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Table 2 Comparison of pathogens reported by routine culture with metagenomics sequencing in respiratory samples

From: Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

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
  1. aReported growth by culture for each pathogen. H= heavy growth, M = moderate growth, L = light growth, S scanty growth
  2. bCriteria for reporting organisms was ≥ 1% of microbial-classified reads and with a centrifuge score ≥ 2504 and > 9 reads for A. fumigatus only