Table 2.
Oligonucleotide primers used in PCR and direct sequencing
| Target gene | Primer ID | Nucleotide sequence (5'-3') | Size (bp) | Ref. no. |
|---|---|---|---|---|
| MTC identification |
|
|
|
|
| 16S rRNA |
285 |
GAGAGTTTGATCCTGGCTCAG |
1028 |
7 |
| |
264 |
TGCACACAGGCCACAAGGGA |
|
|
| |
259 |
TTTCACGAACAACG GACAA |
591 |
|
| cfp32 |
Rv0577F |
ATGCCCAAGAGAAGCGAATACAGGCAA |
786 |
14 |
| |
Rv0577R |
CTATTGCTGCGGTGCGGGCTTCAA |
|
|
| RD9 |
Rv2073cF |
TCGCCGCTGCCAGATGAGTC |
600 |
14 |
| |
Rv2073cR |
TTTGGGAGCCGCCGGTGGTGATGA |
|
|
| RD12 |
Rv3120F |
GTCGGCGATAGACCATGAGTCCGTCTCCAT |
404 |
14 |
| |
Rv3120R |
GCGAAAAGTGGGCGGATGCCAG |
|
|
| RD1 |
ET1 |
AAGCGGTTGCCGCCGACCGACC |
|
15 |
| |
ET2 |
CTGGCTATATTCCTGGGCCCGG |
|
|
| |
ET3 |
GAGGCGATCTGGCGGTTTGGGG |
|
|
| RD4 |
Rv1510F |
GTGCGCTCCACCCAAATAGTTGC |
1033 |
15 |
| |
Rv1510R |
TGTCGACCTGGGGCACAAATCAGTC |
|
|
| RD7 |
Rv1970F |
GCGCAGCTGCCGGATGTCAAC |
1116 |
15 |
| |
Rv1970R |
CGCCGGCAGCCTCACGAAATG |
|
|
| MiD3 |
IS1561F |
GCTGGGTGGGCCCTGGAATACGTGAACTCT |
530 |
15 |
| |
IS1561R |
AACTGCTCACCCTGGCCACCACCATGGACT |
|
|
| Distinguish sub-strains of BCG |
|
|
|
|
| RD2 |
RD2l |
CCAGATTCAAATGTCCGACC |
|
16 |
| |
RD2r |
GTGTCATAGGTGATTGGCTT |
|
|
| RD14 |
RD14l |
CAGGGTTGAAGGAATGCGTGTC |
|
16 |
| |
RD14r |
CTGGTACACCTGGGGAATCTGG |
|
|
| RD15 |
RD8l |
ACTCCTAGCTTTGCTGTGCGCT |
|
16 |
| |
RD8r |
GTACTGCGGGATTTGCAGGTTC |
|
|
| RD16 |
RD16nf |
ACATTGGGAAATCGCTGCTGTTG |
|
17 |
| |
RD16nr |
GGCTGGTGTTTCGTCACTTC |
|
|
| SenX3-RegX3 |
C3 |
GCGCGAGAGCCCGAACTGC |
|
16 |
| |
C5 |
GCGCAGCAGAAACGTCAGC |
|
|
| Sequencing |
|
|
|
|
| mpt64 (Rv1980c) |
mpb64W-F |
ACTCAGATATCGCGGCAATC |
1061 |
this study |
| |
mpb64W-R |
CGATCACCTCACCTGGAGTT |
|
|
| Rv1977 |
Rv1977F |
GTTTCCCGAGATCAGCTCAA |
348 |
this study |
| |
Rv1977R |
ATCTCGTCGTGTGTCACCAG |
|
|
| Rv1981c |
Rv1981F |
GATCGAATGCAGGCTGGTAT |
399 |
this study |
| Rv1981R | ACTACTACCGCGGTGACGAC | |||