TABLE 2.
Oligonucleotide probes and primers used in this study and the probe threshold and detection limits of the biochip assay for the 17 mycobacteria
| Oligonucleotide probe and primer | Sequence (5′-3′)a | Detection limit (CFU/PCR) in: |
|
|---|---|---|---|
| Saline solution | Sputum | ||
| QC | NH2-(T)25-GCAAGACAAGTGGAAGTGTG-HEX | ||
| EC | NH2-(T)25-GCAACCACCACCGGAGG | ||
| NC | NH2-(T)25-CCTCTCTCGGACTAATCGCC | ||
| BC | DMSO | ||
| Mycobacterium spp. | NH2-(T)25-GCGGGCTCATCCCACAC | ||
| M. tuberculosis | NH2-(T)25-ACAAGACATGCATCCCGT | 100 | 100 |
| M. intracellulare | NH2-(T)25-TAAAGACATGCGCCTAAA | 100 | 100 |
| M. avium | NH2-(T)25-GACATGCGTCTTGAGGTC | 200 | 200 |
| M. gordonae | NH2-(T)25-CTTGTGTCCTGTGGTCCT | 50 | 100 |
| M. kansasii | NH2-(T)25-TTATGCCGGTGTGCAG | 50 | 100 |
| M. fortuitum | NH2-(T)25-ATGAAGCGCGTGGTCATA | 50 | 100 |
| M. scrofulaceum | NH2-(T)25-CAACCCACAAAGTGAGCC | 200 | 200 |
| M. gilvum | NH2-(T)25-CACACACCATGAAGCATG | 1,000 | 1,000 |
| M. terrae | NH2-(T)25-CAGAACATGCATCCCA | 500 | 1,000 |
| M. chelonae-M. abscessus | NH2-(T)25-TGGACCACTCACCATGAAGTGTGTG | 1,000 | 1,000 |
| M. phlei | NH2-(T)25-TCCCAGCCATGCAACCAG | 1,000 | 1,000 |
| M. nonchromogenicum | NH2-(T)25-CACACCATGCAGCATG | 200 | 200 |
| M. marinum-M. ulcerans | NH2-(T)25-CAGAGGACATGAATCCCGT | 200 | 200 |
| M. aurum | NH2-(T)25-GACATGCATCGCGTAG | 50 | 50 |
| M. szulgai | NH2-(T)25-CATACGCCTCGGGGTCCT | 100 | 100 |
| M. xenopi | NH2-(T)25-CCTCCGGTGGTGGTTGC | 200 | 200 |
| M. smegmatis | NH2-(T)25-CGACCAGCAGGGTGTATT | 1,000 | 1,000 |
| 16S UT primer | TAMRA-TCACTTGCTTCCGTTGAGGTGGCTCAGGACGAACG (Tm, 66.2; 48.0°C; 0.4 μmol/liter) | ||
| 16S SS primer | AGCCGTGAGATTTCACGAACA (Tm, 50.9°C; 0.2 μmol/liter) | ||
a
HEX, hexachloro-6-carboxy-fluorescein; TAMRA, 6-carboxy-tetramethyl-rhodamine; (T)25, 25 consecutive thymines.