PRIMERS, SNP MARKERS AND METHOD FOR GENOTYPING MYCOBACTERIUM TUBERCULOSIS

BACKGROUND OF THE INVENTION

1. Field of the Invention

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

2. Description of the Related Art

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.

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.

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.

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

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

The present application 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 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.

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.

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

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

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.

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).

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.

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.

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.

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).

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).

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%.

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.

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

DETAILED DESCRIPTION OF THE EMBODIMENTS

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:

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.

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.

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:

(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.

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.

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.

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.

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.

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”.

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 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

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.

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

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

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.

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

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.

Materials and Methods

Bacterial Strains and Molecular Typing

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.

Genome Sequencing of MTB Strains

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.

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%.

Mapping to the Reference Genome H37Rv

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 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

Selection of Strain-Specific SNPs

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.

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.

SNP Genotyping Based on the MassArray System

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.

Linkage Disequilibrium and Phylogenetic Analysis

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.

Results

Genome Sequencing of Six MTB Clinical Isolates

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.

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 3

Genome sequencing and mapping results of the six MTB strains

embedded image

^$depth = totalBases/length of H37Rv genome

*largeContig: contig length >= 1000 bp

avgContigSize & N50ContigSize are calculated from largeContigs

Mapped by 454 gsMapper Release: 2.3

Genetic Variations of the MTB Clinical Isolates

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).

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 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

SNP Genotyping on 156 M. tuberculosis Clinical Isolates

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 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 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

Phylogenetic and Grouping Analysis of MTB Isolates

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.

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.

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 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

Genotyping of MTB by Using 25 tagSNPs

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

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.

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.

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.

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.

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.

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.

PRIMERS, SNP MARKERS AND METHOD FOR GENOTYPING MYCOBACTERIUM TUBERCULOSIS

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