79 Development of the upper respiratory tract microbiome was investigated longitudinally in cystic fibrosis infants and controls 0–6 months of age

Background Cystic Fibrosis (CF) is characterized by early damage of the lungs by infections. The responsible pathogens find their ecological niche in the upper respiratory tract (URT). Information on microbial colonization dynamics in the URT of CF infants is lacking. Objective To examine colonization dynamics of URT microbiota in CF infants over time. Methods Case-control study. Questionnaires and nasopharyngeal (NP) samples were collected monthly from 20 CF patients and 45 controls. We studied the dynamics of URT microbiota from 0–6 months of life by 16SrRNA-based sequencing. Results The bacterial density of URT microbiota is lower in CF infants compared to controls, and inversely correlated with antibiotic use. Also, the microbial community composition is significantly different between groups over the first 6 months of life. Where in CF infants the URT microbiota is initially predominated by Corynebacterium and Staphylococcus followed by Streptococcus and Moraxella, in controls Moraxella, Haemophilus and another Corynebacterium sp. predominate throughout the first 6 months. Multivariate analyses show significantly more Staphylococcus , Pseudomonas , Enterobacteriaceae and Bacillus spp. and less Moraxella, Haemophilus, Dolosigranulum and specific Corynebacterium spp. in CF infants vs. Controls. Antibiotic use is independently associated with increased carriage of Gram-negative bacteria and reduced carriage of non-pathogenic commensals. Conclusion CF infants have a significantly different development of URT microbiota compared to controls from birth on. This information may help to improve targeted therapy, and allows surveillance of ecological side effects of antibiotics.