Oropharyngeal flora in healthy infants: observations and implications for cystic fibrosis care

UMMS Affiliation

Department of Laboratory Medicine; Department of Pediatrics; New England Newborn Screening Program

Publication Date


Document Type



Carrier State; Case-Control Studies; Cystic Fibrosis; Gram-Negative Aerobic Rods and Cocci; Gram-Positive Cocci; Humans; Infant; Infant, Newborn; Oropharynx; Reference Values


Allergy and Immunology | Pediatrics | Respiratory Tract Diseases


OBJECTIVE: The purpose of this preliminary study was to determine normal oropharyngeal flora in healthy, non-CF infants in order to help care givers better interpret culture results obtained from infants with CF.

METHODS: Oropharyngeal cultures were obtained from 104 healthy infants <12 months old. Cultures were obtained using the same methods as for CF patients and were inoculated onto routine CF culture media. Approximately 20 infants from each of 5 age groups>(0-2 days, 3 days to <3 >months, 3 months to <6 >months, 6 months to <9 months or 9 months to><1 >year) were included in the well child sample. In addition, we reviewed serial results of upper airway cultures obtained during the first year of life from 20 CF-affected infants whose diagnosis was suggested by newborn screening.

RESULTS: Well infants in the first 48 hr of life had very few pathogenic organisms found in their oropharyngeal cultures; 1/21 had S. aureus. Of the 83 samples from infants over 48 hr of age, we found that 27% (23/83) had S. aureus in their oropharyngeal cultures. Many infants had polymicrobial cultures. Eleven percent of culture samples had E. coli, E. cloacae, H. influenzae, or M. catarrhalis. Three of 83 cultures were positive for non-mucoid Ps. aeruginosa (3.6%), while 2 others were positive for Ps. putida.

CONCLUSION: Healthy infants can have multiple gram-negative and gram-positive organisms recovered from their oropharynx. S. aureus and enteric gram-negative organisms, including non-mucoid Ps. aeruginosa, can be found in the oropharynx of well children up to 1 year of age. Care should be taken to not over interpret the presence of some of these organisms in the oropharyngeal cultures of asymptomatic CF infants.

DOI of Published Version



Pediatr Pulmonol. 2009 May;44(5):497-502. Link to article on publisher's site

Journal/Book/Conference Title

Pediatric pulmonology

Related Resources

Link to Article in PubMed

PubMed ID