Table 4 Missed detection by metagenomics pipeline in polymicrobial samples
From: Unified metagenomic method for rapid detection of microorganisms in clinical 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 | ||
