TY - JOUR
T1 - Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota
AU - Brown, Perry S.
AU - Pope, Christopher E.
AU - Marsh, Robyn L.
AU - Qin, Xuan
AU - McNamara, Sharon
AU - Gibson, Ronald
AU - Burns, Jane L.
AU - Deutsch, Gail
AU - Hoffman, Lucas R.
N1 - Publisher Copyright:
Copyright © 2014 by the American Thoracic Society
PY - 2014/9/1
Y1 - 2014/9/1
N2 - 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. Objectives: 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. Conclusions: 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.
AB - 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. Objectives: 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. Conclusions: 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.
KW - Cystic fibrosis
KW - Infection
KW - Lobectomy
KW - Microbiota
UR - http://www.scopus.com/inward/record.url?scp=84911888639&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84911888639&partnerID=8YFLogxK
U2 - 10.1513/AnnalsATS.201311-383OC
DO - 10.1513/AnnalsATS.201311-383OC
M3 - Article
C2 - 25072206
AN - SCOPUS:84911888639
SN - 2325-6621
VL - 11
SP - 1049
EP - 1055
JO - Annals of the American Thoracic Society
JF - Annals of the American Thoracic Society
IS - 7
ER -