| Virus-negative(n = 431) | Virus-positive(n = 91) | |
| No microorganisms or colonisation, n (%) | 237 (55.0) | 76 (83.5) |
| Bacterial infection, n (%) | 124 (23.7) | 12 (13.2) |
| Mycobacterium tuberculosis or atypical mycobacteria, n (%)* | 7* (1.6) | 2 (2.2) |
| Pneumocystis jiroveci, n (%) | 14 (3.2) | 1 (1.1) |
*Atypical Mycobacterium was identified in two cases (one lung transplant recipient and one HIV-infected subject).