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Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota

Brown, Perry S., Pope, Christopher E., Marsh, Robyn L., Qin, Xuan, McNamara, Sharon, Gibson, Ronald, Burns, Jane L., Deutsch, Gail and Hoffman, Lucas R. (2014). Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota. Annals of the American Thoracic Society,11(7):1049-1055.

Document type: Journal Article
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IRMA ID 84473293xPUB6
Title Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota
Author Brown, Perry S.
Pope, Christopher E.
Marsh, Robyn L.
Qin, Xuan
McNamara, Sharon
Gibson, Ronald
Burns, Jane L.
Deutsch, Gail
Hoffman, Lucas R.
Journal Name Annals of the American Thoracic Society
Publication Date 2014
Volume Number 11
Issue Number 7
ISSN 2325-6621   (check CDU catalogue open catalogue search in new window)
Start Page 1049
End Page 1055
Total Pages 7
Place of Publication United States of America
Publisher American Thoracic Society
HERDC Category C1 - Journal Article (DIISR)
Abstract Rationale: The airways of people with cystic fibrosis (CF) are chronically infected with a variety of bacterial species. Although routine culture methods are usually used to diagnose these infections, culture-independent, DNA-based methods have identified many bacterial species in CF respiratory secretions that are not routinely cultured. Many prior culture-independent studies focused either on microbiota in explanted CF lungs, reflecting end-stage disease, or those in oropharyngeal swabs, which likely sample areas in addition to the lower airways. Therefore, it was unknown whether the lower airways of children with CF, well before end-stage but with symptomatic lung disease, truly contained diverse microbiota.

To define the microbiota in the diseased lung tissue of a child who underwent lobectomy for severe, localized CF lung disease.

Methods: After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial ribosomal RNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.

Measurements and Main Results:
This analysis identified diverse, and anatomically heterogeneous, bacterial populations in the lung tissue that contained both culturable and nonculturable species, including abundant Haemophilus, Ralstonia, and Propionibacterium species. Routine clinical cultures identified only Staphylococcus aureus, which represented only a small fraction of the microbiota found by sequencing. Microbiota analysis of an intraoperative oropharyngeal swab identified predominantly Streptococcus species. The oropharyngeal findings therefore represented the lung tissue microbiota poorly, in agreement with findings from earlier studies of oropharyngeal swabs in end-stage disease.

These results support the concept that diverse and spatially heterogeneous microbiota, not necessarily dominated by “traditional CF pathogens,” are present in the airways of young, symptomatic children with early CF lung disease.

Keywords Cystic fibrosis
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