Cystic fibrosis (CF) is the most common hereditary life-threatening condition in Belgium. Because of a dysfunctional cystic fibrosis transmembrane conductance regulator (CFTR) channel, chloride is unable to move to the cell surface and mucus becomes more viscous. Consequently, CF patients are not able to clear their lungs efficiently, and trapped bacteria can lead to chronic infection and inflammation of the lungs, and ultimately respiratory failure.

CF lung disease starts at birth due to muco-inflammatory processes and is associated with a significantly altered microbial colonization of the infant airways compared to infants without CF. Additionally, young children with CF suffer from viral infections as often as their healthy peers, but the episodes are more severe and often prolonged. Moreover, frequent viral infections in children with CF contribute towards a more pathogenic airway microbiome at a young age. Although this link has been previously reported, the exact mechanisms by which this occurs need to be elucidated.

A pulmonary exacerbation in CF is characterized by an increase in respiratory symptoms, general symptoms and a decline in lung function. Most young children with CF suffer from a mean of 4 exacerbations per year for which antibiotics are prescribed. Despite the current novel therapies in CF, treatment of respiratory infections stay relevant and is a greater challenge with increasing survival.

The key objective of this study is to gain insights into the mechanisms by which viral infections leading to pulmonary exacerbations induce a more pathogenic microbiome in young children with CF.

About forty participants will be recruited at the paediatric CF clinic of the Antwerp University Hospital. Inclusion criteria are an age of less than 5 years and a diagnosis of CF. There are no exclusion criteria. Duration of the study is 1 year to cover for seasonality of clinical symptoms. Study visits are scheduled at 3-month intervals corresponding with the regular follow up, or unscheduled during an acute pulmonary exacerbation. From all participants, two oropharyngeal swabs (for microbiome analysis and for immunological/mucin analysis) will be collected at set time points. For the linking of the laboratory data to the clinical characteristics, we will examine demographics, environmental exposures, and disease markers of CF. Next to the collection of the oropharyngeal swabs, a history, physical examination, and technical investigations will be performed at the study visits.

Inclusion Criteria:

• Diagnosis of cystic fibrosis

Exclusion Criteria:

• None

Participants will be recruited at the paediatric cystic fibrosis clinic of the Antwerp University Hospital. Inclusion criteria are an age of less than 5 years and a diagnosis of cystic fibrosis (confirmed by sweat chloride levels > 60 mmol/L and/or two pathogenic CFTR variants).