title: Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis.
abstract: Cystic fibrosis (CF) manifests in the lungs resulting in chronic microbial infection. Most morbidity and mortality in CF is due to cycles of pulmonary exacerbations-episodes of acute inflammation in response to the lung microbiome-which are difficult to prevent and treat because their cause is not well understood. We hypothesized that longitudinal analyses of the bacterial component of the CF lung microbiome may elucidate causative agents within this community for pulmonary exacerbations. In this study, 6 participants were sampled thrice-weekly for up to one year. During sampling, sputum, and data (antibiotic usage, spirometry, and symptom scores) were collected. Time points were categorized based on relation to exacerbation as Stable, Intermediate, and Treatment. Retrospectively, a subset of were interrogated via 16S rRNA gene sequencing. When samples were examined categorically, a significant difference between the lung microbiota in Stable, Intermediate, and Treatment samples was observed in a subset of participants. However, when samples were examined longitudinally, no correlations between microbial composition and collected data (antibiotic usage, spirometry, and symptom scores) were observed upon exacerbation onset. In this study, we identified no universal indicator within the lung microbiome of exacerbation onset but instead showed that changes to the CF lung microbiome occur outside of acute pulmonary episodes and are patient-specific.
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
authors.forename: Fiona J
authors.identifier: http://orcid.org/0000-0001-9165-4859
authors.initials: FJ
authors.lastname: Whelan
authors.affiliation: Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada.
authors.forename: Alya A
authors.initials: AA
authors.lastname: Heirali
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
authors.forename: Laura
authors.initials: L
authors.lastname: Rossi
authors.affiliation: Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada.|Department of Medicine, The University of Calgary, Calgary, Canada.
authors.forename: Harvey R
authors.initials: HR
authors.lastname: Rabin
authors.affiliation: Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada.|Department of Medicine, The University of Calgary, Calgary, Canada.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Parkins
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.|Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada.|Department of Medicine, McMaster University, Hamilton, Canada.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Surette
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology / Q000627:therapeutic use; D003550:Cystic Fibrosis / Q000188:drug therapy / Q000382:microbiology* / Q000503:physiopathology; D005260:Female; D006801:Humans; D008137:Longitudinal Studies; D008168:Lung / Q000187:drug effects / Q000382:microbiology*; D008297:Male; D064307:Microbiota / Q000187:drug effects; D013147:Spirometry
chemical_list: D000900:Anti-Bacterial Agents