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Updated: Jul 31, 2025
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Published on: August 3, 2021
Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen
J Kirk Harris1, Brandie D Wagner2, Charles E Robertson3
1Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
Insights
The upper airway microbiota in infants with cystic fibrosis (CF) changes significantly with age. Clinical factors like antibiotics had less impact on the oropharyngeal microbiome during the first year of life.
Area of Science:
- Microbiology
- Pediatrics
- Genetics
Background:
- Upper airway microbiota changes may influence early cystic fibrosis (CF) disease.
- Investigating early airway microbiota in CF infants is crucial.
Purpose of the Study:
- To assess oropharyngeal microbiota in CF infants during their first year.
- To explore relationships between microbiota, growth, and antibiotic use.
Main Methods:
- Longitudinal oropharyngeal swabs from 205 CF infants (1-12 months).
- 16S rRNA gene sequencing for bacterial composition and qPCR for load.
- Statistical analysis including mixed models and canonical correlation.
Main Results:
- Microbiota alpha diversity increased with age, minimally affected by antibiotics.
- Community composition strongly correlated with age, moderately with antibiotics and feeding.
- Streptococcus decreased, while Neisseria and other taxa increased over the first year.
Conclusions:
- Infant age is a primary driver of oropharyngeal microbiota changes in CF.
- Clinical variables, including antibiotics, had less influence than age in the first year.
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.
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