title: Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods.
abstract: BACKGROUND
  Oropharyngeal (OP) swabs and induced sputum (IS) are used for airway bacteria surveillance in nonexpectorating children with cystic fibrosis (CF). Molecular analyses of these airway samples detect complex microbial communities. However, the optimal noninvasive sampling approach for microbiota analyses and the clinical relevance of microbiota, particularly its relationship to airway inflammation, is not well characterized.
  
  
  OBJECTIVE
  The goals of this study were to compare molecular analyses of concurrently collected saliva, OP swabs, IS, and expectorated sputum (ES) from children with CF and to determine the association between microbiota, lung function, and airway inflammation.
  
  
  METHODS
  Saliva, OP swabs, IS, and ES were collected from 16 children with CF. Spirometry was performed.
  
  
  RESULTS
  Respiratory and saliva samples (n = 61) were sequenced for bacterial microbial communities, and total and CF-specific bacterial quantitative PCR assays were performed. Airway samples underwent conventional culture for CF-specific pathogens. Neutrophil elastase, IL-1β, IL-1ra, IL-6, Il-8, TNF-α, and vascular endothelial growth factor were measured in ES and IS. Sequencing results from individual subjects were similar across samples, with greater between-subject than within-subject variation. However, Pseudomonas and Staphylococcus were detected in higher relative abundance from lower airways (ES and IS) compared with paired upper airway samples (OP and saliva). Pseudomonas, Staphylococcus, and Enterobacteriaceae correlated with increased airway inflammation. Divergence between microbiota in upper airway compared with lower airway samples, indicating greater differences between communities, was associated with increased sputum neutrophil elastase.
  
  
  CONCLUSIONS
  Bacteria detected in IS samples resemble ES samples, whereas OP samples may underrepresent bacteria associated with airway inflammation. Divergence of lower airway communities from upper airway was associated with airway inflammation and may portend disease progression.
authors.affiliation: 1 Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado.
authors.forename: Edith T
authors.initials: ET
authors.lastname: Zemanick
authors.forename: Brandie D
authors.initials: BD
authors.lastname: Wagner
authors.forename: Charles E
authors.initials: CE
authors.lastname: Robertson
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Stevens
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Szefler
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Accurso
authors.forename: Scott D
authors.initials: SD
authors.lastname: Sagel
authors.forename: J Kirk
authors.initials: JK
authors.lastname: Harris
mesh_terms: D000293:Adolescent; D002648:Child; D003550:Cystic Fibrosis / Q000276:immunology / Q000382:microbiology* / Q000503:physiopathology; D016207:Cytokines / Q000276:immunology*; D004269:DNA, Bacterial / Q000032:analysis*; D004755:Enterobacteriaceae / Q000235:genetics / Q000302:isolation & purification; D004756:Enterobacteriaceae Infections / Q000276:immunology / Q000382:microbiology; D005260:Female; D006801:Humans; D007249:Inflammation; D008297:Male; D064307:Microbiota / Q000235:genetics / Q000276:immunology; D009960:Oropharynx / Q000276:immunology / Q000382:microbiology*; D011549:Pseudomonas / Q000235:genetics / Q000302:isolation & purification; D011552:Pseudomonas Infections / Q000276:immunology / Q000382:microbiology; D012141:Respiratory Tract Infections / Q000276:immunology / Q000382:microbiology; D012463:Saliva / Q000276:immunology / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013147:Spirometry; D013183:Sputum / Q000276:immunology / Q000382:microbiology*; D013203:Staphylococcal Infections / Q000276:immunology / Q000382:microbiology; D013210:Staphylococcus / Q000235:genetics / Q000302:isolation & purification; D055815:Young Adult
chemical_list: D016207:Cytokines; D004269:DNA, Bacterial
keywords: DNA sequencing; bacterial infection; microbiome; oropharyngeal swab; sputum