Table 2. Mean Ct values derived from real time RT-PCR analyses of nucleic acid extracts prepared by different extraction methods using the blood, stool and sputum test panels.
Shaded and non-shaded rows represent spiked (positive) and non-spiked (negative) samples, respectively; A–F represent coded identifiers of the six developers; the CDC used the Roche MagNaPure platform; PATH used the Qiagen extraction kits except for MTB; SP, sputum; BL, blood; ST, stool; ND no amplification detected; a 1–2 false negative RT-PCR replicate(s) detected within a confirmed positive member; b false positive RT-PCR replicate(s) detected within negative sample; Sens, mean sensitivity across all nine replicates; Spec, mean specificity across all nine replicates; CI, confidence interval. Dark shading indicates spiked samples; NC, not calculated.
| Developer | Developer | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | B | C | D | E | F | CDC | PATH | A | B | C | D | E | F | CDC | PATH | |
| Panel | Influenza A | M. tuberculosis | ||||||||||||||
| SP1 | ND | ND | 37.4 | ND | 32.6 a | ND | 32.2 | 33.9 | 15.2 | 28.5 | 17.6 | 33.6 a | 20.9 | 16.7 | 16.9 | 16.8 |
| SP2 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | 36.5 b | ND | ND | ND | ND |
| SP3 | ND | ND | ND | ND | 24.8 b | ND | ND | ND | 15.2 | 29.9 | 17.5 | 34.9 a | 21.9 | 16.7 | 16.6 | 17.1 |
| SP4 | 22.3 | ND | 21.8 | ND | 23.3 | 24.8 | 21.2 | 19.6 | 37.5 b | ND | ND | ND | ND | ND | ND | ND |
| SP5 | ND | ND | ND | ND | ND | ND | ND | ND | 34 | ND | 36.1 a | ND | 37.9 a | 35.3 a | 36.1 | 33.9 |
| SP7 | 22 | ND | 26.4 | ND | 23.5 | 25 | 21.2 | 19.6 | 34 | ND | 36.2 a | ND | 41.3 a | ND | 34.9 | 35.9 |
| SP8 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| SP9 | ND | ND | ND | ND | ND | ND | ND | ND | 22.9 | ND | 26.1 | ND | 32.1 | 25.0 | 25.9 | 26.4 |
| SP10 | 29.1 | ND | 28.8 | ND | 30.3 | 31.9 | 28.2 | 26.5 | ND | ND | ND | ND | ND | ND | ND | ND |
| Sens 95% CI |
0.75 0.58,0.88 |
0.00 0.00,0.10 |
1.00 0.90,1.00 |
0.00 0.00,0.10 |
0.86 0.71,0.95 |
0.75 0.58,0.88 |
NC | NC | 1.00 0.92,1.00 |
0.40 0.26,0.56 |
0.86 0.71,0.95 |
0.33 0.20,0.49 |
0.76 0.60,0.87 |
0.71 0.56,0.84 |
NC | NC |
| Spec 95% CI |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
0.93 0.82,0.99 |
1.00 0.92,1.00 |
NC | NC | 0.86 0.71,0.95 |
1.00 0.90,1.00 |
1.00 0.90,1.00 |
0.92 0.78,0.98 |
1.00 0.90,1.00 |
1.00 0.90,1.00 |
NC | NC |
| Rank | 3 | 5 | 1 | 6 | 2 | 3 | 1 | 5 | 1 | 6 | 3 | 4 | ||||
| Panel | MS2 bacteriophage | S. pneumoniae | ||||||||||||||
| BL1 | 31.0 | 32.4 a | ND | ND | 36.5 a | 32.8 | 33.4 | 32.3 | 20.6 | 27.6 | 25 | 30.5 | 23.9 | 21.9 | 19.2 | 20.9 |
| BL2 | ND | 34.9 b | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| BL3 | ND | 34.8 b | ND | ND | ND | ND | ND | ND | 20.8 | 27.8 | 24.7 | 29.7 | 24.2 | 22.5 | 19.1 | 20.8 |
| BL4 | 17.5 | 23.6 | 34 | ND | 23.2 | 18.8 | 19.4 | 19.7 | ND | ND | ND | ND | ND | ND | ND | ND |
| BL5 | ND | 36.4 b | ND | ND | ND | ND | ND | ND | 32.1 | ND | 37.1 a | 37.0 a | 35.8 | 37.0 a | 31.9 | 33.3 |
| BL6 | 31.1 | 35.6 | ND | ND | 36.5 a | 32.7 | 33.3 | 33.5 | ND | ND | ND | ND | ND | ND | ND | ND |
| BL7 | 17.0 | 23.8 | 33.9 a | 38.1 a | 22.5 | 19.4 | 19.6 | 20.7 | 34.5 | ND | 35.7 a | 37. a | 36.6 a | 37.0 | 32 | 33.0 |
| BL8 | ND | 36.1 b | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | 40.4 b | ND | ND |
| BL9 | ND | 36.2 b | ND | ND | ND | 37.6 b | ND | ND | 28 | 34.1 | 30.3 | 36.6 a | 29.9 | 30.8 | 26.1 | 28.0 |
| BL10 | 24.0 | 30.9 | ND | ND | 29.8 | 26.7 | 26.5 | 24.9 | ND | ND | ND | ND | ND | 39.3 b | ND | ND |
| Sens 95% CI |
1.00 0.92,1.00 |
0.93 0.82,0.99 |
0.36 0.22,0.51 |
0.07 0.01,0.18 |
0.87 0.73,0.95 |
1.00 0.92,1.00 |
NC | NC | 1.00 0.92,1.00 |
0.60 0.44,0.74 |
0.73 0.58,0.85 |
0.60 0.44,0.74 |
0.96 0.85,0.99 |
0.98 0.88,1.00 |
NC | NC |
| Spec 95% CI |
1.00 0.92,1.00 |
0.02 0.00,0.12 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
0.98 0.88,1.00 |
NC | NC | 1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.85,0.99 |
0.91 0.79,0.98 |
NC | NC |
| Rank | 1 | 6 | 4 | 5 | 3 | 2 | 1 | 5 | 4 | 5 | 2 | 3 | ||||
| Panel | MS2 bacteriophage | S. Typhimurium | ||||||||||||||
| ST1 | 38.1 a | ND | 38.6 a | ND | ND | 41.6 a | 36 | 34.4 | 24.5 | 28.7 | 35.3 | 32.1 a | 26 | 25.5 | 26.4 | 22.7 |
| ST2 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| ST3 | ND | ND | ND | ND | ND | ND | ND | ND | 21 | 29.6 | 30.1 | 29.3 a | 25 | 26.6 | 26.5 | 23.2 |
| ST4 | 21.1 | 23 | 24.3 | 27.5 | 23.9 | 22.1 | 22.6 | 16.3 | ND | ND | ND | ND | ND | ND | ND | ND |
| ST5 | ND | 38.0 a | ND | ND | ND | ND | ND | ND | 30.7 | ND | ND | 39.0 a | ND | ND | ND | 32.9 |
| ST6 | 36.8 a | ND | 37.8 | 37.9 a | ND | 42.4 a | 36 | 32.1 | ND | ND | ND | ND | ND | ND | ND | ND |
| ST7 | 20.9 | 23.8 | 23.9 | 27.9 | 25.5 | 21.8 | 22.8 | 15.9 | 30.4 | ND | ND | 37.3 a | ND | ND | ND | 33.0 |
| ST8 | ND | 31.2 b | 38.4 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| ST9 | ND | 35.5 b | ND | ND | ND | ND | ND | ND | 25.6 | 31.3 | ND | 32.4 | 29.0 | 30.9 | 31.6 | 27.9 |
| ST10 | 29.3 | 31.1 | 32.9 | 38.7 a | 35.1 | 30.8 | 32.9 | 24.2 | ND | ND | ND | ND | ND | ND | ND | ND |
| Sens 95% CI |
0.84 0.71,0.94 |
0.60 0.44,0.74 |
0.73 0.58,0.85 |
0.60 0.44,0.74 |
0.67 0.50,0.80 |
0.80 0.65,0.90 |
NC | NC | 1.00 0.92,1.00 |
0.60 0.44,0.74 |
0.40 0.26,0.56 |
0.64 0.49,0.78 |
0.57 0.41,0.72 |
0.60 0.44,0.70 |
NC | NC |
| Spec 95% CI |
1.00 0.92,1.00 |
0.53 0.38,0.68 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
NC | NC | 1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
1.00 0.92,1.00 |
NC | NC |
| Rank | 1 | 6 | 3 | 5 | 4 | 2 | 1 | 3 | 6 | 2 | 5 | 3 | ||||