Table 2.
Comparison of pathogens reported by routine culture with metagenomics sequencing in respiratory samples
| Patient ID | Sample ID | Semi-quantitative routine culture reporta | Pathogens identified by metagenomic sequencing | Pathogen readsb identified by metagenomic sequencing | Microbial readsb identified by metagenomic sequencing |
|---|---|---|---|---|---|
| 26 | S35 | Acinetobacter spp. (L) | A. baumannii | 99 | 853 |
| 100 | S39 | C.koseri (H) |
C. koseri K. pneumoniae |
23,870 284 |
26,251 |
| 121 | S37 |
P.mirabilis (M) M.morganii (M) |
P. mirabilis M morgannii K. pneumoniae |
397 28,300 876 |
45,395 |
| 177 | S36 | S. aureus (H) | S. aureus | 109,767 | 119,881 |
| 196 | S42 | B. cenocepacia (L) | Burkholderia spp. | 34,347 | 51,551 |
| 400 | S49 | K. pneumoniae (M) | K. pneumoniae | 594 | 2202 |
| 408 | S20 | S. aureus (M) | S. aureus | 36,281 | 38,708 |
| 441 | S21 | E. cloacae (M) | E. cloacae | 62,314 | 75,866 |
| S51 |
S. aureus (L) C. koseri (L) |
S. aureus C. koseri |
5203 2262 |
8582 | |
| 550 | S10 | K. pneumoniae (M) | K. pneumoniae | 69,029 | 75,350 |
| 563 | S28 | Aspergillus (S) |
A. fumigatus S. aureus |
2649 3165 |
44,684 |
| 613 | S18 | Negative | Negative | 0 | 22,776 |
| 618 | S45 | K. aerogenes (S) | – | 104 | 1228 |
| 677 | S52 | K. aerogenes (L) | K. aerogenes | 5277 | 38,854 |
| S54 | Negative | Negative | 1758 | 3015 | |
| S63 | K. pneumoniae (M) | K. pneumoniae | 17,034 | 147,379 | |
| 727 | S53 | Negative | Negative | 0 | 0 |
| 740 | S30 | Negative | Negative | 0 | 759 |
| S59 | K. pneumoniae (M) | K. pneumoniae | 99,186 | 119,458 | |
| 749 | S40 | Negative | Negative | 0 | 1157 |
| S62 | K. aerogenes (L) | K. aerogenes | 184 | 1021 | |
| 815 | S25 | Negative | Negative | 0 | 1413 |
| S46 | C. koseri (M) | C. koseri | 237 | 462 | |
| 855 | S41 | Negative | S. aureus | 1365 | 31,067 |
| 872 | S11 | K. pneumoniae (H) | K. pneumoniae | 16,828 | 35,668 |
| S61 |
P. mirabilis (H) K. pneumoniae (M) |
P. mirabilis K. pneumoniae C. koseri |
29,797 14,118 815 |
47,924 | |
| 1033 | S8 | A. fumigatus (S) |
A. fumigatus K. oxytoca |
77 44 |
1399 |
| 1036 | S5 | Negative | Negative | 0 | 0 |
| 1054 | S31 | K. pneumoniae (L) | K. pneumoniae | 28,056 | 31,800 |
| 1065 | S16 | Negative | S. aureus | 1768 | 43,692 |
| S19 | Negative | Negative | 0 | 10,371 | |
| 1069 | S17 | P. aeruginosa (M) | P. aeruginosa | 1457 | 1905 |
| 1082 | S14 | Negative | Negative | 0 | 205 |
| 1092 | S27 | Negative | Negative | 0 | 1413 |
| 1262 | S29 | Negative | Negative | 0 | 759 |
| 1292 | S44 |
S. marcescens (L) K. aerogenes (S) |
S. marcescens C. freundii |
53,082 6082 |
65,078 |
| 1346 | S56 |
A. fumigatus (S) P. mirabilis (L) |
A. fumigatus P. mirabilis |
79 11,323 |
36,658 |
| 1440 | S33 | Negative | Negative | 0 | 1176 |
| 1457 | S64 | Negative | Negative | 0 | 24,484 |
| S65 | Negative | Negative | 0 | 45,990 | |
| 1503 | S1 | K. aerogenes (L) | K. aerogenes | 138,626 | 145,195 |
| 1512 | S34 | K. pneumoniae (L) | K. pneumoniae | 38,758 | 82,796 |
| 1538 | S55 | Negative | A. fumigatus | 16 | 9146 |
aReported growth by culture for each pathogen. H= heavy growth, M = moderate growth, L = light growth, S scanty growth
bCriteria for reporting organisms was ≥ 1% of microbial-classified reads and with a centrifuge score ≥ 2504 and > 9 reads for A. fumigatus only