• Cystic Fibrosis

Lung disease in cystic fibrosis (CF) is characterised by chronic airway infection and inflammation.1 Advances in sequencing technology have expanded our understanding of airway infection in CF, with complex polymicrobial bacterial communities frequently detected along with typical CF bacterial pathogens such as Pseudomonas aeruginosa.2 Investigations of CF airway microbiota rely on interrogation of airway samples, most commonly expectorated sputum. Young children with CF rarely expectorate sputum spontaneously, leaving clinicians with the option of oropharyngeal swabs which may not reflect lower airway bacteriology or bronchoalveolar lavage fluid (BALF) collection which requires an invasive procedure with anaesthesia.3

Microbial diversity, a measure that takes into account the number of different bacterial taxa and the relative amount of each taxa detected within a community, has been associated with disease status in CF with lower diversity associated with lower lung function, the presence of pathogenic bacteria and increased airway inflammation.4–6 Microbial analyses of CF samples from younger, healthier patients often show highly diverse bacterial communities,7 whereas lung explants from patients with end-stage lung disease reveal extremely low diversity with typically only one or two pathogenic bacteria detectable.8 The transition from a diverse community to one dominated by CF pathogens likely begins early, but difficulty with airway sampling hinders our ability to study changes in young children.

Lung disease begins early in CF with airway infection, inflammation and bronchiectasis, evident as early as 3 months.9 Airway inflammation is tightly linked to development of bronchiectasis, as the presence of BALF neutrophil elastase (NE) in early infancy is strongly associated with bronchiectasis in young children. Airway inflammation is also increased in the presence of known CF pathogens such as P. aeruginosa and Staphylococcus aureus, with less inflammation seen with bacteria detected by molecular approaches but not on conventional routine culture. …