Table 2:
Direct sequencing analyses with treatment impact
| Patient ID | Test ID | Clinical syndrome | Assay | Test indication | Sample type | Turnaround time (days) | Test result | Final clinical diagnosis | Clinical impact |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | Infected sclerosing peritonitis | Bacterial | NCWA | Ascites | Unknown | Haemophilus influenzae | Infected sclerosing peritonitis | TM (levofloxacin introduction) |
| 2 | 2 | Sinusitis | Fungal | First-line test | Sinus mucosal biopsy | Unknown | Negative | Bacterial sinusitis | TC (isavuconazole cessation) |
| 3 | Sinusitis | Fungal | First-line test | Bone sample | Unknown | Negative | Bacterial sinusitis | TC (isavuconazole cessation) | |
| 4 | Sinusitis | Fungal | First-line test | Bone sample | Unknown | Negative | Bacterial sinusitis | TC (isavuconazole cessation) | |
| 3 | 5 | Infective myositis | Fungal | Unknown | Soft tissue | Unknown | Negative | Cicatricial changes | TC (fluconazole cessation) |
| 4 | 6 | Meningoencephalitis | Bacterial | NCWA | Cerebrospinal fluid | Unknown | Technical limitations | Non-infectious condition | TC (Meropenem cessation) |
| 5 | 7 | Spondylodiscitis | Bacterial | NCWA | Intervertebral disc sample | 17 | Haemophilus parainfluenzae | Spondylodiscitis | TM (ceftriaxone, vancomycin and metronidazole changed for ceftriaxone) |
| 6 | 8 | Osteomyelitis | Bacterial | First-line test | Bone sample | Unknown | Negative | Non-infectious condition | TC (cefazolin cessation) |
| 7 | 9 | Encephalitis | Bacterial | First-line test | Cerebral biopsy | 17 | Streptococcus intermedius | Encephalitis | TM (meropenem and vancomycin changed for penicillin) |
| 10 | Cerebral abscess | Bacterial | First-line test | Cerebral collection | 17 | Streptococcus intermedius | Cerebral abscess | TM (meropenem and vancomycin changed for penicillin) | |
| 8 | 11 | Endovascular prosthesis infection | Bacterial | NCWA | Endovascular prosthesis | Unknown | Winkia neuil | Endovascular prostheses infection | TM (ertapenem changed for penicillin) |
| 12 | Endovascular prosthesis infection | Bacterial | NCWA | Perivascular collection | Unknown | Winkia neuil | Endovascular prostheses infection | TM (ertapenem changed for penicillin) | |
| 9 | 13 | Cerebral abscess | Bacterial | NCWoA | Cerebral collection | 32 | Nocardia sp | Cerebral abscess | TM (meropenem changed for linezolid and moxifloxacin) |
| 10 | 14 | Multisystemic disease | Fungal | NCWA | Whole blood | 25 | Saccharomyces cerevisiae | Fungal multisystemic disease | TM (voriconazole and caspofungin changed for voriconazole and amphotericin B) |
NCWA = Negative culture with antimicrobial at the time of sampling; NCWoA = Negative culture without antimicrobial at the time of sampling; TC = Treatment cessation; TM = Treatment modification