TABLE 2.
Analytes detected by NGS workflows but not by provider-ordered testinga
| Workflow, result, and organism type | Analyte | No. of samples with analyte detected |
|---|---|---|
| Metagenomic NGS workflow | ||
| True positive | ||
| Bacteria | Corynebacterium striatum b | 1 |
| Enterococcus faecium c | 1 | |
| Ureaplasma parvum | 1 | |
| Viruses | CMV | 5 |
| EBV | 16 | |
| HSV-1 | 4 | |
| HHV-6 | 5 | |
| HHV-7 | 4 | |
| Rhinovirus | 1 | |
| SARS-CoV-2 | 2 | |
| False positive | ||
| Bacteria | Achromobacter xylosoxidans | 2 |
| Acinetobacter haemolyticus | 1 | |
| Clostridium tetani | 1 | |
| Cupriavidus gilardii | 1 | |
| Listeria monocytogenes | 2 | |
| Orientia tsutsugamushi | 1 | |
| Rhodococcus sp. | 1 | |
| Stenotrophomonas maltophilia | 1 | |
| Mycobacteria | Mycobacterium avium complex | 1 |
| Fungi | Coccidioides posadasii | 2 |
| Cryptococcus neoformans | 1 | |
| Pneumocystis jirovecii | 1 | |
| Rhizophagus irregularis | 1 | |
| Scedosporium apiospermum | 1 | |
| Trichosporon asahii | 2 | |
| Viruses | CMV | 2 |
| EBV | 2 | |
| HSV-1 | 1 | |
| HHV-7 | 3 | |
| SARS-CoV-2 | 2 | |
| RPIP targeted NGS workflow | ||
| True positive | ||
| Bacteria | Corynebacterium striatum b | 1 |
| Enterococcus faecium c | 1 | |
| Tropheryma whipplei | 1 | |
| Ureaplasma parvum | 1 | |
| Viruses | EBV | 12 |
| HSV-1 | 4 | |
| HHV-6 | 4 | |
| Rhinovirus | 1 | |
| SARS-CoV-2 | 3 | |
| False positive | ||
| Bacteria | Burkholderia cepacia complex | 1 |
| Enterococcus faecalis | 2 | |
| Escherichia coli | 1 | |
| Fusobacterium nucleatum | 1 | |
| Ralstonia pickettii | 1 | |
| Stenotrophomonas maltophilia | 1 | |
| Fungi | Microascus cirrosus | 3 |
| Viruses | Human metapneumovirus | 1 |
| EBV | 1 | |
| SARS-CoV-2 | 5 | |
a
Counts represent the number of samples in which the analyte was detected per workflow.
b
Isolated from blood cultures.
c
Isolated from pleural fluid; vancomycin resistant by phenotypic testing and associated with a van gene by RPIP analysis.