TABLE 2.
Summary of sputum microbiology; pilot data (n = 23), sputum differential (neutrophilia >61%, eosinophilia >3%), FeNO (high: >45 ppb), culture, MALDI-TOF speciation, DNA sequencing by Oxford Nanopore; RT-qPCR for Eubacteria 16S and specific pathogens: H. influenzae, S. pneumoniae, M. catarrhalis, P. aeruginosa, S. aureus (positive >1 × 106 copies/mL)a
| PID | Age (yrs) | Sex | Smoking status (pack yrs) | H. inf culture | H. inf reads (% total bacterial reads) | H. inf qPCR (×106 copies/mL) | S. pneu qPCR (×106 copies/mL) | M. cat qPCR (×106 copies/mL) | P. aeru qPCR (×106 copies/mL) | S. aur qPCR (×106 copies/mL) | Total 16S qPCR (×106 copies/mL) | Sputum neutrophils (%) | Sputum eosinophils (%) | FeNO (ppb) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1054 | 53 | M | Ex (10) | + | 93.5 | 983.80 | 1.89 | − | − | − | 8510 | 93.2 | 0.5 | nd |
| 278 | 50 | M | Ex (40) | + | 86.5 | 435.40 | − | 0.79 | − | − | 2832 | 84.7 | 0 | 11 |
| 133 | 60 | F | Never | + | 66.6 | 91.70 | 1.99 | − | − | − | 1643 | 98.2 | 0 | 29 |
| 297 | 76 | F | Never | + | 66.6 | 40.00 | 1.72 | − | − | − | 1042 | 75 | 0 | 21 |
| 288 | 67 | M | Ex (9) | + | 58.0 | 31.00 | − | − | − | 0.02 | 572 | 96.7 | 0.2 | 169 |
| 29 | 76 | F | Ex (10) | + | 47.1 | 16.50 | 0.17 | − | − | − | 633 | 62.7 | 0.5 | 9 |
| 214 | 54 | M | Ex (<1) | + | 17.1 | 12.50 | − | − | − | − | 338 | 99.5 | 0 | 20 |
| 1049 | 57 | F | Never | − | 51.3 | 12.40 | − | − | − | − | 297 | 91.7 | 2 | 20 |
| 235 | 57 | M | Never | − | 3.3 | 0.70 | − | − | − | − | 335 | 20.5 | 0.5 | 37 |
| 306 | 69 | F | Never | − | 0.03 | 0.30 | − | − | − | − | 1006 | 82.2 | 1 | 85 |
| 187 | 66 | M | Ex (12) | − | 0.05 | 0.03 | − | − | − | − | 1822 | 25.2 | 7.5 | 300 |
| 1052 | 79 | M | Never | − | 0.1 | 0.02 | − | 35.63 | − | − | 695 | 65.2 | 1.2 | 125 |
| 294 | 62 | F | Never | − | 0.05 | 0.02 | − | − | − | − | 43 | nd | 0.5 | 28 |
| 1055 | 70 | F | Ex (15) | − | 0.6 | 0.01 | − | − | − | − | 91 | 58.2 | 15.5 | 138 |
| 1053 | 59 | M | Ex (10) | − | 0.5 | 0.01 | − | − | − | − | 1754 | 85.7 | 0.7 | 64 |
| 1041 | 73 | F | Ex (8) | − | 1.0 | 0.01 | − | − | − | − | 286 | 43.2 | 0.5 | 8 |
| 5 | 67 | M | Never | − | 0.07 | − | − | − | − | − | 661 | 53.7 | 11 | 8 |
| 275 | 76 | F | Never | − | 2.8 | − | 5.95 | − | − | − | 696 | 83.7 | 0.7 | 20 |
| 315 | 61 | M | Never | − | 0.05 | − | − | − | − | − | 115 | 22.2 | 0.2 | 78 |
| 1060 | 86 | M | Ex (8) | − | 0.0 | − | − | − | − | − | 58 | 32.7 | 22.9 | 16 |
| 279 | 60 | F | Never | − | 0.05 | − | − | − | − | − | 216 | nd | nd | 48 |
| 295 | 81 | M | Ex (20) | − | 0.4 | − | − | − | − | − | 191 | 72 | 0 | 78 |
| 1058 | 72 | M | Ex (3) | − | 1.0 | − | − | − | − | − | 95 | 41.5 | 15.1 | 89 |
a
Values above indicated thresholds levels shown in bold denotes pathogen not detected by PCR. Participants are ranked according to detection of H. influenae by quantitative PCR. +, denotes pathogen detected; −, denotes pathogen not detected by standard culture or by PCR.