Introduction: Airway colonisation with Aspergillus fumigatus increases with age in CF, however its significance in lung disease progression remains uncertain. Molecular methods provide a dynamic approach in characterising the CF airway microbiome in relation to fungal culture (FC) positivity.

Objectives: To characterise the change in bacterial and fungal microbiota in relation to fungal airway colonisation.

Methods: A prospective, single-centre longitudinal study over a six-year period, including paediatric and adult CF patients. Annual spontaneous and induced sputum samples were collected.

Results: Seventy patients provided 235 respiratory samples. Median age at recruitment was 17 years (range 0.5?59 years) with a median percent predicted FEV₁ of 88% (range 26?135%). 60% of participants were FC positive, of which 3% were persistently colonised. 68% of the FC naïve group were aged <15 years. FC positivity was independently associated with reduced bacterial diversity. Streptococcus and Pseudomonas were the predominant taxa across both FC groups. Rare bacterial and fungal taxa were more abundant within the FC negative cohort. Participants with persistent fungal airway colonisation displayed differences in bacterial and fungal community structure, and demonstrated a steeper decline in fungal diversity over time. This cohort also demonstrated a predominance of Candida paraspsilosis, C. albicans and A. fumigatus.

Conclusion: Chronic Aspergillus fumigatus airway colonisation is associated with a change in bacterial and fungal community structure and diversity in CF. Further comparative studies are needed to understand the impact of fungal airway colonisation on the post modulator CF airway microbiome.