Table 2.
The results of microbiological tests in patients in the BALF mNGS/CMT group
| Patient No. | Sex/Age | Conventional microbiological tests | mNGS tests | Symptomatic infection duration before bronchoscopy, days | Treatment before bronchoscopy | Treatment adjustment upon mNGS tests | Outcomes | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | M/80 | Fungal spores (sputum culture)/ BALF GM(+)/hMPV (throat swab PCR) | Aspergillus fumigatus | 12 | PE, prednisolone, antibiotics | voriconazole, prednisolone withdrawal | death | ||||
| 2 | M/63 | none | none | 0 | - | plasmapheresis, prednisolone, RTX | survival | ||||
| 3 | M/66 | Serum G(+)/Pneumocystis cysts (BALF smear)/RhV (throat swab PCR) | Pneumocystis jirovecii/RhV-A | 4 |
PE, MP pulse, prednisolone, RTX, antibiotics |
SMZ/TMP, prednisolone withdrawal | survival | ||||
| 4 | F/66 | Serum G(+)/Pneumocystis cysts (BALF smear)/BALF GM(+)/BALF CMV-DNA(+) | Bca/Hin/Aspergillus fumigatus/Pneumocystis jirovecii/CMV/HHV-7 | 5 | MP pulse, prednisolone, RTX, antibiotics | antibiotics upgrading, voriconazole, SMZ-TMP, prednisolone withdrawal | death | ||||
| 5 | M/65 | none | Sps/CMV | 6 |
MP pulse, prednisolone AZA |
antibiotics, immunosuppressive therapy continuance | survival | ||||
| 6 | F/48 | none | none | 4 | PE, prednisolone, RTX, antibiotics | antibiotics discontinuance | survival | ||||
| 7 | F/57 | Pae (BALF culture) | Pae/Sep | 9 | prednisolone, AZA | antibiotics, immunosuppressive therapy continuance | survival | ||||
| 8 | F/65 | Serum G(+)/Pneumocystis cysts (BALF smear) | Pneumocystis jirovecii/P. chrysogenum species complex/CMV/HHV-6B | 6 | prednisolone, CTX, antibiotics | SMZ-TMP, ganciclovir, prednisolone withdrawal | death | ||||
| 9 | M/71 | none | Pae/Nocardia pneumoniae /Candida albicans | 4 | prednisolone, AZA |
antibiotics, SMZ-TMP, immunosuppressive therapy continuance |
survival | ||||
| 10 | F/67 | none | none | 1 | prednisolone, antibiotics | antibiotics discontinuance, immunosuppressive therapy intensification | survival | ||||
| 11 | F/65 | Candida albicans (sputum culture) | Sho/ HCov-OC43/ Candida albicans | 9 | prednisolone, CTX, antibiotics | antibiotics upgrading, prednisolone withdrawal | death | ||||
| 12 | F/71 | Pae (sputum and BALF culture) | Pae | 13 |
PE, MP pulse, prednisolone, CTX |
antibiotics, prednisolone withdrawal | survival | ||||
| 13 | M/58 | Serum G(+) | Pneumocystis jirovecii | 4 | MP pulse, prednisolone, CTX, antibiotics | SMZ-TMP, prednisolone withdrawal | survival | ||||
| 14 | F/60 | Serum G(+)/BALF CMV-DNA(+) | Efa/ Pneumocystis jirovecii/CMV/EBV | 4 | prednisolone, antibiotics | antibiotics upgrading, SMZ-TMP, prednisolone withdrawal | survival, ESRD | ||||
| 15 | M/61 | none | Pae | 8 | prednisolone |
antibiotics, PE, immunosuppressive therapy continuance |
survival | ||||
| 16 | M/70 | BALF EBV-DNA(+) | Sps/EBV/ Candida albicans | 0 | - |
prednisolone, CTX, antibiotics |
survival | ||||
| 17 | F/77 | none | none | 1 | antibiotics | antibiotics discontinuance prednisolone, CTX | survival | ||||
| 18 | M/67 | Pae (sputum and BALF culture) | Pae/ Achromobacter xylosoxidans/RhV-A | 9 | prednisolone, antibiotics | antibiotics upgrading, prednisolone withdrawal | survival, ESRD | ||||
| 19 | M/82 | BALF CMV-DNA(+) | C. amycolatum | 0 |
prednisolone, ganciclovir |
antibiotics, immunosuppressive therapy continuance | survival | ||||
| 20 | F/54 | Candida tropicalis (sputum culture) | Bca/C. striatum/ Candida albicans/ Candida tropicalis | 5 |
PE, prednisolone |
antibiotics, prednisolone withdrawal | survival | ||||
| 21 | F/76 | none | none | 3 | prednisolone | immunosuppressive therapy intensification | survival | ||||
| 22 | F/44 | none | none | 4 | prednisolone | immunosuppressive therapy intensification | survival | ||||
| 23 | M/71 | BALF CMV-DNA(+) | Efa/Sho /HCov/EBV/CMV/Candida parapsilosis | 7 |
PE, prednisolone, antibiotics |
antibiotics adjustment, ganciclovir, prednisolone withdrawal |
survival, ESRD | ||||
| 24 | F/59 | none | Sau/Sma | 4 | prednisolone, antibiotics | antibiotics upgrading, prednisolone withdrawal | survival | ||||
| 25 | F/75 | Serum PIV IgM (+)/Pneumocystis cysts (BALF smear)/BALF EBV-DNA(+) | Pneumocystis jirovecii/ EBV/CMV/RSV | 0 | prednisolone, CTX | SMZ-TMP, ganciclovir, antibiotics, prednisolone withdrawal | survival | ||||
| 26 | F/75 | none | none | 2 | antibiotics, prednisolone | antibiotics discontinuance, immunosuppressive therapy intensification | survival | ||||
| 27 | F/72 | Sho (BALF culture)/ Serum G(+)/BALF GM(+) |
Sho/Kpn/Pneumocystis jirovecii/ Aspergillus terreus EBV/CMV |
0 | fluconazole, SMZ-TMP, antibiotics, prednisolone | voriconazole, antibiotics adjustment, prednisolone withdrawal | survival | ||||
Abbreviation: AZA, azathioprine; Bca, Moraxella catarrhalis; C. amycolatum, Corynebacterium amycolatum; CMV, cytomegalovirus; C. striatum, Corynebacterium striatum; CTX, cyclophosphamide; EBV, human gammaherpesvirus 4; Efa, Enterococcus faecium; ESRD, end-stage renal disease; HCov, human coronavirus; HHV, human herpesvirus; Hin, Haemophilus influenza; hMPV, human metapneumovirus; Kpn, Klebsiella pneumoniae; MP, methylprednisolone; mNGS, metagenomic next-generation sequencing; Pae, Pseudomonas aeruginosa; P. chrysogenum, Penicillium chrysogenum; PE, plasmapheresis; PIV, parainfluenza virus; RhV-A, rhinovirus A; RSV, respiratory syncytial virus; RTX, rituximab; Sau, Staphylococcus aureus; Sep, Staphylococcus epidermidis; Sho, Staphylococcus hominis; Sma, Stenotrophomonas maltophilia; SMZ-TMP, sulfamethoxazole and trimethoprim; Sps, Streptococcus pseudopneumoniae;