TABLE 3.
Performance characteristics of targeted and metagenomic NGS workflows
| Performance category | No. of samples categorized as: |
Accuracy (%) (95% confidence interval) | PPA (%) (95% confidence interval) | NPA (%) (95% confidence interval) | |||
|---|---|---|---|---|---|---|---|
| TP | FP | TN | FN | ||||
| Metagenomic NGS workflow | |||||||
| Overall | 69 | 29 | 98 | 53 | 67.1 (60.9–72.9) | 56.6 (47.3–65.5) | 77.2 (68.9–84.1) |
| Bacterial | 20 | 10 | 153 | 24 | 83.6 (77.8–88.3) | 45.5 (30.4–61.2) | 93.9 (89.0–97.0) |
| Mycobacterial | 3 | 1 | 188 | 5 | 97.0 (93.5–98.9) | 37.5 (8.5–75.5) | 99.5 (97.1–100.0) |
| Fungal | 0 | 8 | 185 | 12 | 90.2 (85.3–93.9) | 0.0 (0.0–26.5) | 95.9 (92.0–98.2) |
| Viral | 46 | 10 | 116 | 12 | 88.0 (82.5–92.4) | 79.3 (66.6–88.8) | 92.1 (85.9–96.1) |
| RPIP targeted NGS workflow | |||||||
| Overall | 56 | 17 | 102 | 66 | 65.6 (59.2–71.5) | 45.9 (36.8–55.2) | 85.7 (78.1–91.5) |
| Bacterial | 20 | 7 | 158 | 24 | 85.2 (79.6–89.7) | 45.5 (30.4–61.2) | 95.8 (91.5–98.3) |
| Mycobacterial | 1 | 0 | 189 | 7 | 96.4 (92.8–98.6) | 12.5 (0.3–52.7) | 100 (98.1–100.0) |
| Fungal | 0 | 3 | 187 | 12 | 92.6 (88.0–95.8) | 0.0 (0.0–26.5) | 98.4 (95.5–99.7) |
| Viral | 35 | 7 | 115 | 23 | 83.3 (77.1–88.5) | 60.3 (46.6–73.0) | 94.3 (88.5–97.7) |