Accurate identification of lower respiratory tract pathogens is standard of care in the management of CF patients and it is therefore recommended to perform regular bacterial cultures, at least once a year, but some even recommend monthly cultures. This can be done through different methods, of which sputum and bronchoalveolar lavage (BAL) are the gold standard. However, BAL is an invasive method, not designated to repeat monthly. Therefore, the diagnosis of lower respiratory tract infections can be challenging in the non-expectorating CF patient. Other methods, such as induced sputum (IS), cough swabs and nasal swabs, have been developed to obtain bacterial cultures in these patients. Studies have investigated the reliability of these different sampling methods, however, with controversial conclusions.

I. Protocol design:

The current protocol is designed to compare:

• Group 1: nasal swab, cough swab and spontaneous expectorated sputum in expectorating CF patients
• Group 2: nasal swab, cough swab and induced sputum in non-expectorating CF patients
• Group 3: nasal swab, cough swab, induced sputum and BAL in both expectorating and non-expectorating CF patients requiring clinically indicated bronchoscopy

II. Flow chart:

1. Nasal swab obtained by the physiotherapyst (PT)

2. Patient rinses his mouth with water, followed by autogenic drainage

3. Cough swab obtained by the PT

4. Obtainment of 3rd (4th) sample:

   • Group 1: Sputum sample voluntary expectorated by the patient
   • Group 2 and 3: Induced sputum sample --> voluntary coughed up and expectorated by the patient after inhalation of 4ml of HS OR
   • Group 3: BAL -->obtained by the pulmonologist during bronchoscopy

5. Filling out questionnaire on acceptability of the different sampling methods by patients >6 years of age (not in Group 3)

III. Analysis of the samples:

(Induced) Sputum samples, cough and nasal swabs are aseptically collected in the appropriate disposable and are immediately sent to the Laboratory for Microbiology and Infection Control of the Universitair Ziekenhuis Brussel, where analyses are carried out within 24h post-sampling.

These analyses include:

• Culture and identification of respiratory pathogens on selective and non-selective media
• Each type of colony will be identified by MALDI-TOF mass spectrometry, completed by other identification tests if needed
• When appropriate, susceptibility tests will be performed on the isolated bacteria

IV. Statistical analysis:

• Determination of sensitivity, specificity, positive predicted value, negative predicted value of the different sampling methods
• Preference for one method over another: crosstabs, Chi-square test
• Pain experienced with any method (Yes/No): Student's t-test
• VAS-scale pain per method: ANOVA

Inclusion Criteria:

• Both expectorating and non-expectorating CF patients with confirmed diagnosis (sweat test / genotyping)
• All ages
• Attending the UZ Brussel CF Clinic
• Written informed consent from each participant and/or his parents or legal guardian

Exclusion Criteria:

• CF patients who underwent lung transplantation
• Denial of participation to the study

CF patients

All data will be analysed and shared as an original article, individual data will only be available upon motivated request