Studies including samples from CF patients were approved by the Ethics Committee of the University of Heidelberg (study number S-370/2011). Informed written consent was obtained from the patients, parents, or legal guardians of all subjects. Airway samples from CF patients (sputum, throat swab) were obtained during routine visits at the CF Center at the University Hospital Heidelberg as previously described (54). The diagnosis of CF was based on established diagnostic criteria. Samples were used for isolation of P. aeruginosa strains (n = 51) and sputum, nose or throat swabs were analyzed for virus infection by multiplex PCR (Seegene, Korea, AllplexTM respiratory panels 1–4) or by targeted RT-PCR after RNA extraction using TRIZOL and cDNA synthesis as described above. Infection status with P. aeruginosa (intermittent or chronic) was classified according to the following definition (69): Intermittent infection was defined as positive microbial culture of P. aeruginosa in at least one and <50% of the samples in the last 12 months and no detection of anti-Pseudomonas antibodies (against alkaline protease, elastase, and exotoxin A). Chronic infection was defined as persistent culture presence of P. aeruginosa for at least 6 months, or less when combined with a positive finding (titer >1,250) of two or more antibodies.