Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis

Sabine M P J Prevaes, Karin M de Winter-de Groot, Hettie M Janssens, Wouter A A de Steenhuijsen Piters, Gerdien A Tramper-Stranders, Anne L Wyllie, Raiza Hasrat, Harm A Tiddens, Mireille van Westreenen, Cornelis K. van der Ent, Elisabeth A M Sanders, Debby Bogaert

Research output: Contribution to journalArticleAcademicpeer-review


RATIONALE: Cystic Fibrosis (CF) is characterized by early structural lung disease caused by pulmonary infections. The nasopharynx of infants is a major ecological reservoir of potential respiratory pathogens.

OBJECTIVE: To investigate the development of nasopharyngeal microbiota profiles in infants with CF compared with those of healthy controls during the first 6 months of life.

METHODS: We conducted a prospective cohort study, collecting questionnaires and 324 nasopharynx samples of 20 CF infants and 45 age-matched healthy controls from diagnosis. Microbiota profiles were characterized by 16S-rRNA-based sequencing.

MAIN RESULTS: We observed significant differences in microbial community composition (PERMANOVA, p<0.0002) and development between groups; in infants with CF, early Staphylococcus aureus and to a lesser extent, Corynebacterium spp. and Moraxella spp. dominance was followed by a switch to Streptococcus mitis predominance after 3 months of age, versus Moraxella spp. enrichment throughout the first 6 months of life in controls. In a multivariate analysis S. aureus, S. mitis, Corynebacterium accolens and bacilli. were significantly more abundant in CF whereas Moraxella spp., Corynebacterium pseudodiphtericum/propinquum and Haemophilus influenzae were significantly more abundant in controls, after correction for age, antibiotic use, and respiratory symptoms. Antibiotic use was independently associated with increased colonization of gram-negative bacteria such as Burkholderia and Enterobacteriacae spp. and reduced colonization of potential beneficial commensals.

CONCLUSION: From diagnosis onwards, we observed distinct patterns of nasopharyngeal microbiota development in infants with CF under 6 months of age versus controls and a marked effect of antibiotic therapy towards a gram-negative microbial composition.

Original languageEnglish
JournalAmerican Journal of Respiratory and Critical Care Medicine
Early online date2015
Publication statusPublished - 2015


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