The effect of exacerbations on the airway microbiota in children with non-CF bronchiectasis

<b>Background:</b> Bronchiectasis is a significant health problem affecting New Zealand children. Bacteria are presumed to play a role in the development, progression and exacerbation of bronchiectasis. Culture independent methods are capable of detecting subtle shifts in bacterial composition which need to be defined further in children with exacerbations. <b>Aim:</b> To characterise the airway microbiota in children with bronchiectasis at the time of an acute exacerbation and following treatment. <b>Method:</b> Nasal swab and sputum samples were collected from children presenting with bronchiectasis exacerbations to the Starship Bronchiectasis Clinic. Samples were also obtained at the end of antibiotic treatment. Bacterial DNA was extracted and the V3-V4 region of the 16S rRNA gene was amplified and sequenced using Illumina MiSeq. The relative abundance of taxa and alpha diversity was calculated. <b>Result:</b> Substantial inter-patient variability was observed among the 28 children studied (median age 5.5years). At presentation Proteobacteria were the most abundant phyla in nasal and sputum samples (relative abundance 77% and 60% respectively). After antibiotic treatment the relative abundance of Proteobacteria was reduced in the nasal (55%) and sputum (39%) samples with Firmicutes becoming more abundant in the sputum (44%). <i>Moraxella</i> was the most abundant genera in the nasal samples. In sputum samples <i>Haemophilus</i> was the most abundant genera at the time of exacerbation (30%) which reduced to 17% after antibiotics. <b>Conclusion:</b> The airway microbiota in children with bronchiectasis exacerbations is dynamic with a reduction in Proteobacteria and <i>Haemophilus</i> following antibiotic treatment.