TABLE 1.
Comparison of qPCR-positive whole-blood samples to sequencing results from plasma samples
| Pathogena | No. of samples (mean CT, range) for samples that were positive by qPCR and: |
No. of samples negative by qPCR and: |
Sequencing vs qPCR sensitivity/specificity | ||
|---|---|---|---|---|---|
| mNGS positive | mNGS negative | mNGS positive | mNGS negative | ||
| Viral pathogens | |||||
| CMV | 7 (26.8, 21–31.4) | 59 (32.3, 20.9–37) | 1 | 187 | 11%/99% |
| Dengue virus | 0 | 5 | 0 | 249 | 0%/100% |
| EBV* | 3 (21, 17.9–23.3) | 107 (35.4, 28.6–39.8) | 0 | 144 | 3%/100% |
| Hepatitis B virus* | 14 (15.2, 10.7–22) | 28 (32.4, 22.2–35.3) | 0 | 212 | 33%/100% |
| Hepatitis E virus | 0 | 1 | 1 | 252 | 0%/100% |
| HIV* | 124 (28.3, 21.4–37.3) | 52 (32.7, 23–39.2) | 6 | 72 | 70%/92% |
| Bacterial pathogens | |||||
| S. pneumoniae | 1 | 17 | 1 | 235 | 6%/100% |
| E. coli | 0 | 4 | 0 | 250 | 0%/100% |
| Rickettsia spp. | 1 | 5 | 0 | 248 | 17%/100% |
| P. aeruginosa | 0 | 1 | 9 | 244 | 0%/96% |
| K. pneumoniae | 0 | 2 | 0 | 252 | 0%/100% |
| S. aureus | 0 | 2 | 2 | 250 | 0%/99% |
| Salmonella spp. | 0 | 2 | 0 | 252 | 0%/100% |
| Leptospira spp. | 0 | 2 | 0 | 252 | 0%/100% |
| Coxiella spp. | 0 | 1 | 0 | 253 | 0%/100% |
| M. tuberculosis | 1 | 43 | 0 | 207 | 2%/100% |
| Other pathogens | |||||
| Plasmodium | 2 | 15 | 0 | 234 | 12%/100% |
| Cryptococcus | 0 | 6 | 0 | 248 | 0%/100% |
| Toxoplasma | 0 | 2 | 0 | 252 | 0%/100% |
a
Asterisks denote pathogens detected by qPCR with plasma sample following sequencing.