Table 1. .
Result Summary of Shotgun Metagenomics and Quantitative Real-time PCR on the Patient Samples
| Sample (Hospital Day) | Shotgun Metagenomics Results | Quantitative Real-time PCR Results | ||||
|---|---|---|---|---|---|---|
| Total NGS Reads | Reads After Host DNA Removal | Reads Aligned to Bacterial Database | Reads Aligned to Nonbacterial Database | Pathogens Detected After Filtering, Reads | Viral Load, Copies/mL | |
| BAL (HD3) | 5 834 434 | 95 300 | 484 | 2865 | Adenovirus (1301) | 2 814 889 |
| BAL (HD9) | 2 028 030 | 43 139 | 2483 | 367 | Adenovirus (10), Acinetobacter baumannii (1666) | 211 743 |
| Blood (HD3) | 4 867 325 | 125 375 | 4648 | 2450 | Adenovirus (795) | 21 655 |
| Blood (HD9) | 4 076 330 | 114 449 | 7774 | 337 | Negative (0) | Not detected |
| CSF (HD30) | 3 492 920 | 107 793 | 1985 | 1302 | HSV-1 (844) | 20580 |
| CSF (HD44) | 2 934 620 | 80 613 | 4398 | 328 | Negative (0) | Not detected |
Abbreviations: BAL, bronchoalveolar lavage; CSF, cerebrospinal fluid; NGS, next-generation sequencing; HSF-1, herpes simplex virus–1; PCR, polymerase chain reaction.