Early development of the airway microbiota in infants with cystic fibrosis

The pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood. We aimed to identify changes in the airway microbiota in infancy that could underpin deterioration and could potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening were followed up for up to two years. Throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits). Quantitative PCR and sequencing of the 16S rRNA bacterial gene was performed using the Illumina MiSeq. Data analyses were performed in QIIME and Phyloseq in R.