Background: Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables.
Methods: Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis.
Results: 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year.
Conclusions: Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
Competing Interests: Declaration of Competing Interest Dr. Harris reports grants from the Cystic Fibrosis Foundation during the conduct of the study Dr. Wagner has nothing to disclose Dr. Robertson has nothing to disclose Dr. Lingard has nothing to disclose Dr. Borowitz has nothing to disclose Dr. Leung reports other from Merck, grants and other from Gilead, grants from Abbvie, grants from CF Foundation, outside the submitted work Dr. Heltshe has nothing to disclose Dr. Ramsey has nothing to disclose Dr. Zemanick reports grants from Cystic Fibrosis Foundation, NIH/NCATS, NIH/NHLBI, Savara and Calithera Biosciences during the conduct of the study, grants and fees from Vertex Pharmaceuticals, Cystic Fibrosis Foundation outside the submitted work
(Copyright © 2023. Published by Elsevier B.V.)