| Thresholds |  | mNGS | Diagnosis | ||||
---|---|---|---|---|---|---|---|---|
 | SDSMRN | RAR | CF |  |  |  +  | − | |
Non-mycobacterium | Â | Â | Â | Â | Â | Â | ||
All |  |  |  | NPV = 76% |  +  | 26 | 26 | |
 |  |  |  | PPV = 50% | − | 44 | 143 | |
Sputum | 4000 | 65 | 3 | NPV = 66% |  +  | 18 | 14 | |
 |  |  |  | PPV = 56% | − | 26 | 50 | |
BALF | 4500 | 60 | 6 | NPV = 80% |  +  | 6 | 6 | |
 |  |  |  | PPV = 50% | − | 11 | 45 | |
Lung tissue | 6000 | 55 | 4 | NPV = 85% |  +  | 1 | 5 | |
 |  |  |  | PPV = 17% | − | 5 | 28 | |
Pleural fluid | 1000 | 35 | 8 | NPV = 91% |  +  | 1 | 1 | |
 |  |  |  | PPV = 50% | − | 2 | 20 | |
Mycobacterium | Â | Â | Â | Â | Â | Â | Â | |
All |  |  |  | NPV = 76% |  +  | 45 | 29 | |
 |  |  |  | PPV = 61% | − | 51 | 166 | |
Sputum | MRN = 3 |  |  | NPV = 69% |  +  | 14 | 11 | |
 |  |  |  | PPV = 56% | − | 28 | 62 | |
BALF | MRN = 3 |  |  | NPV = 79% |  +  | 17 | 11 | |
 |  |  |  | PPV = 61% | − | 15 | 58 | |
Lung tissue | MRN = 13 |  |  | NPV = 81% |  +  | 10 | 4 | |
 |  |  |  | PPV = 71% | − | 4 | 23 | |
Pleural fluid | MRN = 2 |  |  | NPV = 85% |  +  | 4 | 3 | |
 |  |  |  | PPV = 57% | − | 4 | 23 | |
Fungi | Â | Â | Â | Â | Â | Â | Â | |
All |  |  |  | NPV = 85% |  +  | 19 | 44 | |
 |  |  |  | PPV = 30% | − | 37 | 212 | |
Sputum | 400 | 85 | 7.5 | NPV = 87% |  +  | 4 | 9 | |
 |  |  |  | PPV = 31% | − | 20 | 131 | |
BALF | 100 | 90 | 9.5 | NPV = 80% |  +  | 3 | 5 | |
 |  |  |  | PPV = 38% | − | 12 | 47 | |
Lung tissue | 600 | 80 | 8 | NPV = 76% |  +  | 2 | 6 | |
 |  |  |  | PPV = 25% | − | 12 | 37 | |
Pleural fluid | 50 | 80 | 8.5 | NPV = 91% |  +  | 1 | 1 | |
 |  |  |  | PPV = 50% | − | 2 | 20 |