Table 1 Clinical microbiology results and sequencing information for patients who were positive for S. pneumonia by mNGS
| Â | Clinical microbiology tests | mNGS | qPCR | |||||
|---|---|---|---|---|---|---|---|---|
Patient | Pathogen | Culture (blood/CSF) | Antigen test | Pathogen | Reads | Coverage% | Depth | |
P1 | SP | – | + | SP | 262 | 1.1 | 1 | ND |
P2 | SP | + | + | SP | 1105 | 11 | 1.1 | ND |
P3 | SP | + | + | SP | 573 | 2.6 | 1 | + |
P4 | SP | + | + | SP | 429 | 1.9 | 1 | + |
P5 | SP | – | + | SP | 425 | 1.9 | 1 | + |
P6 | SP | – | + | SP | 176 | 1.8 | 1 | ND |
P7 | SP | + | ND | SP | 162 | 0.75 | 1 | + |
P8 | SP | + | + | SP | 38 | 0.16 | 1 | ND |
P9 | SP | – | + | SP | 21 | 0.12 | 1 | ND |
P10 | SP | + | + | SP | 13 | 0.066 | 1 | ND |
P11 | SP | + | + | SP | 11 | 0.052 | 1 | ND |
P12 | SP | + | + | SP | 7 | 0.048 | 1 | – |
P13 | SP | + | + | SP | 6 | 0.034 | 1 | – |
P14 | SP | + | + | SP | 4 | 0.041 | 1 | ND |
P15 | SP | – | + | SP | 4 | 0.016 | 1 | – |
P16 | SP | – | + | SP | 3189 | 28 | 1.3 | ND |
P17 | SP | – | + | SP | 23,247 | 75 | 3.9 | ND |
P18 | SP | + | + | SP | 25 | 0.19 | 1 | + |
P19 | SP | + | + | SP | 2603 | 7.25 | 1.06 | ND |
P20 | SP | + | + | SP | 341,303 | 86.68 | 36.57 | + |
P21 | SP | + | + | SP | 165 | 0.7413 | 1.01 | + |
P22 | SP | + | + | SP | 1335 | 12.03 | 1.09 | + |
P23 | SP | + | + | SP | 456 | 5.41 | 1.04 | + |
P24 | SP | + | + | SP | 32 | 0.0744 | 1 | ND |
P25 | SP | + | + | SP | 218 | 1.04 | 1 | ND |
P26 | SP | + | + | SP | 20 | 0.1488 | 1 | – |
P27 | – | – | – | SP | 33 | 0.31 | 1 | ND |
P28 | SA | SA | ND | SP | 27 | 0.15 | 1 | – |
P29 | – | – | – | SP | 24 | 0.12 | 1 | ND |
P30 | – | – | ND | SP | 12 | 0.95 | 1 | ND |
P31 | – | – | – | SP | 6 | 0.055 | 1 | ND |
P32 | – | – | – | SP | 4 | 0.011 | 1 | – |