LATE-BREAKING ABSTRACT: Symptomatic rhinovirus infections are associated with a lower diversity of the nasopharyngeal microbiota in infants

Background: Respiratory infections with Rhinovirus (RV) are very frequent in infancy and thought to be relevant for asthma development. Recently, an important role of the respiratory microbiota in chronic lung diseases has also been suggested. It thus seems useful to better understand a possible interaction of RV infections and the nasopharyngeal microbiome in infancy to fully appraise their respective roles in disease development. Methods: 32 unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 570) were taken; the microbiome was analysed by 16s rRNA pyrosequencing (454 technology) and 12 viruses were characterised by multiplex PCR. In weekly telephone interviews respiratory symptoms were recorded. The association between RV infections and the microbiome was assessed using multilevel multivariable regression analysis. Results: In contrast to asymptomatic RV colonization, symptomatic RV infections were associated with 0.4 units lower bacterial diversity (Shannon Diversity index) (95%-CI -0.6 to -0.2; p=0.001) and 10.6 units higher bacterial density (PCR concentration) (95%-CI 3.3 – 17.9; p=0.005) of the microbiota. This change persisted up to three weeks after an infection. Findings were robust after adjustment for age, season and other risk factors. Conclusion: Only symptomatic RV infections were associated with a change in bacterial density and diversity of the microbiota. This indicates an interaction between RV infections and the respiratory microbiota in early life, of possible importance for later disease development.