TABLE 2.
Experiment B: variability of sensitivity depending on different extraction methods
| DNA extraction methoda | No. of PCR replicates/ exptb | Result for a mycobacterial concentrationc (CFU/ml) of:
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 300
|
30
|
3
|
1
|
||||||||||
| No. of pos replicates/ expt | Proportion of pos replicates/ expt | Sensitivity/ replicates (%) | No. of pos replicates/ expt | Proportion of pos replicates/ expt | Sensitivity/ replicate (%) | No. of pos replicates/ expt | Proportion of pos replicates/ expt | Sensitivity/ replicates expt | No. of pos replicates/ expt | Proportion of pos replicates/ expt | Sensitivity/ replicate (%) | ||
| Guanidine | 8 | 8 | 1.00 | 91 | 5 | 0.62 | 54 | 4 | 10.50 | 45 | 2 | 0.25 | 20 |
| 8 | 6 | 0.75 | 4 | 0.50 | 4 | 0.50 | 2 | 0.25 | |||||
| 8 | 8 | 1.00 | 4 | 0.50 | 3 | 0.37 | 1 | 0.12 | |||||
| NaOH (PCI-purified DNA) | 8 | 6 | 0.75 | 58 | 2 | 0.25 | 20 | 1 | 0.12 | 8 | 0 | 0.00 | 0 |
| 8 | 4 | 0.50 | 2 | 0.25 | 1 | 0.12 | 0 | 0.00 | |||||
| 8 | 4 | 0.50 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | |||||
| NaOH (not-purified DNA) | 8 | 2 | 0.25 | 20 | 2 | 0.25 | 12 | 1 | 0.12 | 4 | 0 | 0.00 | 0 |
| 8 | 2 | 0.25 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | |||||
| 8 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | |||||
| PK (PCI-purified DNA) | 8 | 2 | 0.25 | 16 | 0 | 0.00 | 0 | 0 | 0.00 | 0 | 0 | 0.00 | 0 |
| 8 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | |||||
| 8 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | |||||
| PK (not-purified DNA) | 8 | 2 | 0.25 | 12 | 0 | 0.00 | 0 | 0 | 0.00 | 0 | 0 | 0.00 | 0 |
| 8 | 1 | 0.12 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | |||||
| 8 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | |||||
a
DNA was extracted from SDS-lysate pellets by three methods; a DNA purification step was provided by kit instructions when the guanidine method was used.
b
Total of three experiments.
c
Pos, positive.