and non-PE/PPE gene families, respectively, comparing to the H37Rv reference strain. In the present application, lineage specific SNPs were used as markers to design a novel strain classification scheme and conduct the phylogenetic analyses. The performance of this genotyping panel was compared with the current standard test, spoligotyping patterns specific for 156 Mycobacterium tuberculosis complex (MTBC) isolates.

[0040] Materials and Methods

[0041] Bacterial Strains and Molecular Typing

[0042] MTB isolates were collected between 2004 and 2007 from the mycobacteriology laboratories of five general hospitals located in four geographical regions in Taiwan, namely, Taipei Tri-Service General Hospital (northern region), Mennonite Christian Hospital (eastern region), Wan-Ciao Veterans Hospital (central region), Tainan Chest Hospital (southern region), and Kaohsiung Veterans General Hospital (southern region). The bacterial strains used in this study are representative of the diversity of MTB in Taiwan as shown previously (Chang J R et al., Clin Microbiol Infect 2011, 17(9):1391-1396; Dou H Y et al., BMC Infect Dis 2008, 8:170; Dou H Y et al., Infect Genet Evol 2008, 8(3):323-330; Dou H Y et al., J Microbiol Methods 2009, 77(1):127-129). Spoligotyping and MIRU-VNTR genotyping assays were performed based on internationally standardized protocols. A total of 156 isolates (of the Beijing, EAI, Haarlem, LAM, T, MANU, and unclassified strains) that had all genotype data available were used for the subsequent analyses.

[0043] Genome Sequencing of MTB Strains

[0044] Six MTB strains, W6, M3, M7, A27, A18 and M24, belong to the genogroups modern Beijing, Haarlem, Latin-American Mediterranean (LAM), T, East African-Indian (EAI), and ancient Beijing, respectively. They represent the major types of clinical strains isolated from three different ethnic groups in Taiwan and were taken to whole genome sequencing using the 454 pyro-sequencing approach (Margulies M et al., Nature 2005, 437(7057):376-380). TB strains were sequenced 14 to 28-fold depth of the genome separately using a Genome Sequencer 20 (GS-20) or a Genome Sequencer FLX (GS-FLX) instrument (454 Life Sciences, Roche) with a 500-800 base-pair shotgun library for each strain.

[0045] DNA libraries of six MTB Haarlem and six T clinical isolates were prepared using Nextera DNA sample preparation kit (Illumina, CA, USA), and were multiplex sequenced (2×100 bp) at one lane of flow cell using HiSeq2000 sequencer. After performing de-multiplex procedure, the average sequence size of each sample was 3.38 Gb, and the depths of these samples were ranged from 568 to 1068-fold when mapping to H37Rv reference sequence, resulting in that the reference coverage of these samples was from 99.44% to 99.82%.

[0046] Mapping to the Reference Genome H37Rv

[0047] The 454 sequencing raw data (sff files) from each strain were collected into a specific folder as the read source to align the reference genome of the strain H37Rv. H37Rv genome sequence and the annotated gene information were downloaded from the NCBI ftp site for Microbial Genome Assembly/Annotation Projects (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Mycobacterium_--tuberculosis- _H37Rv_uid57777/). 454 GS Reference Mapper (Roche) software (version 2.3) was used to map 454 reads to the reference sequence (see Table 2 for detail information) and generate high-confidence variations between the reference and each of our six MTB clinical strains.

TABLE-US-00005 TABLE 2 Statistics of lineage-specific single nucleotide polymorphisms (SNPs) # of PE/PPE gene family non-PE/PPE gene family lineage-specific synonymous non-synonymous synonymous non-synonymous intergenic Isolate Lineage SNPs SNPs SNPs SNPs SNPs SNPs M3 Haarlem 133 3 3 55 56 16 W6 modern 270 4 7 78 150 31 Beijing M7 LAM 317 10 7 93 163 44 A18 EAI 1,260 37 60 368 639 156 A27 T 136 2 2 48 69 15 M24 ancient 260 6 10 78 138 28 Beijing Sum 2,376 62 89 720 1,215 290

[0048] Selection of Strain-Specific SNPs

[0049] Based on the result which contains "High-Confidence" differences with at least three non-duplicate reads that (a) show the differences, (b) have at least five bases on both sides of the difference, (c) have few other isolated sequence differences in the read, and (d) have at least one aligned in the forward direction and at least one aligned in the reverse direction. Besides, only those variation sites that all six strains have at least three reads covered and the variation rate larger or equal to 80% were considered as valid. Home-made scripts were used to merge the mapping results of all six strains and parse those valid differences into a MySQL database for further analysis. Strain-specific (observed only in single strain) SNPs were selected and grouped into two categories: PE/PPE protein family and non-PE/PPE. According to the location of the variations, they can be synonymous or non-synonymous to the coding sequences. And in non-PE/PPE group, the variations can also locate at non-coding sequences, which are intergenic regions. To further confirmation using MassARRAY Analyzer (Sequenom), the number of the variations was reduced with criteria that both total depth and variation depth must larger than 15 and the variation frequency must larger than 90% for each variation site.

[0050] For SNP calling of Illumina HiSeq2000 sequence data, mapped sequence data of each sample was analyzed using CLC Genomics Workbench software (Aarhus, Denmark) with default parameters. We applied an additional filter to identify highly reliable SNPs with more than 30-fold depth and >95% variant frequency.

[0051] SNP Genotyping Based on the MassArray System

[0052] PCR and extension primers were designed for 60 PE/PPE and 60 randomly-selected non-PE/PPE SNPs using the MassArray Assay Design 3.1 software (Sequenom, San Diego, Calif.). Five of them were excluded due to difficult sequences. PCRs contained, in a volume of 5 ul per well, 1 pmol of the corresponding primers, 5 ng genomic DNA, and HotStar reaction Mix (Qiagen) in 384-well plates. Three wells were needed for each sample. PCR conditions were as follows: 94° C. for 15 min, followed by 40 cycles of 94° C. (20 s), 56° C. (30 s), 72° C. (60 s), and a final extension of 72° C. for 3 min. In the primer extension procedure, each sample was denatured at 94° C., followed by 40 cycles of 94° C. (5 s), 52° C. (5 s), 72° C. (5 s). The mass spectrum from time-resolved spectra was retrieved by using a MassARRAY mass spectrometer (Sequenom), and each spectrum was then analyzed using the SpectroTYPER software (Sequenom) to perform the genotype calling. After analyzing the genotype profiles, the clustering patterns of five SNPs could not be used to correctly perform genotype calling, and the data of 110 SNPs (57 PE/PPE and 53 non-PE/PPE) were finally used in the following analyses.

[0053] Linkage Disequilibrium and Phylogenetic Analysis

[0054] Based on the haploview software, the Lewontin D' measure was used to estimate the intermarker coefficient of linkage disequilibrium (LD) as shown in FIG. 2. An extra stringent criteria, r2=1 between each pair markers, was used to select 25 tagSNPs from 110 SNPs. We applied the Phylip software to calculate the Nei's distance using SNP data, and then constructed a phylogenetic tree using the neighbor joining approach.

[0055] Results

[0056] Genome Sequencing of Six MTB Clinical Isolates

[0057] The overall scheme for selecting lineage-specific DNA markers is shown in a flowchart (FIG. 1). Based on our previous study of the MTB stains in Taiwan (Dou, et al), we selected representative strains for whole-genome sequencing. The initial grouping of these bacteria was based on spoligotyping and MIRU, also we consider the ethnic background of the patients that were infected with MTB. We applied whole-genome shotgun approach to generate high coverage sequences using the 454 technology. Genome sequence of the representative strain was compared to the reference to generate variant sequences for each of the isolate. A total of 120 SNPs were used to form a genotyping panel to investigate 150 additional clinical isolates, which were characterized by both spoligotyping and MIRU. After phylogenetic analysis and the analysis for decision tree, we grouped these 156 isolates (6+150) with selected markers. To improve the genotyping panel and broaden the basis of selecting lineage-specific SNPs, we further sequenced those that could not be classified with the minimum set of SNP markers. The sequence data was then used for comparative analysis to refine the process. To obtain genome contents of representative MTB isolates from local ethnic groups and to reveal their differences with the reference strain H37Rv, we performed whole genome shotgun sequencing of six isolates using the 454 platform. Three isolates W6, M3, M7 were sequenced by the 454 GS20 sequencer with average read length of 96 base-pair. With the sequencing technique evolving, another three isolates A27, A18, M24 were sequenced by the 454 FLX sequencer with longer average read length of 227 base-pair and fewer runs of sequencing experiments. The sequencing depths were about 14X˜23X in 454 GS20 data and about 16X˜28X in 454 FLX data.

[0058] The mapping results were summarized in Table 3. All six isolates got at least 95.8% of mapped reads that covered 97% and above of the reference sequence. The total contig numbers for the three isolates sequenced by 454 GS20 were 214-305; while for the three isolates sequenced by 454 FLX they were 290-299. The large contig (>=1,000 bp) numbers were 134-158 for the three isolates sequenced by 454 GS20 and 196-200 for the three isolates sequenced by 454 FLX, indicating that large contigs ratio were higher for the three isolates sequenced by 454 FLX. The base quality of Phred score 40 and above (Q40Bases) for large contigs were 99.48% to 99.95% in the six isolates, indicating that the sequencing quality is high enough.

TABLE-US-00006 TABLE 3 Genome sequencing and mapping results of the six MTB strains ##STR00001## .sup.$depth = totalBases/length of H37Rv genome *largeContig: contig length >= 1000 bp avgContigSize & N50ContigSize are calculated from largeContigs Mapped by 454 gsMapper Release: 2.3

[0059] Genetic Variations of the MTB Clinical Isolates

[0060] We totally extracted 9,003 high-confidence (HC) variations (for the definition of HC variants, please see the Method section), including SNPs, multiple nucleotide polymorphisms (MNPs), insertions and deletions (INDELs), from the mapping results of the six isolates. After sorting these variations with reference positions, and at least one isolate with over 80% of variation frequency, there are 3,819 reference positions that all the six isolates got at least three reads covered. For simplicity, 3,582 reference positions contained only SNPs were chose for the following analysis (other 27 positions were INDELs and 210 positions were MNPs).

[0061] Among these 3,582 SNPs, 404 SNPs co-exist in all the six isolates, and 13, 19, 232, 538 SNPs exist in five, four, three, and two of the six isolates, respectively (details were shown in Table 4). The most abundant SNPs are 2,376 strain-specific (HC differences exist only in one of the six strains) and we used them as candidates for seeking lineage-specific SNPs. These candidate SNPs, according to their locations in coding or non-coding regions, are divided into three main categories: PE/PPE gene family, non-PE/PPE gene family, and intergenic SNPs (as shown in Table 2). For those SNPs in coding regions, non-synonymous SNPs seem to have more or equal number them synonymous SNPs, except in M7 isolate. And as we know that the presence of the two novel gene families PE/PPE comprises about 10% of the coding capacity of the TB genome, thus the SNPs in PE/PPE family are commonly much less than those in other non-PE/PPE gene families. A18, belongs to the EAI lineage, has 4-10 times higher numbers of specific SNPs than other five isolates, suspects that the lineage may evolve at a higher mutation rate and quickly adapt to changes in their host environment.

TABLE-US-00007 TABLE 4 High-confidence SNPs with total depth ≧3 and variation rate ≧80% for each site of each strain Comparing to the reference # of SNPs M3 W6 M7 A18 A27 M24 Differences 2,376 133 270 317 1,260 136 260 in 1 strain Differences in 538 205 325 2 9 206 329 2 strains Differences in 232 3 228 4 229 3 229 3 strains Differences in 19 6 19 16 14 3 18 4 strains Differences in 13 13 12 8 12 9 11 5 strains Differences in 404 404 404 404 404 404 404 6 strains Sum 3,582 764 1,258 751 1,928 761 1,251

[0062] SNP Genotyping on 156 M. tuberculosis Clinical Isolates

[0063] In order to characterize SNPs in 156 clinical isolates for phylogenetic analysis, 120 lineage-specific SNPs with high confidence scores were selected to design primers for Sequenom MassArray assays. These 120 lineage-specific SNPs were unequally selected from six lineage samples as shown in Table 5, which was caused by the difference in the total numbers of lineage-specific SNP between them. These 120 SNPs were divided into two categories: [5] all of 60 SNPs within PE/PPE gene family; [8] 60 of 1,215 non-synonymous SNPs within in non-PE/PPE gene family (details were shown in Table 6). Five of 120 SNPs were not designable in Sequenom matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) systems because of high GC contents and/or primer dimmers. 115 of 120 SNPs were designed into 10 multiplex reactions, and were genotyped in 156 clinical M. tuberculosis isolates. We excluded five SNPs with low call rate (<95%) and bad clustering pattern, and the remaining 110 SNPs are used in the following analysis. The false-positive and false-negative rates were both 0% when comparing Sequenom and 454 sequencing data, and the average call rate of each of 110 SNPs in 156 samples were 97%. There were strong correlations between these SNPs in the MTB genomes based on linkage disequilibrium analysis as shown in FIG. 2. These 110 lineage-specific SNPs were completely tagged by 25 tagSNPs with r2=1.

TABLE-US-00008 TABLE 5 Selection of lineage-specific SNPs for strain typing Strain M24 W6 A18 M7 M3 A27 Lineage ancient modern Beijing Beijing EAI LAM Haarlem T No of original 260 270 1,260 317 133 136 lineage-specific SNPs No of 25 17 31 17 16 14 designed SNPs No of actual 22 17 29 15 15 12 genotyped SNPs No of SNPs 7 3 19 3 0 0 with 100% variant frequency in other isolates

TABLE-US-00009 TABLE 6 SNP number of genotyping panel used in Sequenom MassArray Isolate (lineage) M24 W6 (ancient (modern A18 M7 M3 A27 Gene family Substitution Beijing) Beijing) (EAI) (LAM) (Haarlem) (T) Sum PE/PPE synonymous 5 1 5 4 3 2 60 non-synonymous 10 6 16 3 3 2 non-PE/PPE non-synonymous 10 10 10 10 10 10 60 Sum 25 17 31 17 16 14 120

[0064] Phylogenetic and Grouping Analysis of MTB Isolates

[0065] To trace the relationships between 156 clinical isolates, phylogenetic trees were constructed based on 110-SNP or 25-tagSNP information as shown in FIG. 3(A) and FIG. 3(B). The positions of 110-SNP and 25-tagSNP were shown in FIG. 3(C) and FIG. 3(D). Although the total numbers of markers used were different between these two trees, the morphology of 25-tagSNP phylogenetic tree was the same as that of 110-SNP tree, indicating that 25 tagSNPs can well represent the genomic variances between strains. Based on the preliminary lineage information from spoligotyping, 10 ancient Beijing, 51 modern Beijing, 11 EAI and 3 LAM strains were grouped into the corresponding branches in both phylogenetic trees. In addition, 6 spoligotype-unclassified isolates were suggested to belong to modern Beijing (n=2), EAI (n=2) and LAM (n=2) lineage based on the nodes of phylogenetic trees.

[0066] Combination of spoligotyping and SNP genotyping data, we characterized the allele frequencies these 110 SNPs in 51 modern Beijing, 25 Haarlem, 11 EAI, 10 ancient Beijing, 7 T and 3 LAM isolates as shown in FIG. 4. All these 110 SNPs were lineage specific in these strains, and showed polymorphic in the corresponding lineage. Importantly, the variants of 32 SNPs were consensus in MTB lineage (Table 5), 7 SNPs were lineage-specific with 100% variant allele frequency in ancient Beijing, 3 in modern Beijing, 19 in EAI and 3 in LAM. Therefore, each of these 32 SNPs can be used to represent MTB lineage of ancient Beijing, modern Beijing, EAI and LAM, decision tree was constructed based on four lineage-specific SNP markers (FIG. 5). Based on the decision tree, 75 of 107 (70%) spoligotype-classified isolates can be correctly grouped into the corresponding lineage, and 6 of 49 (10.1%) spoligotype-unclassified isolates were grouped into known lineage.

[0067] 32 of 107 (30%) spoligotype-classified isolates were poorly classified using these 25 tagSNPs, and these isolates all belong to Euro American lineage (25 and 7 were classified as Haarlem and T strains based on spoligotype data, respectively). We hypothesized that there are high genetic heterozygosities of spoligotype-classified within Haarlem or T strains, resulting there was no leaf for Haarlem and T strains of decision tree (FIG. 5). To explore the genomic diversities of Euro American lineage, we took whole-genome sequencing to characterize genomic profiles of six Haarlem and six T strains. There were 4,419 SNPs found in these 12 Euro American strains (Table 7). We combined SNP information of M3, A27 (454 sequencing data) and these 12 samples (HiSeq2000 sequencing data) to construct phylogenetic tree and perform principal component analysis, and found the same spoligotype-classified strains were not well clustered (FIG. 6). These results demonstrated that there were high homozygosities within Euro American lineages, including Haarlem and T subtypes, and this findings was also supported by 24-MIRU-VNTR phylogenetic tree (FIG. 7). Importantly, M3 and A27 isolates, which were used to identify lineage-specific SNPs and construct decision tree (FIG. 6), were clustered together, but some Haarlem and T isolates were distant from M3 and A27, accounting for no leaf of decision tree for classifying these two subtypes. In addition, there were two major clusters of phylogenetic tree (FIG. 8), and we named these two clusters as EuAm1 and EuAm2 subtypes. Based on new proposed hypothetic definition of EuAm subtypes, there were high homozygosity within each EuAm subtype as shown in FIG. 9, and two SNPs were only needed to classify Euro American strains into two hypothetic subtypes.

TABLE-US-00010 TABLE 7 SNP discovery in Haarlem and T subtypes of Euro American lineage PE/PPE gene family non-PE/PPE gene family Total # synonymous non- synonymous non- Data source Isolate Lineage Sublinage of SNPs SNPs synonymous SNPs synonymous Intergenic SNPs HiSeq2000 A005 Haarlem h3(st227) 2261 126 206 646 1053 230 D065 Haarlem h3(st742) 984 76 75 308 438 87 A073 Haarlem h3(st742) 1651 107 154 460 744 186 B042 Haarlem st36 1645 106 153 449 753 184 C015 Haarlem h3(st50) 1579 114 113 451 719 182 W70 Haarlem h3(st50) 1009 65 71 351 435 87 A074 T T1(st102) 1615 127 148 450 721 169 B010 T T2-T3(st73) 1638 106 154 457 739 182 B029 T T2(st52) 1590 117 160 426 730 157 W21 T T1, st53 896 69 81 257 397 92 KVGH295 T T1 like 1039 59 91 318 460 111 KVGH458 T T3 like 958 78 84 286 421 89 454 M3 Haarlem h3(st742) 813 41 49 276 399 48 A27 T T1, st53 865 40 41 277 405 102

[0068] Genotyping of MTB by Using 25 tagSNPs

[0069] As described above, the 25 tagSNPs can well represent the genomic variants between strains. PCR and extension primers for 25 tagSNPs were designed using the MassArray Assay Design 3.1 software (Sequenom, San Diego, Calif.). The PCR primers, the extension primers, the positions and the correspondent alleles for the 25 tagSNPs are shown in FIG. 10. PCRs contained, in a volume of 5 ul per well, 1 pmol of the corresponding primers, 5 ng genomic DNA, and HotStar reaction Mix (Qiagen) in 384-well plates. Three wells were needed for each sample. PCR conditions were as follows: 94° C. for 15 min, followed by 40 cycles of 94° C. (20s), 56° C. (30s), 72° C. (60s), and a final extension of 72° C. for 3 min. In the primer extension procedure, each sample was denatured at 94° C., followed by 40 cycles of 94° C. (5s), 52° C. (5s), 72° C. (5s). The mass spectrum from time-resolved spectra was retrieved by using a MassARRAY mass spectrometer (Sequenom), and each spectrum was then analyzed using the Sequenom Typer 4.0 software (Sequenom) to perform the SNP genotype calling.

DISCUSSION

[0070] Tuberculosis remains a major public health issue in Taiwan and throughout the world. Over the past years, the development of genotyping methods for molecular epidemiology study of tuberculosis has advanced our understanding of the transmission of MTB in human populations. Classification of strains into sub-lineages provides perspective on the phenotypic consequences of genetic variations of the MTB strains. Phylogenic analyses of MTB strains have also offered new insights regarding the evolution of MTB and the existence of distinct clades. From public health perspective, an ideal methodology to determine the genetic variation of MTB clinical isolates should be simple, affordable, have a rapid turnaround time, and the result should be transferable in a format that can be easily shared between laboratories. In this study, we have designed a selection scheme of lineage-specific markers by genome sequencing, comparative analysis, and genotyping with DNA mass spectrometry, and also demonstrated the utility and accuracy of this new typing protocol. Because of its speed and ease of laboratory operation and the simple data format for exchange and comparison, the protocol reported here has the potential to become a new standard method. It should prove valuable for the development of an effective infection-control policy.

[0071] Although spoligotyping analysis is a straightforward technique, it is less discriminatory than IS6110 RFLP. Moreover, it is a labor-intensive and time-consuming procedure. Even through strain classification based on spoligotyping can assign MTBC strains to the correct phylogenetic lineages in about 90% of the cases, some strains cannot be classified at all, and others might be misclassified as shown in this study (FIG. 7). Analysis of MIRU-VNTR loci is reproducible and sensitive, and it provides a better resolution than spoligotyping. However, dependent on the context, such investigations can be less than or as discriminatory as IS6110 RFLP. Strain-specific SNP typing can provide precise sequence-based information, and could be automated for large-scale studies of molecular epidemiology and phylogenetics. The combination of spoligotyping and MIRU-typing can be considered a cost-effective method for TB genotyping. However, the spoligotype is still only about 20-40% strains that cannot be sorted, and nothing in this law to compensate for this shortcoming. The proposed MIRU-VNTR typing method could not sufficiently differentiate M. tuberculosis strains comprising many Beijing genotype strains. Therefore, this typing method could not be used for routine epidemiological study in areas where the Beijing genotype is prevalent. The addition of several VNTR loci is required to use VNTR typing as a routine epidemiological tool without doing RFLP analysis.

[0072] Additional genotyping of M. tuberculosis isolates is essential for understanding the dynamics of transmission. Genetic information will help determine precise quantitative measures for transmission dynamics and augment classical epidemiological models. The ability to assess the inter-strain genetic relationships provides a powerful means of resolving a number of epidemiological issues, such as tracing of chains of transmission, determining sources of infection, differentiating recent transmission from reactivation and reinfection from relapse or treatment failure, detecting laboratory cross-contaminations, monitoring the geographic distribution and spread of particular genetic strains (including those of special epidemiological importance), or investigating the evolution of M. tuberculosis.

[0073] The proposed workflow of selecting lineage-specific DNA marker (FIG. 1) is an effective and logistical way to discriminate MTB isolates into genetic subtypes. Importantly, the concept of our workflow is also applicable in other fields of microbial projects, e.g., searching highly conserved domains of variable clinical isolates for vaccine development.

[0074] FIG. 11 shows the comparisons of the present application and the conventional genotyping methods. For the 25 tagSNPs genotyping method of the present application, the sample needed for the detection is as low as 20 ng of DNA sample for PCR. Based on the MALDI-TOF technology, the specificity and the sensitivity of sequence detection is able to achieve almost 100%, but conventional PCR-based spoligotyping and MIRU cannot. By using 25 tagSNPs genotyping method of the present application, detection of 192 samples can be completed within 48 hours. Accordingly, advantages of the 25 tagSNPs genotyping method described herein include excellent specificity and sensitivity, less sample requirements, rapid and large scale detection.

[0075] While the present invention is disclosed by reference to the preferred embodiments and examples detailed above, it is to be understood that these examples are intended in an illustrative rather than in a limiting sense. It is contemplated that modifications and combinations will readily occur to those skilled in the art, which modifications and combinations will be within the spirit of the invention and the scope of the following claims and its equivalent systems and methods.

Sequence CWU 1

1

100130DNAArtificial SequencePrimer 1acgttggatg ttctggacga cctgtcctac 30229DNAArtificial SequencePrimer 2acgttggatg agctgcgcca aggttcgtg 29330DNAArtificial SequencePrimer 3acgttggatg ttgtagctgc ccaaattgcc 30429DNAArtificial SequencePrimer 4acgttggatg ggcttcaatc tcggcttgg 29530DNAArtificial SequencePrimer 5acgttggatg tattcaacac cggcatcggg 30630DNAArtificial SequencePrimer 6acgttggatg tcgcctggtc gtggaagaac 30729DNAArtificial SequencePrimer 7acgttggatg atcggacagc agaaggcac 29829DNAArtificial SequencePrimer 8acgttggatg actcccgcgg aacgtggtg 29929DNAArtificial Sequenceprimer 9acgttggatg caacaccggc aacttcaac 291030DNAArtificial SequencePrimer 10acgttggatg aattagcgtc tcctccgttg 301129DNAArtificial SequencePrimer 11acgttggatg tcgaacccgc cgacaaatg 291230DNAArtificial SequencePrimer 12acgttggatg tcgattggtc gcatgcactg 301330DNAArtificial SequencePrimer 13acgttggatg aaacctcggc atagggatcg 301430DNAArtificial SequencePrimer 14acgttggatg tcgacaggac tattggtagc 301530DNAArtificial SequencePrimer 15acgttggatg aagacgacgg gccggatatg 301630DNAArtificial SequencePrimer 16acgttggatg cgtcaagagc ttcccaaatc 301730DNAArtificial SequencePrimer 17acgttggatg catccgggaa caccgtaaac 301830DNAArtificial SequencePrimer 18acgttggatg atcaccttct tatcgggtgg 301930DNAArtificial SequencePrimer 19acgttggatg cctggatttc agatattgcc 302029DNAArtificial SequencePrimer 20acgttggatg tggccagccc tagcaagtc 292130DNAArtificial SequencePrimer 21acgttggatg agaacaaacg cgggattcac 302230DNAArtificial SequencePrimer 22acgttggatg tctcccggag atcaccattc 302329DNAArtificial SequencePrimer 23acgttggatg gttgtttttg gccgggcag 292430DNAArtificial SequencePrimer 24acgttggatg atcgagcaga ctcagcgctt 302530DNAArtificial SequencePrimer 25acgttggatg tgctaccgcc aatgttcaac 302630DNAArtificial SequencePrimer 26acgttggatg atggcgttga cataactcgg 302730DNAArtificial SequencePrimer 27acgttggatg atagcaagca cgattgcgac 302829DNAArtificial SequencePrimer 28acgttggatg accccccgct gagggcgta 292930DNAArtificial SequencePrimer 29acgttggatg gattcgattg gggaaacggc 303030DNAArtificial SequencePrimer 30acgttggatg ttccacattg gtgatcagcg 303130DNAArtificial SequencePrimer 31acgttggatg caaacggcgt cactttggtc 303230DNAArtificial SequencePrimer 32acgttggatg tgaaatgtgg gcccaagacg 303330DNAArtificial SequencePrimer 33acgttggatg cgatttcgat cgggatgttg 303430DNAArtificial SequencePrimer 34acgttggatg caatcacgat cccctcaatc 303530DNAArtificial SequencePrimer 35acgttggatg aggcaaagga aaatcgaccg 303630DNAArtificial SequencePrimer 36acgttggatg ttgacaaact gaaacaccgc 303729DNAArtificial SequencePrimer 37acgttggatg acaaccggcc gcagcgttt 293830DNAArtificial SequencePrimer 38acgttggatg aagaacaccg aaagtggctg 303930DNAArtificial SequencePrimer 39acgttggatg tgcattggcc actaaagctc 304030DNAArtificial SequencePrimer 40acgttggatg tcgatgacta tctgcggatg 304130DNAArtificial SequencePrimer 41acgttggatg acccatttgc cgaacgtgtc 304230DNAArtificial SequencePrimer 42acgttggatg tgcttggcga ctttgtgcag 304329DNAArtificial SequencePrimer 43acgttggatg agcgtgaaga agacgacga 294430DNAArtificial SequencePrimer 44acgttggatg gtctgttgtc attacgggag 304530DNAArtificial SequencePrimer 45acgttggatg acatcaggtg atggtcatgc 304630DNAArtificial SequencePrimer 46acgttggatg cgaagggaac aatggatgtg 304730DNAArtificial SequencePrimer 47acgttggatg tatgccaacc gatttgcctg 304830DNAArtificial SequencePrimer 48acgttggatg acatattgtc caccgcgtag 304929DNAArtificial SequencePrimer 49acgttggatg tcttggcagc ggcatggac 295030DNAArtificial SequencePrimer 50acgttggatg ccgaatttcc agtctcacag 305125DNAArtificial SequenceExtension primer 51gacctgtcct acgaaccggt gatgg 255220DNAArtificial SequenceExtension primer 52cgttgcccac gttgttggcg 205323DNAArtificial SequenceExtension primer 53caccggccaa cgtctcgggc atg 235421DNAArtificial SequenceExtension primer 54cccccgaccg gccgttcttc g 215517DNAArtificial SequenceExtension primer 55ttcaacggcg gcatcat 175617DNAArtificial SequenceExtension primer 56gccgaaacaa gatttgc 175717DNAArtificial SequenceExtension primer 57ccttctgcgt ctccaat 175817DNAArtificial SequenceExtension primer 58gatatggggc cgcggat 175923DNAArtificial SequenceExtension primer 59accgtaaacg ggcctaaccc tcc 236018DNAArtificial SequenceExtension primer 60ttggggctgg gaactggg 186119DNAArtificial SequenceExtension primer 61attcacgtga aaaccctcg 196221DNAArtificial SequenceExtension primer 62agctcagcgc gcggctggtg t 216323DNAArtificial SequenceExtension primer 63caaaatacgg cgatcatcat ggg 236417DNAArtificial SequenceExtension primer 64ccaccagtac ttgccgc 176517DNAArtificial SequenceExtension primer 65atcggggtga cgatgag 176622DNAArtificial SequenceExtension primer 66gccgaggagc ccgcgtaacc gt 226718DNAArtificial SequenceExtension primer 67tgttgatcgg cccgaggc 186820DNAArtificial SequenceExtension primer 68gcgggcgtgg aacgctggtc 206920DNAArtificial SequenceExtension primer 69agcgtttcca ggtcaccgca 207017DNAArtificial SequenceExtension primer 70ccagagcgca acaacaa 177118DNAArtificial SequenceExtension primer 71cacgctggca tcaagttc 187222DNAArtificial SequenceExtension primer 72gaagacgacg aggacgactg gg 227318DNAArtificial SequenceExtension primer 73gacgattccg ggcatgcg 187417DNAArtificial SequenceExtension primer 74tgcctgcctg gtatgac 177517DNAArtificial SequenceExtension primer 75ggcatggacg ggatcgg 1776601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 76tgccgggccg cctccagtcg acgtcgggta gtcgctaccg ccggcaccac cacccggcgc 60accagctggt cctgctcggc gaatagctcg gcggccgccg cctcggctcg caatcgttgt 120accccaccgg tgatcgcgtt gaccgtcatc acgcccgcta ccagtagcgc gtcgatattg 180ctgccgacaa tcgccgatgc tgcggcgccc accgccagga tcggagtcag cggatcggcc 240agttcatggc gggtggccac cgccagctgc gccaaggttc gtgccgggcc gcgcagcggc 300tccatcaccg gttcgtagga caggtcgtcc agaatgcgcc gccaggccgg gattccgggt 360tcgacggcca agggtcggga gccgccggct agccgcgagt agacgatctc ggggtccagc 420gcgtgccagg cggtcagcgg ttgcggggtg gggtcgggca tccgcagcac cttggcggcc 480gaccacattc cggacaccaa agccgttgcg gcagcggcat tgaccggatt gagccagcga 540cggaagctgg ctgggttggt ggttttgtcc tgctcaccgg tgaccaacaa cagcccggcc 600a 60177601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 77agcgttggga cccagcgaga tgaggtgctg catttccagg gacgcgatga cggcgctctg 60cgaatagccg aacacggtga cgtggtttcc ggcgttgatt tgctcccaaa tcgcgccgtc 120gagaatctgt aggcccaact gcaccgaggt ttggaagggc agggatttga cgccggtgat 180cggatatagc tcttcgggcg tcaccagcgc tttgacgacc ggattcgaga cgacggggtc 240gatgaacaag gtcgtgatgg cgttgacata actcggcgtg ggtatcggtg acccggtgcc 300acccatgatg atcgccgtat tttggttgaa cattggcggt agcaccgggg gtgaggttgg 360cttaaagagt ccggccgtcg cctcctgcac cagcgcgctc gtgttggtgg cctcggcatt 420gacaaatgcg tttgcggccg ccgccaacct ctgggtgaat tcgttgtgaa acgccgcaac 480ctgtgcgctg atcgcctgga actgctggcc gtacgcgccg aacagcgtgg caagggccgt 540ggacacttcg tccgcggcag ccgccgccag gccggttgtc ggggccgcga cggccgccgt 600a 60178601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 78ccgacaacac cggcccaccc ggcagcgtgg tgctcagcga gttggcggcg tagaaggcgg 60cctccgaccg ccattgcttg acgtgcaccc cggcggattt cagcagggtt cgctgaatct 120gggcgaagct gtgcatcgag gcgcccgcgg ctgccaccgc ggccagcaac caccaccact 180tggcgcgata caagctcacc caggccttgg cgagctggtc ccagcccaac gccacctcta 240tagcaagcac gattgcgacg atggccagta ccgcccatcg caaccaccag tacttgccgc 300acgggggtac gccctcagcg gggggtgccc ccacccgcgt gcgagggagt gcccccacgc 360gctggcggag gttgcgggcg ggggcgtcgt gcgacacgtg cttaagggta accgtgcagg 420tggcgccgta atcgcgatac atcgctaacc gtgtcagcct cgttgggggg tcgtgaccgg 480atcgtgccgc ctggcaaagt aactatgcgg gctcgacgcg acccgccgcg accttacgac 540gccgccgttc ccgttacgct tgccggatgt cggcgagcct ggatgacgct tcggtcgcac 600c 60179601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 79cgaggccagg ttccaaaagc ccgaagcgcc gccgccgaag ttgccgaagc ccgaggcggt 60gccggcgcca gcgttgaaga agcccgacga cgggctggtg gtcgagttcc cgaagcccgg 120ggccgccgga atcttgatga gcgggatgct gacgcccccc accatgccgg tgaggttgcc 180gtcgatcgtg gtggttggtc cgcccacggt gatcgtcacc gtgggaaggg tgagcgtgga 240ttgcgggagc tcgaccgggc cgtagtaaac aacgaaggga acaatggatg tgaagggcaa 300gcgcatgccc ggaatcgtca tcacgcttcc gggcatgacc atcacctgat gtatcggcat 360gctgaatagc tgcgcgttta tcggaatggc gggaatctcg agggcgatat cggcaccgat 420caggccttgg tagtcgcccc gccacaagac gccgttgctg tagttgccgg cgatgaaggc 480gccggtgttg acgttgccgg tgttggccac tccagtgttg tagtcgccgg tgttgaagta 540gccggtgttg tagttacctg cgttgaagct gccggtgttg tagttgccgg tgttgaagtt 600c 60180601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 80ttgaacaacc cgacgtttcc gctgccggag ttgaacaggc cgatgttgtg gctgcccgag 60ttgaagctgc cgaacccgat ctgtccgttg ccggtgagcc cgatgccgac attgttgctg 120cccgtattcc caaagccgac attgttgctg ccggtgttcg caaagccgat gttgtggccg 180cccaggttgg ccaaacccag gttgtcgctg cccaggtttg caaagccgag gttgtagctg 240cccaaattgc cgaagccgac gttgaacacg ccgacgtttc cgttgcccac gttgttggcg 300gcgacgtttg ccaagccgag attgaagccc gccgcgctcg gggggccggc agcggctgcc 360gcggcgctgg tcagccgctc cgataggccc gccagcttct tcagctgctg ggtgaacggc 420atcaacgcgg agacggccgc cgacgctcca gcgtgatagc caaccatcgc ggccacatcc 480tgggcccaca tccgctcata ggcggcctcg gtggccgcga tcgccggagc gttgaatccc 540agcagattcg agctcaccag cgacaccagc acggcgcggt tggccgcgac gatcgccgga 600t 60181601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 81agtcgccggc gttgccgaat ccgaagttgt agctgcccag gttgcctagg ccgatgttgt 60agttacccag gttcgccggg ccgatgttgt atgagccctg gtttccgccg aagacgttga 120agctgccgag gttgccgctg ccgaggttga agctgccgat gttcgccaag ccggcgttgc 180tgtcgcctac gttggagaag ccgacgttga attggccgat gtttcccagg ccgaggttga 240acatcgacat cccggtcgcc tggtcgtgga agaaccccgc gaggttgctg ccgatgttga 300gcatgcccga gacgttggcc ggtgccccga tgccggtgtt gaatacgccc gagacggtat 360cgcccaggtt cgccagtccc gattgcagcg agccgtagtt gttgaagccc gaggtcgcgg 420agttcgcgac gttctggaag ccggaaatgt tggcgccgat gttggcgatg cccgatacgg 480ttccggggcc gccgttgaag aagcccgagg acggatcggt ggtggcgttg aaaaagcccg 540tggtagccgc aatgttgacg aacgtgacat cgaagggacc gacgcttgcg gtggccggga 600t 60182601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 82taaagctcaa cggctacaac accgcccagt tcggcaagtg ccacgaagtc ccggtctggc 60agaccagccc ggtcgggccg ttcgacgcgt ggcccagcgg cggcggtggt ttcgaatact 120tctacgggtt tatcggtggc gaggctaacc agtggtatcc gagtctgtac gagggcacca 180cgccggtcga ggtgaaccgc acgcccgagg agggttacca tttcatggcg gacatgaccg 240acaaggccct cggctggatc ggacagcaga aggcactggc ccccgaccgg ccgttcttcg 300cgtacttcgc cccgggcgcc acccacgcgc cccaccacgt tccgcgggag tgggccgaca 360agtaccgggg ccgcttcgat gtgggctggg acgcactgcg agaggaaacc ttcgcccggc 420aaaaggaact cggggtgatc ccggcggact gccagctgac cgcgcggcac gccgaaatcc 480cggcgtggga cgacatgccg gaggacctca aacccgtgct atgccggcag atggaggtct 540acgcgggctt tctggaatac accgaccacc acgtcggccg gctcgtcgac ggcctgcagc 600g 60183601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 83gttggcgaag cccgagattt gtaaattacc aacgttttgg gcgccggagt ttcccctacc 60agaattattg aaacccgaat ttccactgcc ggcgtttccg aatcccgagt tttcgcccag 120cccatcggta gtattgccga aaccggtgtt caggttgccc gcgttaaagc cgcccgtgtt 180gatattgcca gaatttgcga agccggtgtt cgtcaggcca gagttcaaga aaccagaatt 240agcgtctcct ccgttgaagc tgcctgagtt gaatgcaccc gagttgaagc taccggtgtt 300gatgatgccg ccgttgaagt tgccggtgtt gaaatcgccc gcgttcccta tgccggtatt 360ggcctgacct gagttgccaa agccagtgtt gacgcttaac gcgttcccga agccggtgtt 420gataaagccg gagtttccga agccggtgtt gatgttgcct gagttggcta cgcccgtgtt 480ggtgacgccc gagttgccca cgccgaagtt gccgctgccc gagttgaaga agccgatgtt 540cccggtgccc gagttaccaa atcctatatt accgctaccg gaattcagtc cgccaaagcc 600g 60184601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 84ttgtccgcag gagtgttgag tgaggcggcc agcgccgtgt agtagtcacg gtgacgtgcg 60tgcacatcgg cctcgccgga gtcgcccagt ttttccagcg cgtaccgacg caccgtttcc 120agcagccggt accgcgtgcg gccctggcag tcgtcggcca ccaccagcga cttgtctacc 180agcagggtca gctgatcaag caccgaaaac ggatccaggt cgctaccggc ggcgaccgcc 240cgcaccgcgg cgaggtcgaa cccgccgaca aatggcgcca gtcgccgaaa caagatttgc 300ccggtctcgg tcagcagtgc atgcgaccaa tcgatcgagg cgcgaagtgt ctgctggcgc 360tgcaccgcgc cccgcacacc gccggccaac agccggaaac agtcgtccag accgtcggca 420atctcgagcg gtgacatcga ccgcacccgt gcggcagcga actcgatcgc cagcggtatg 480ccgtctagcc gccggcagat ctcgccgacg gccgcggcgt tgtgattggc gatggtgaac 540ccgggctgaa ctcggctggc tcggtcagca aacaattcga ctgcttcgtc ggttatcgac 600a 60185601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 85tccaactcga agattgttgt cccgattggc cattgcaatc ggaatgcacg ggaatccaat 60cctgcagcca agatgaccac ctgcttcatg ccggcggccg ttgcccggga gaaatactcg 120tcgaaatacc tggtgcgggc accttggaag ttgacgaaat gctcaccgaa gtccccggtt 180gtcagatagt gatcgggcag cttgccgtcc aatacgtcgg cccattcacc acctgcggca 240cggcagaaaa cctcggcata gggatcgatg gccagcggat cggccttctg cgtctccaat 300actcttgcgg cggctaccaa tagtcctgtc gaaccaacac tcgtggtgac atcccagcta 360tcgtcctcgg tccgcattca tcgaactcta gttgctccag tccgcccacc gctgtcggta 420tcccagcgca gtcggccgtg cacacatatc tgcgcggtgg acttggtact tctacgcgca 480ttcgccgatg ttttgcgatc cgcggcgggt ctatggtgcc atttatgtgc caggatcggt 540cttcaataac aacgtcgcga agcgaggggt cgtgacgtga gagggctcgc ttatgccggc 600g 60186601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 86gagcgctacc ttggatgttg agggagttga actccggcgg aaaaattgtg aaatccattg 60tcgctcaacc gctgtctagg tggaggtgcc cgcgcggttg gctaattcgg tgagccaata 120cgaagtcttg ctggtctgaa gtgtttggac aaatgactcg tggatcacat gggcctggcg

180cgcgatcgcc ttgtacagct cgccgtgcat ggaaaacagc atcgacgtca cgatggacac 240aagatcgtgg gcgggggatt ccacattggt gatcagcggc gtgaccccgt catcatgggc 300actcatcgtc accccgatct cgtggaggtt ggcggccgtt tccccaatcg aatcgggccg 360tgtggtgaca aaagacacgc gtgcatctcc ttccactgac gtggtctgat ggtgggggtc 420agcgacgact tggggttccg cacggcattg tagacggaat cgttcactaa ggtattttca 480ccataacggc ttcggtcaca aaacggtagc gattctgttg aggaattttt tcgacgctcg 540cccggtaggg tgcctccatg tctgagacgc cgcggctgct gtttgttcat gcacaccccg 600a 60187601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 87tctgtgggtg gtcccggatg tcgcggcccg cggagccgat cttgcccatg tcccagtggt 60gacgctggtc ggaagcgccc ggcactattg gggcgcggtg gcggcggtgt tggcggcagt 120gtgtgctttg ctcgctgccg tcttcttgat gagttcggcg gcgattcgcg ggtcggctgg 180cgaggacatg gcgagatatg cggcgccccg cgcccgccgg tcgattgccc ggcgccagca 240ctcgaatgcg gccggccggg cggctccgca agacgacggg ccggatatgg ggccgcggat 300atcggagcga atgatttggg aagctcttga cgagggccgt gacccgaccg atcgggagca 360ggagtctgac accgaggggc ggtgacggac cgcgcgctga cggtcgctac ccttcatgga 420cgtcgtcgaa attgacgagc gcgtgtgggt gacagtggga agggaacggc aggcatgagt 480ccggcaaccg tgctcgactc catcctcgag ggagtccggg ccgacgttgc cgcgcgtgaa 540gcctcggtga gcctgtcgga gatcaaggct gccgccgctg cggcgccgcc gccgctcgac 600g 60188601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 88aacccacggt gttgtaaaac agctgtgata tcggcagata ccagttgatg aaccattcca 60gccaccccgg ggtcgcggcg gcggtcaacg cggacgacag gggcgaggtg aggcccagca 120gcgtgttggg caagtgggcg atcagctccg ctattgcgct ctgcgccgcg ccggctgagg 180tgccggcggc tttggcgact gcggacaact gcgtcgccgc ggcggatggg ctggtggtgt 240tcggcggcgg ggcaaacggc gtcactttgg tcgcggtcgc cgaggagccc gcgtaaccgt 300gcatggccat ggcgtcttgg gcccacattt cagcgtattg agcttcggtg gccgcgattg 360atgcggtgtt ttgaccgaac acgttatgcg tgaccagcga cgtgagccgc gcgcgattgg 420ccgcgatcag cggcgggggc acaatggcgg caaacgcggt ttcgtaagcg gccgccgccg 480cacgcgcctg actggctgcc tgctcagctt ggatggcggt ggctcgcatc cacgccacat 540acggggcgac cgcttcgacc atcaacgtcg acgccggacc cagccattct tcggtttgca 600g 60189601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 89ccggccacct gtggcaccag cgtctatgtc tacccattcg accttgccga cgaggtcttt 60acctgggccc gcgcggtcag cgccgaagtc gaccctcggg tcgagctgca agcccttgcc 120tcccgcggtg aaccgagcat gggcatcgac gtccccgtca tctcccttgc ctcgcccgct 180ttcgctgact cgcccgaaga ggccgaacag gccctcgccc tgttcggcac ctgcccggtt 240gtcgagcagg cactggtcaa agtcccttat atgccaaccg atttgcctgc ctggtatgac 300atcgcgatga cccactacct gtcagaccat cactacgcgg tggacaatat gtggacgtcg 360gcgtccgctg aggacctgct gccgggtatc cgctcaatcc tggacacgct gcccccgcat 420ccggcgcact tcctctggct gaactggggt ccatgccctc cccgtcaaga catggcctat 480agcatcgaag ccgacatcta cttggcgctc tacggctcct ggaaggatcc ggccgacgag 540gcgaagtacg ccgactgggc gcggtcccac atggccgcga tgtcgcatct ggcggtcggc 600a 60190601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 90tgttaccgac gccggagtga aaggccgatg tcgctaggcc cagcgtgctg gtgttgtaga 60ggcctgagac tgtgttgccg aagttcaaga ttcccgatgt cagtggcccg acgttaagga 120atccggagtt gccgagattc ccagcaatgt tccagaagcc agatccgccc gaaccgacgt 180tcccgaaacc cgatgtgccg cccgtaccgc tgttgaagaa gcccgatgac ggggtggtgg 240tcgagtttcc gaagcctggg gtgcccgcga tttcgatcgg gatgttgatc ggcccgaggc 300ggccggacac gtcgatgccc aacgggattg aggggatcgt gattggcggg gtagtgaggg 360ggccgatggc gccgcccaca tcaataccca acgggattgc cggaagtgag tagccatccg 420ggaacaccgt aaacgggcct aaccctccgc ccacatcaat acccaacggg attgccggaa 480gtgagtagcc atccgggaac accgtaaacg ggcctaaccc tccgcccaca tcaataccca 540acgggattgc cggaagtgag tagccatccg ggaacaccgt aaacgggcct aaccctccac 600c 60191601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 91gctgccggac acgtcgatgc ccaacgggat tgaggggatc gtgattggcg gggtagtgag 60ggggccgatg gcgccgccca catcaatacc caacgggatt gccggaagtg agtagccatc 120cgggaacacc gtaaacgggc ctaaccctcc gcccacatca atacccaacg ggattgccgg 180aagtgagtag ccatccggga acaccgtaaa cgggcctaac cctccgccca catcaatacc 240caacgggatt gccggaagtg agtagccatc cgggaacacc gtaaacgggc ctaaccctcc 300gcccacatca atacccaacg gaatagccgg caaactataa ccacccgata agaaggtgat 360gggaccgatt tgaccactca ctgtcacgta atctggaggg aatccgggga aaaatggcgg 420aatcgcggga atctcaggag tgcctagctg tatcgatatg ctacccgggc ctatgctgcc 480aacggtggga tttacgccga ataagccgat cgcaagcgga gacgcgggga tcgaaatcga 540tcccacgtta atgacctgga acgccgatag ctctaggcca atagaattta gagtgatcgg 600c 60192601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 92ccatgcggtg ccgcggtggt ccagccagcg ccctgcagtg tgctggtgct cgataccagg 60ttggcctgtc ccgcccagct gggcggcacc gacaatgcgc cgattgacga cgcccgacta 120aggccggcgg ctagcggagc cgcacccaga ccggccgcga tcggcgcctc gccgacggcc 180gcctccgccg cccccagctc cgataggccc gcgccctcca agccctcctc gagggcggct 240tcctcggcag ccggaagaag accaccgctg gccagcccta gcaagtccga cgcggcggag 300acccagttcc cagccccaat gttgaagata ttggcaatat ctgaaatcca ggagggcacc 360ttcccgggcg tggaacccaa gatgctcgcg atacccgaca acggcgaagc ggccgcggat 420gagttggcgg cctcggtggc cgcataggtg ccagcgctga cccccagggt cttcacaaac 480aggtcgtata ccgcagctgc ttcagcactg acctgctggt agagagtgcc gtacgcggtg 540aacaacggcg cctgtagcac tgatatctca tcagcggcgg cgggaatcac gcccgtggtg 600g 60193601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 93acgtcgagcc aaccccactt cagtgggtag gtgaactcgt ccagcagata gaagtcgtga 60cgttgcgtgg ccagccggag cgcgatctcg gcccaaccgt ccgccgccgc ggccgcacga 120tcgacgtcgg tgccggcctt gcgagacgta cgtgtccagg accagcccgc acccatcttg 180tgccactcca ccgctccgcc gatcccgtgc tggtcgtgca gccggcccag ttgacgaaac 240gccgcctcct cacccacttt ccacttagcg ctcttgacaa actgaaacac cgcgatgtcc 300cgaccagcgt tccacgcccg caacgccatt ccgaacgccg cggtcgattt tcctttgcct 360tcaccggtgt gtaccgccag tatcggcatg ttgcgccggg cccgggtggt caggccatcg 420ttgggcactg cgagcggatt gccctgcggc atgtgtggtt acctatccat cgtcaagcca 480cgccacgcac ggcatgcact agataatccg cgtgcaactg ctccaaccga accaccggcg 540cacccagctg acgagccagt tgcgctgcca aacccagccg tacatacgac gtttcgcagt 600c 60194601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 94ctgcgagtgg gccgaccgat aggcccgatg ctggcacaga ccgcgaccag cgtccatgat 60gcactcgaac gtcacggcgg cacaaccatt ttcgaggcta aactagacgg cgcgcgagtg 120cagatccacc gggcaaacga ccaggtcagg atctacaccc gaagcctgga cgacgtcact 180gcccggctgc ccgaggtggt ggaggcaaca ctggcactgc cggtccggga tctagtggcc 240gacggcgagg cgatcgcgct gtgcccggac aaccggccgc agcgtttcca ggtcaccgca 300ccacggttcg gccgatcggt cgatgttgcg gctgcccgcg cgacgcagcc actttcggtg 360ttcttcttcg acatcctgca tcgggatggt accgacttgc tcgaagcgcc gaccaccgag 420cggctggccg ccctggacgc actggtgccg gctcggcacc gcgtggaccg gctgatcacg 480tccgatccaa cggacgcggc caacttcctg gatgcgacgc tggccgccgg ccacgagggg 540gtgatggcca aggcaccggc cgctcgttac cttgcgggtc gccgcggagc gggctggctg 600a 60195601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 95acggtgaggc cggccgggaa caaggccaag gacgatgtgg acagattgaa agtcgcgccg 60aacgggccgg ggatcgtgcc cgggccgccg tagctgccga tgatgggtcc attgatctgc 120aggtcgctga tgctgaggta gaacgacccg gaggggaatt tcgcgccggg tgggcctagc 180ggcgggccgt agtggtcgat cgtgatgaac gggtccggca agacgaccgg gtccgcggtg 240atttctgcca tggcggtttg cccgaaaaga acaaacgcgg gattcacgtg aaaaccctcg 300tggccgacgg ttccggtcac gtggatcggg atcgcgggaa tggtgatctc cgggagagtg 360aattcgcgga tcccgatgaa tcccccggtg atttgtatgt cgaatgccgg aatatcgatg 420ggctggacgt ggatgggacc gatcccgcca atcacctgca ggtcaatggg gatttcggaa 480atggtgaaaa gggtgccggg ggtgaagggg gccaggacgt tgatgttgtt gcccgttaag 540aagaaaccgg tgttgtggct tcccgaattg aatacgccca aattcccggt gccggagttg 600a 60196601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 96acaagcgcgg tagcccgctc gacatcgctt gctgtcattg cggcaggtgc ttgatagagg 60gccgccaatt cggtcgccgc ttcggatcgc gagttcaggg cggcaacaac tggcagtgtc 120gccttacgtc gggcaaggtc gttgccgacc ggctttcccg tcacaccagg gtcaccccag 180atgccgatca gatcgtcgac gcattgaaac gcaagaccca actcatggcc aaaacgctcc 240aacgcagcaa tcgtcgcgtc gtctgcattg gccactaaag ctcccagagc gcaacaacaa 300tcggtcaggg cggccgtctt gcccgcggcc atccgcagat agtcatcgac tgtaacttcg 360ggctgtccct ccaataaaca atcctcaaac tggccgatac acaagtccag gcacgacatc 420tgcaatcgcc ttatcgccct gaccgccaca cactcgtcgg tcaggccggt cagtatccga 480acggccgtgg cgtgcaacgc atctcccaac aggatcgcga cgcccacacc ccacacactc 540cataccgtcg gccgtcccct gcgagtcgca tccccatcca tcacatcgtc atgcaacaac 600g 60197601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 97gtcagccagt cgttgcgaac atcgtcgtcc acgtagggct gtatctgttg gcgaaccact 60tcgacggccg tcggccgatc tgccccctcc gtcgtgagcg cttcggccgc agccaaccat 120gccggccgct gcgccagggc acgctcgtcg atcgcaatgg ccgtcgcgac tttggagtcc 180accagctgcc agaggttgtc gcgcagcgat tcgcagcgtt gggccgcggc acggacttcg 240gtgaccaccg aatttccagt ctcacagtga cgctgcacaa agtgcaccgc cgcgtcggcc 300tccgatcccg tccatgccgc tgccaagacg gcgacctggc tacgctccat ccgcagcgcc 360tccatgagca cactggcggc agcccgcagc tgcgcgcagt cagcgtcgag cgcgtgcagg 420tcaagtccgt cttcgctgcc gtaccagtcg tggatctggg cagggtaggc ggtcaggtcg 480ggatgttggt agcccaccag gtggcaagcc cgcacgtagc tttgcgtgtg ctcggctgcg 540ggcctgccct cggcgagacg ctcagcgacg ttcaaccggt cagccaccct cacccgatcc 600g 60198601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 98cgccagcacc gcggggctcg ccgccggggt cgtggcggtc caaacggccg gaaccttcaa 60tcccccgacc gacgccgcct gaccgacggc gcccgcaacg ccgctcaggc cagcactcgg 120aatggccgga acggcggccg gcaacgcctt ggcggcctca ccggcggctt tggcgccttc 180actcgcccac ttcggcaggt cgtgcgccag gccaaagtag tccttgaatt gggtgaccat 240gagccgagcg ggcgagaccc atttgccgaa cgtgtccatg gccacgctgg catcaagttc 300tgccgacccg gtcacaccct gcacaaagtc gccaagcact ccgcccacga tgagcccgct 360accgtccgag gaccaggtgt gcccggtcaa accgagcgcc ttgccaaggt cggtgagcca 420aggcggttca ttggtgaaga ttccgctaag cccaaacaac gctttaggaa tgtcggtgag 480tgcttgcgca tttgcggccc cgctgacagc ttgtccgaca gatgcggcct ggctggccag 540cccggccggg ttgatggtct gcgccgccgg attgaatggc gacaactgcg tcgccgccgc 600c 60199601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 99tgcgcgatgc cgacgatgcc gcgctgcttg ccgcaatcga ggactgcgcg cgtgccgagg 60tggccgccgg cgcccgccgc ctgtcagcga tcgccgaact caccagccgg cgcaccggca 120atgaccagcg ggccgactgg gcgtgcgacg gctgggactg cgcggccgcc gaggtggccg 180ccgcactgac cgtaagccac cgtaaggcct ccgggcagat gcatctgagc ctcaccctaa 240accgactgcc ccaggtggcg gcgttgtttt tggccgggca gctcagcgcg cggctggtgt 300tgatcatcgc ctggcgcacc tacctggttc gcgaccccga agcgctgagt ctgctcgatg 360ccgccctcgc caaacacgcc acagcgtggg gtccgctgtc ggcccccaaa ctggaaaagg 420ctatcgactc ctggattgat cggtacgatc ccgccgcact gcgacgcacc cgtatctcgg 480cccgcagccg cgacctgtgc atcggtgatc ccgacgaaga tgccggcacc gccgcactat 540ggggccggtt gtttgccacc gacgccgcca tgctggataa gcgcctcacc cagctggccc 600a 601100601DNAMycobacterium tuberculosisvariation(301)..(301)Single-nucleotide polymorphism marker 100atccgctggc tggtggatca ggccccagcg cgggcgcggg cctgctgcgc gcggagtcgc 60tacctggcgc aggtgggtcg ttgacccgca cgccgctgat gtctcagctg atcgaaaagc 120cggttgcccc ctcggtgatg ccggcggctg ctgccggatc gtcggcgacg ggtggcgccg 180ctccggtggg tgcgggagcg atgggccagg gtgcgcaatc cggcggctcc accaggccgg 240gtctggtcgc gccggcaccg ctcgcgcagg agcgtgaaga agacgacgag gacgactggg 300ccgaagagga cgactggtga gctcccgtaa tgacaacaga cttcccggcc acccgggccg 360gaagacttgc caacattttg gcgaggaagg taaagagaga aagtagtcca gcatggcaga 420gatgaagacc gatgccgcta ccctcgcgca ggaggcaggt aatttcgagc ggatctccgg 480cgacctgaaa acccagatcg accaggtgga gtcgacggca ggttcgttgc agggccagtg 540gcgcggcgcg gcggggacgg ccgcccaggc cgcggtggtg cgcttccaag aagcagccaa 600t 601

Claims

1. A primer set for genotyping Mycobacterium tuberculosis selected from one of the group consisting of: TABLE-US-00011 Primer set 1: (SEQ ID No. 1) ACGTTGGATGTTCTGGACGACCTGTCCTAC and (SEQ ID No. 2) ACGTTGGATGAGCTGCGCCAAGGTTCGTG, Primer set 2: (SEQ ID No. 3) ACGTTGGATGTTGTAGCTGCCCAAATTGCC and (SEQ ID No. 4) ACGTTGGATGGGCTTCAATCTCGGCTTGG, Primer set 3: (SEQ ID No. 5) ACGTTGGATGTATTCAACACCGGCATCGGG and (SEQ ID No. 6) ACGTTGGATGTCGCCTGGTCGTGGAAGAAC, Primer set 4: (SEQ ID No. 7) ACGTTGGATGATCGGACAGCAGAAGGCAC and (SEQ ID No. 8) ACGTTGGATGACTCCCGCGGAACGTGGTG, Primer set 5: (SEQ ID No. 9) ACGTTGGATGCAACACCGGCAACTTCAAC and (SEQ ID No. 10) ACGTTGGATGAATTAGCGTCTCCTCCGTTG, Primer set 6: (SEQ ID No. 11) ACGTTGGATGTCGAACCCGCCGACAAATG and (SEQ ID No. 12) ACGTTGGATGTCGATTGGTCGCATGCACTG, Primer set 7: (SEQ ID No. 13) ACGTTGGATGAAACCTCGGCATAGGGATCG (SEQ ID No. 14) ACGTTGGATGTCGACAGGACTATTGGTAGC, and Primer set 8: (SEQ ID No. 15) ACGTTGGATGAAGACGACGGGCCGGATATG and (SEQ ID No. 16) ACGTTGGATGCGTCAAGAGCTTCCCAAATC, Primer set 9: (SEQ ID No. 17) ACGTTGGATGCATCCGGGAACACCGTAAAC and (SEQ ID No. 18) ACGTTGGATGATCACCTTCTTATCGGGTGG, Primer set 10: (SEQ ID No. 19) ACGTTGGATGCCTGGATTTCAGATATTGCC and (SEQ ID No. 20) ACGTTGGATGTGGCCAGCCCTAGCAAGTC, Primer set 11: (SEQ ID No. 21) ACGTTGGATGAGAACAAACGCGGGATTCAC and (SEQ ID No. 22) ACGTTGGATGTCTCCCGGAGATCACCATTC, Primer set 12: (SEQ ID No. 23) ACGTTGGATGGTTGTTTTTGGCCGGGCAG and (SEQ ID No. 24) ACGTTGGATGATCGAGCAGACTCAGCGCTT, Primer set 13: (SEQ ID No. 25) ACGTTGGATGTGCTACCGCCAATGTTCAAC and (SEQ ID No. 26) ACGTTGGATGATGGCGTTGACATAACTCGG, Primer set 14: (SEQ ID No. 27) ACGTTGGATGATAGCAAGCACGATTGCGAC and (SEQ ID No. 28) ACGTTGGATGACCCCCCGCTGAGGGCGTA, Primer set 15: (SEQ ID No. 29) ACGTTGGATGGATTCGATTGGGGAAACGGC and (SEQ ID No. 30) ACGTTGGATGTTCCACATTGGTGATCAGCG, Primer set 16: (SEQ ID No. 31) ACGTTGGATGCAAACGGCGTCACTTTGGTC and (SEQ ID No. 32) ACGTTGGATGTGAAATGTGGGCCCAAGACG, Primer set 17: (SEQ ID No. 33) ACGTTGGATGCGATTTCGATCGGGATGTTG and (SEQ ID No. 34) ACGTTGGATGCAATCACGATCCCCTCAATC, Primer set 18: (SEQ ID No. 35) ACGTTGGATGAGGCAAAGGAAAATCGACCG and (SEQ ID No. 36) ACGTTGGATGTTGACAAACTGAAACACCGC, Primer set 19: (SEQ ID No. 37) ACGTTGGATGACAACCGGCCGCAGCGTTT and (SEQ ID No. 38) ACGTTGGATGAAGAACACCGAAAGTGGCTG, Primer set 20: (SEQ ID No. 39) ACGTTGGATGTGCATTGGCCACTAAAGCTC and (SEQ ID No. 40) ACGTTGGATGTCGATGACTATCTGCGGATG, Primer set 21: (SEQ ID No. 41) ACGTTGGATGACCCATTTGCCGAACGTGTC and (SEQ ID No. 42) ACGTTGGATGTGCTTGGCGACTTTGTGCAG, Primer set 22: (SEQ ID No. 43) ACGTTGGATGAGCGTGAAGAAGACGACGA and (SEQ ID No. 44) ACGTTGGATGGTCTGTTGTCATTACGGGAG, Primer set 23: (SEQ ID No. 45) ACGTTGGATGACATCAGGTGATGGTCATGC and (SEQ ID No. 46) ACGTTGGATGCGAAGGGAACAATGGATGTG, Primer set 24: (SEQ ID No. 47) ACGTTGGATGTATGCCAACCGATTTGCCTG and (SEQ ID No. 48) ACGTTGGATGACATATTGTCCACCGCGTAG, and Primer set 25: (SEQ ID No. 49) ACGTTGGATGTCTTGGCAGCGGCATGGAC and (SEQ ID No. 50) ACGTTGGATGCCGAATTTCCAGTCTCACAG.

2. The primer set of claim 1, which is applied in polymerase chain reaction to amplify a DNA fragment containing a single-nucleotide polymorphism (SNP) of M. tuberculosis.

3. An extension primer for genotyping Mycobacterium tuberculosis selected from one of the group consisting of: TABLE-US-00012 (SEQ ID No. 51) GACCTGTCCTACGAACCGGTGATGG, (SEQ ID No. 52) CGTTGCCCACGTTGTTGGCG, (SEQ ID No. 53) CACCGGCCAACGTCTCGGGCATG, (SEQ ID No. 54) CCCCCGACCGGCCGTTCTTCG, (SEQ ID No. 55) TTCAACGGCGGCATCAT, (SEQ ID No. 56) GCCGAAACAAGATTTGC, (SEQ ID No. 57) CCTTCTGCGTCTCCAAT, (SEQ ID No. 58) GATATGGGGCCGCGGAT, (SEQ ID No. 59) ACCGTAAACGGGCCTAACCCTCC, (SEQ ID No. 60) TTGGGGCTGGGAACTGGG, (SEQ ID No. 61) ATTCACGTGAAAACCCTCG,, (SEQ ID No. 62) AGCTCAGCGCGCGGCTGGTGT, (SEQ ID No. 63) CAAAATACGGCGATCATCATGGG, (SEQ ID No. 64) CCACCAGTACTTGCCGC, (SEQ ID No. 65) ATCGGGGTGACGATGAG, (SEQ ID No. 66) GCCGAGGAGCCCGCGTAACCGT, (SEQ ID No. 67) TGTTGATCGGCCCGAGGC, (SEQ ID No. 68) GCGGGCGTGGAACGCTGGTC, (SEQ ID No. 69) AGCGTTTCCAGGTCACCGCA, (SEQ ID No. 70) CCAGAGCGCAACAACAA, (SEQ ID No. 71) CACGCTGGCATCAAGTTC,, (SEQ ID No. 72) GAAGACGACGAGGACGACTGGG, (SEQ ID No. 73) GACGATTCCGGGCATGCG, (SEQ ID No. 74) TGCCTGCCTGGTATGAC, and (SEQ ID No. 75) GGCATGGACGGGATCGG.

4. The extension primer of claim 3, which is applied in polymerase chain reaction to amplify a DNA fragment having a single-nucleotide polymorphism (SNP) of M. tuberculosis as a terminal nucleotide of the DNA fragment.

5. A combination of single-nucleotide polymorphism markers of M. tuberculosis is selected from the group consisting of "T" at position 301 of SEQ ID No.76, "A" at position 301 of SEQ ID No. 77, "A" at position 301 of SEQ ID No. 78, "G" at position 301 of SEQ ID No. 79, "G" at position 301 of SEQ ID No. 80, "G" at position 301 of SEQ ID No. 81, "C" at position 301 of SEQ ID No. 82, "G" at position 301 of SEQ ID No. 83, "C" at position 301 of SEQ ID No. 84, "A" at position 301 of SEQ ID No. 85, "A" at position 301 of SEQ ID No. 86, "A" at position 301 of SEQ ID No. 87, "G" at position 301 of SEQ ID No. 88, "A" at position 301 of SEQ ID No. 89, "G" at position 301 of SEQ ID No. 90, "G" at position 301 of SEQ ID No. 91, "A" at position 301 of SEQ ID No. 92, "C" at position 301 of SEQ ID No. 93, "C" at position 301 of SEQ ID No. 94, "T" at position 301 of SEQ ID No. 95, "T" at position 301 of SEQ ID No. 96, "T" at position 301 of SEQ ID No. 97, "T" at position 301 of SEQ ID No. 98, "T" at position 301 of SEQ ID No. 99, and "C" at position 301 of SEQ ID No.100.

6. A method for genotyping Mycobacterium tuberculosis comprising obtaining a sample, amplifying and obtain at least one of first DNA fragment by using one or more primer sets selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), amplifying and obtain at least one of second DNA fragment by using the obtained first DNA fragment as template and using one or more extension primers selected from the group consisting of SEQ ID Nos. 51 to 75, and detecting the second DNA fragment by using mass spectrometry.

7. The method of claim 6, which further comprising analyzing the mass spectrometry data based on the single-nucleotide polymorphism markers selected from the group consisting of combination of single-nucleotide polymorphism markers of M. tuberculosis is selected from the group consisting of "T" at position 301 of SEQ ID No.76, "A" at position 301 of SEQ ID No. 77, "A" at position 301 of SEQ ID No. 78, "G" at position 301 of SEQ ID No. 79, "G" at position 301 of SEQ ID No. 80, "G" at position 301 of SEQ ID No. 81, "C" at position 301 of SEQ ID No. 82, "G" at position 301 of SEQ ID No. 83, "C" at position 301 of SEQ ID No. 84, "A" at position 301 of SEQ ID No. 85, "A" at position 301 of SEQ ID No. 86, "A" at position 301 of SEQ ID No. 87, "G" at position 301 of SEQ ID No. 88, "A" at position 301 of SEQ ID No. 89, "G" at position 301 of SEQ ID No. 90, "G" at position 301 of SEQ ID No. 91, "A" at position 301 of SEQ ID No. 92, "C" at position 301 of SEQ ID No. 93, "C" at position 301 of SEQ ID No. 94, "T" at position 301 of SEQ ID No. 95, "T" at position 301 of SEQ ID No. 96, "T" at position 301 of SEQ ID No. 97, "T" at position 301 of SEQ ID No. 98, "T" at position 301 of SEQ ID No. 99, and "C" at position 301 of SEQ ID No.100.

8. The method of claim 6, wherein the mass spectrometry is matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

9. The method of claim 6, wherein the sample is bacterial culture, nasal mucus, phlegm saliva, blood, section of tissues or organ, and/or biopsy.

10. A kit for genotyping Mycobacterium tuberculosis comprising: at least one primer set selected from the group consisting of primer sets 1 to 25 (SEQ ID Nos. 1 to 50), and at least one extension primer selected from the group consisting of SEQ ID Nos. 51 to 75.

11. The kit of claim 10, which further comprises a database of genotypes of M. tuberculosis based on single-nucleotide polymorphism markers.

12. The kit of claim 11, wherein the single-nucleotide polymorphism markers is selected from the group consisting of the combination of single-nucleotide polymorphism (SNP) markers of M. tuberculosis can be selected from the group consisting of "T" at position 301 of SEQ ID No.76, "A" at position 301 of SEQ ID No. 77, "A" at position 301 of SEQ ID No. 78, "G" at position 301 of SEQ ID No. 79, "G" at position 301 of SEQ ID No. 80, "G" at position 301 of SEQ ID No. 81, "C" at position 301 of SEQ ID No. 82, "G" at position 301 of SEQ ID No. 83, "C" at position 301 of SEQ ID No. 84, "A" at position 301 of SEQ ID No. 85, "A" at position 301 of SEQ ID No. 86, "A" at position 301 of SEQ ID No. 87, "G" at position 301 of SEQ ID No. 88, "A" at position 301 of SEQ ID No. 89, "G" at position 301 of SEQ ID No. 90, "G" at position 301 of SEQ ID No. 91, "A" at position 301 of SEQ ID No. 92, "C" at position 301 of SEQ ID No. 93, "C" at position 301 of SEQ ID No. 94, "T" at position 301 of SEQ ID No. 95, "T" at position 301 of SEQ ID No. 96, "T" at position 301 of SEQ ID No. 97, "T" at position 301 of SEQ ID No. 98, "T" at position 301 of SEQ ID No. 99, and "C" at position 301 of SEQ ID No.100.