Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability

• Published in: Journal of Bacteriology 2012-09, Vol.194 (17), p.4709-4717
• Main Authors: Filkins, L. M, Hampton, T. H, Gifford, A. H, Gross, M. J, Hogan, D. A, Sogin, M. L, Morrison, H. G, Paster, B. J, O'Toole, G. A
• Format: Article
• Language: English
• Subjects: Adult; Anti-Bacterial Agents - administration & dosage; Anti-Bacterial Agents - therapeutic use; Bacteria; bacterial communities; Bacteriology; Base Sequence; Biological and medical sciences; Cystic fibrosis; Cystic Fibrosis - microbiology; DNA; DNA, Bacterial - genetics; Female; Fundamental and applied biological sciences. Psychology; genes; Genetic diversity; Humans; Lung - microbiology; Lungs; Male; Metagenome; microarray technology; Microbiology; Middle Aged; Miscellaneous; mouth; patients; Polymerase chain reaction; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Pseudomonas aeruginosa - isolation & purification; quantitative polymerase chain reaction; ribosomal RNA; RNA, Ribosomal, 16S - genetics; sequence analysis; Sequence Analysis, DNA; Sputum - microbiology; Streptococcus - classification; Streptococcus - genetics; Streptococcus - isolation & purification; Streptococcus milleri; Streptococcus parasanguinis; Streptococcus salivarius; tobramycin; Tobramycin - administration & dosage; Tobramycin - therapeutic use; Young Adult
• ISSN: 0021-9193; 1098-5530; 1067-8832
• DOI: 10.1128/JB.00566-12

Diverse microbial communities chronically colonize the lungs of cystic fibrosis patients. Pyrosequencing of amplicons for hypervariable regions in the 16S rRNA gene generated taxonomic profiles of bacterial communities for sputum genomic DNA samples from 22 patients during a state of clinical stability (outpatients) and 13 patients during acute exacerbation (inpatients). We employed quantitative PCR (qPCR) to confirm the detection of Pseudomonas aeruginosa and Streptococcus by the pyrosequencing data and human oral microbe identification microarray (HOMIM) analysis to determine the species of the streptococci identified by pyrosequencing. We show that outpatient sputum samples have significantly higher bacterial diversity than inpatients, but maintenance treatment with tobramycin did not impact overall diversity. Contrary to the current dogma in the field that Pseudomonas aeruginosa is the dominant organism in the majority of cystic fibrosis patients, Pseudomonas constituted the predominant genera in only half the patient samples analyzed and reported here. The increased fractional representation of Streptococcus in the outpatient cohort relative to the inpatient cohort was the strongest predictor of clinically stable lung disease. The most prevalent streptococci included species typically associated with the oral cavity (Streptococcus salivarius and Streptococcus parasanguis) and the Streptococcus milleri group species. These species of Streptococcus may play an important role in increasing the diversity of the cystic fibrosis lung environment and promoting patient stability.