TABLE 3.
Detection of pathogenic bacteria and antimicrobial resistance genes in cultured blood samples
| Sample | No. of raw reads |
Total no. of mapped reads |
Bacterium identified |
Genome coverage (%) |
AST profilea | Significant AMR gene(s) detected |
|---|---|---|---|---|---|---|
| 1 | 2,833,697 | 2,709,612 |
Pseudomonas
aeruginosa |
87 | TET (R), MERO (I) |
mexA to -N, -P, -Q, -S, -V, and -W
combined with oprM |
| 2 | 8,322,222 | 7,126,518 |
Escherichia
coli |
81 | AMP (I), CEF (I) | TEMs (115, 4, 80, 6, 153, 143, 79), combined with numerous efflux pump antiporters (including most prominently acrF, cpxR, or H-NS) |
| 3 | 5,768,129 | 5,096,360 |
Morganella
morganii |
90 | AMP (R), CEPH (R), AZT (I) |
Numerous DHA complex β-lactamases (DHA-20, -17, -21, -1, -19), combined with efflux pump antiporters acrB and smeB; cpxR, related to aztreonam resistance |
| 4 | 5,749,637 | 4,774,301 |
Haemophilus
influenzae |
92 | NA | hmrM |
a
Antimicrobial sensitivity test (AST) profile: AMP, ampicillin; AZT, aztreonam; CEF, cefoxitin; CEPH, cefazolin/ceftazidime/ceftriaxone; MERO, meropenem; TET, tetracycline. R, resistant; I, intermediate rating; NA, not applicable.