Table 4.
Missed detection by metagenomics pipeline in polymicrobial samples
| Sample number | Sample type | Routine testing detections (Ct values for viral detections or bacterial/fungal culture growth) | 2 h of sequencing | ||||
|---|---|---|---|---|---|---|---|
| Microorganisms sequenced | Number of microbial reads | Percentage of bacterial reads | |||||
| 1 | NTS |
SARS-CoV-2 (Ct 20/22) PIV3 (Ct 29) |
SARS CoV-2 Human gammaherpesvirus 4 |
2878 1188 |
57.514 23.741 |
||
| 79 | BAL | B.cepacia (L) | B. cepacia | 53 | 0.671 | ||
| 73 | Sputum |
E. faecalis (H) E. coli (S) C. albicans (S) B-glucan positive |
E. faecalis A. fumigatus C. albicans P. jirovecii |
119 18 4 1 |
1.277 N/A N/A N/A |
||
| 88 | BAL |
A. baumanii (H) P. aeruginosa (H) E. meningoseptica (L) |
P. aeruginosa A. baumannii S. maltophilia |
483 412 123 |
4.178 3.564 1.064 |
||
| 42 | BAL |
Enterovirus/Rhinovirus (Ct 35) Seasonal coronavirus (Ct 30) |
P.melaninogenica S. salivarius S. sp. FDAARGOS_192 S. equinus N. mucosa V. parvula R. mucilaginosa P. jejuni P. salivae P. scopos S. odontolytica S. viridans G. sanguinis Human coronavirus 229E |
1465 441 325 150 123 118 105 104 84 69 67 65 38 30 |
40.481 12.186 8.98 4.145 3.399 3.261 2.901 2.874 2.321 1.907 1.851 1.796 1.05 N/A |
||
H high growth, L light growth, S scanty growth.