Table 2.
mNGS findings of the 10 patients.
| Patient#/gestation age, wk | Conventional method results | mNGS results | Therapy | Follow-up (Mo)/outcome | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Culture | Antigen | PCR | Sample | TAT (h) | Initial Host index | Pathogens | IR | Initial Microbial index | FR | Final Host index | Final Microbial index | Antibiotics, d | Other | ||
| 1/39 | Sputum/Blood/CSF(−) | Respiratory/TORCH (−) | EV/CA (−) | Blood | 13 | 28826.85 | Mtb | 59 | 10723.30 | ND | / | / | Isoniazid/ rifampicin/pyrazinamide,67 | Ventilation 7d | 3/recovered |
| 2/40 | Sputum/Blood/CSF/BALF(−) | Respiratory/TORCH (−) | EV(−) | Blood | 22.5 | 29143.69 | LP | 361 | 13653.88 | NF | 29485.81 | NF | Erythromycin,19 | Plasma transfusion Ventilation 12d | 2/recovered |
| 3/40+3 | Sputum(MP)/Blood (−) | Respiratory/TORCH (−) | EV/CA (−) | Blood | 41.7 | 28392.78 | Mcat | 110 | 10994.57 | NF | 21320.92 | NF | Amikacin/Ceftazidime/Linezolid,24 | Ventilation 3d | 5/recovered |
| 4/38+1 | Sputum/Blood (−) | Respiratory/TORCH (−) | EV(−) | Sputum | 40.7 | 26006.36 | CT | 1,330 | 13036.10 | NF | 19779.90 | NF | Erythromycin,11 | Salbutamol nebulization | 5/recovered |
| 5/31 | Sputum/Blood (−) | TORCH (−) | EV/CA (−) | Sputum | 21 | 26180.42 | UP | 65 | 8430.86 | 6 | 22020.46 | 1784.12 | Erythromycin,7 | Bishop’s fistula of ileum and santulli fistulaVentilation 10d PICC 30d | 4/recovered |
| 6/39+1 | Sputum/Blood (−) | Respiratory/TORCH (−) | EV(−) | Sputum | 18 | 27934.48 | S. mitis | 1,286 | 15876.97 | NF | 26254.30 | NF | Oxacillin/Vancomycin,14 | Repair of VSD and PFO, ligation of PDA Ventilation 10d | 4/recovered |
| 7/40+1 | Sputum/Blood/CSF(−) | RSV(+) | EV(−) | Blood | 17.7 | 23752.90 | S. pasteuri& HHV-5 | 6/12 | 2661.86/3543.13 | ND | / | / | Vancomycin/Acyclovir,43 | NCPAP 4d DEX 4d | 2/recovered |
| CSF | 17.7 | 31468.11 | S. pasteuri& HHV-5 | 32/1 | 12767.09/7773.50 | 4/11 | 28348.48 | 7672.03/9126.95 | |||||||
| 8/39+5 | Sputum/blood/CSF(−) | Respiratory/TORCH(−) | EV(−) | blood | 43.5 | 27536.51 | E. coli | NF | / | ND | / | / | Meropenem/Cefotaxime,40 | phenobarbitone 7d/midazolam 3d/prednisone 7d | 1/recovered |
| CSF | 43.5 | 31482.51 | E. coli | 13 | 9777.09 | NF | 25699.22 | NF | |||||||
| 9/38+3 | Sputum/blood/CSF/stool(−) | Respiratory/TORCH(−) | EV(−) | blood | / | / | / | ND | / | ND | / | / | Penicillin,26 | phenobarbitone 16d/midazolam 3d DEX 4d | 1/encephalomalacia in left side of brain |
| CSF | 18.6 | 27271.33 | GBS | 15,611 | 15390.84 | NF | 27033.76 | NF | |||||||
| 10/34+2 | Sputum/blood/CSF(−) | RSV(±) | EV/CA (−) | Blood | 21 | 32275.98 | B. cereus | 4 | 9508.34 | ND | / | / | Gentamicin/Vancomycin,17 | Ventilation 3d phenobarbitone 8d | 1/diffused encephalomalacia |
| CSF | 21 | 29712.14 | B. cereus | 61 | 9559.24 | 2 | 24454.21 | 804.66 | |||||||
wk, week; CSF, cerebral spinal fluid; MP, Mycoplasma pneumonia; TORCH, Toxoplasma, Rubella, cytomegalovirus, herpes, and others; Respiratory, including influenza A/B virus, parainfluenza virus, adenovirus, and respiratory syncytial virus; RSV, respiratory syncytial virus; EV, Enterovirus; CA, Coxsackie Virus; TAT, turn-around time; Mtb, Mycobacterium tuberculosis; LP, Legionella pneumophila; Mcat, Moraxella catarrhalis; CT, Chlamydia trachomatis; UP, Ureaplasma parvum; S. mitis, Streptococcus mitis; S. pasteuri, Streptococcus pasteuri; HHV-5, Human betaherpesvirus 5; E. coli, Escherichia coli; GBS, Streptococcus agalactiae; B. cereus, Bacillus cereus; IR, Initial reads; FR, Finial reads; NF, not found; ND, not done; PICC, peripherally inserted central catheter; VSD, ventricular septal defect; PFO, patent foramen ovale; PDA, patent ductus arteriosus; DEX, dexamethasone; and Mo, months.