M MIKA¹, I KORTEN², W QI³, N REGAMEY², U FREY⁴, C CASAULTA², P LATZIN², M HILTY¹, SCILD STUDY GROUP<sup>5

1</sup>Institute for Infectious Diseases, University of Bern, Bern, Switzerland, ²Division of Respiratory Medicine, Department of Pediatrics, Inselspital and University of Bern, Bern, Switzerland, ³Functional Genomics Center, Swiss Federal Institute of Technology Zurich/ University of Zurich, Zurich, Switzerland, ⁴University Children`s Hospital (UKBB), Basel, Switzerland, ⁵SCILD Study Group, Switzerland

Background: Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis (CF). However, there is a lack of information regarding the microbial composition of the respiratory tract in infants with CF. Our aim was to perform an in-depth characterization of the upper respiratory tract microbiota in infants with CF, who were followed throughout their first year of life.
Methods: Microbiota characterization was performed using 16S rRNA pyrosequencing of nasal swabs (n=461) collected biweekly from 30 infants with CF. Data was compared to an age-matched cohort of 47 healthy infants (n=872 samples). Additionally, the influence of antibiotic therapy on the microbiota of infants with CF was investigated.
Results: The microbiota of infants with CF differed compositionally from the microbiota of healthy infants (permutational MANOVA, P=0.001). This was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae, which persisted during antibiotic therapy. The mean relative abundance of Moraxellaceae decreased significantly, while a spectrum of various bacterial families emerged (multivariable linear regression model, P=0.03 and <0.001, respectively). There was also an increase in bacterial diversity (Shannon Diversity Index) upon antibiotic administration (P=0.02).
Conclusions: This study describes compositional differences in the microbiota of CF infants and healthy controls, and the disordering of the microbiota upon antibiotic administration. These findings improve our understanding of the microbiota and its manipulation in the prevention of early disease progression in infants with CF.