title: Nasopharyngeal microbiota in infants with acute otitis media.
abstract: BACKGROUND
  Interspecies interactions of the nasopharyngeal microbiota are likely to be involved in the pathogenesis of acute otitis media (AOM). Capturing the breadth of microbial interactions requires a detailed description of the microbiota during health and AOM.
  
  
  METHODS
  The nasopharyngeal microbiota of 163 infants with (n = 153) or without (n = 10) AOM was characterized using nasopharyngeal swabs and multiplexed pyrosequencing of 16S rRNA. Nasopharyngeal swab specimens were collected during 4 winter seasons from 2004 through 2010 for infants with AOM and during 2010 for controls.
  
  
  RESULTS
  Fifty-eight bacterial families were identified, of which Moraxellaceae, Streptococcaceae, and Pasteurellaceae were the most frequent. Commensal families were less prevalent in infants with AOM than in controls. In infants with AOM, prior exposure to antimicrobials and administration of the heptavalent conjugated pneumococcal polysaccharide vaccine (PCV7) were also associated with reduced prevalence of distinct commensal families (Streptococcaceae and Corynebacteriaceae). In addition, antimicrobial exposure increased the prevalence of Enterobacteriaceae and the abundance of Pasteurellaceae. Other factors, such as age, sex, day care, and a history of recurrent AOM, did not influence the microbiota.
  
  
  CONCLUSIONS
  Infants' nasopharyngeal microbiota undergoes significant changes during AOM and after exposure to antimicrobials and PCV7, which is mainly attributable to reduced prevalence of commensal bacterial families.
authors.affiliation: Institute for Infectious Diseases, University of Berne, Berne, Switzerland. markus.hilty@ifik.unibe.ch
authors.forename: Markus
authors.initials: M
authors.lastname: Hilty
authors.forename: Weihong
authors.initials: W
authors.lastname: Qi
authors.forename: Silvio D
authors.initials: SD
authors.lastname: Brugger
authors.forename: Laurence
authors.initials: L
authors.lastname: Frei
authors.forename: Philipp
authors.initials: P
authors.lastname: Agyeman
authors.forename: Pascal M
authors.initials: PM
authors.lastname: Frey
authors.forename: Suzanne
authors.initials: S
authors.lastname: Aebi
authors.forename: Kathrin
authors.initials: K
authors.lastname: Mühlemann
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification*; D044822:Biodiversity; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D008969:Molecular Sequence Data; D009305:Nasopharynx / Q000382:microbiology*; D010033:Otitis Media / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S