Table 1.
Results of CMT and mNGS of various samples for patients with PID.
| Patients | Specimen for mNGS | Culture results | Other microbiogical testing results | mNGS results (pathogenic) | SMRN | Genomic coverage (%) |
|---|---|---|---|---|---|---|
| P1 | CSF | Negative (CSF and blood) | Negative | JC polyomavirus | 1526 | 97.563 |
| BK Virus | 20 | 30.063 | ||||
| Acidovorax temperans | 3301 | 11.166 | ||||
| Comamonas testosteroni | 591 | 1.453 | ||||
| Malassezia globosa | 119 | 0.168 | ||||
| Acanthamoeba triangularis | 890 | 0.241 | ||||
| P2 | CSF | Negative (CSF and blood) | Negative | JC polyomavirus | 5 | 14.6 |
| Acidovorax temperans | 30 | 0.119 | ||||
| Ralstonia mannitolilytica | 18 | 0.053 | ||||
| P3 | CSF | Negative (CSF and blood) | Negative | Toxoplasma gondii | 151 | 0.01 |
| P4 | sputum | Negative (sputum and blood) | CMV-DNA (+) | Acinetobacter junii | 567 | 1.44 |
| Stenotrophomonas maltophilia | 118 | 0.21 | ||||
| Pneumocystis jirovecii | 2 | 0.0018 | ||||
| Cytomegalovirus | 2 | 0.064 | ||||
| P5 | blood | Negative (blood) | CMV-DNA (+) | Cytomegalovirus | 18 | 1.139 |
| P6 | Liver tissue | Negative (blood) | EBV-DNA(+) | Epstein-barr virus | 18 | 0.757 |
| P7 | BALF | Klebsiella pneumoniae (BALF) | Negative | Klebsiella pneumoniae | 18957 | 3.0 |
| P8 | BALF | Negative (BALF and blood) | Mycoplasma pneumoniae (+) | Epstein-barr virus | 45 | 2.781 |
| Mycoplasman pneumonia | 154 | 2.479 | ||||
| P9 | BALF | Streptococcus pneumoniae | Negative | Streptococcus pneumonia | 67 | 0.434 |
| Pseudomonas aeruginosa | Pseudomonas aeruginosa | 6 | 0.014 | |||
| (BALF) | Haemophilus influenza | 3 | 0.024 | |||
| Epstein-barr virus | 2 | 0.159 | ||||
| P10 | BALF | Klebsiella aerogenes | Negative | Stenotrophomonas maltophilia | 364 | 1.221 |
| Candida albicans | Klebsiella aerogenes | 156 | 0.444 | |||
| (BALF) | Candida albicans | 3380 | Copies/ml | |||
| Cytomegalovirus | 61 | 3.761 | ||||
| P11 | BALF | Negative (BALF and blood) | Negative | Haemophilus parainfluenzae | 6 | 0.100 |
| Sphingomonas paucimobilis | 2 | 0.007 | ||||
| Escherichia coli | 2 | 0.005 | ||||
| P12 | Pus | Staphylococcus aureus (Pus) | Negative | Stenomonas maltophilia | 19 | 0.03 |
| Staphylococcus aureus | 5 | 0.02 | ||||
| P13 | sputum | Multiple drug resistant pseudomonas aeruginosa (Sputum) | Negative | Pseudomonas aeruginosa | 1599 | 3.572 |
| Torque teno virus | 56 | 13.687 | ||||
| Epstein-barr virus | 376 | 10.228 | ||||
| Cytomegalovirus | 23 | 1.378 | ||||
| P14 | Bone biopsy tissue | Negative | PPD (+) | Nocardia farcinica | 752 | 0.73 |
| (Blood) | T-SPOT (+) | Mycobacterium avium | 2 | 0.01 | ||
| P15 | CSF | Negative (CSF and blood) | Negative | Negative | / | / |
| P16 | CSF | Negative | Sputum X-pert (+) | Mycobacterium | 2 | 0.01 |
| (CSF and blood) | Rasamsonia emersonii | 1 | 0.01 |
CMV, Cytomegalovirus; EBV, Epstein-barr virus; SMRN, strictly map reads number.