title: Concordance between upper and lower airway microbiota in infants with cystic fibrosis.
abstract: Nasopharyngeal and oropharyngeal samples are commonly used to direct therapy for lower respiratory tract infections in non-expectorating infants with cystic fibrosis (CF).We aimed to investigate the concordance between the bacterial community compositions of 25 sets of nasopharyngeal, oropharyngeal and bronchoalveolar lavage (BAL) samples from 17 infants with CF aged ∼5 months (n=13) and ∼12 months (n=12) using conventional culturing and 16S-rRNA sequencing.Clustering analyses demonstrated that BAL microbiota profiles were in general characterised by a mixture of oral and nasopharyngeal bacteria, including commensals likeStreptococcus,Neisseria,VeillonellaandRothiaspp. and potential pathogens likeStaphylococcus aureus,Haemophilus influenzaeandMoraxellaspp. Within each individual, however, the degree of concordance differed between microbiota of both upper respiratory tract niches and the corresponding BAL.The inconsistent intra-individual concordance between microbiota of the upper and lower respiratory niches suggests that the lungs of infants with CF may have their own microbiome that seems seeded by, but is not identical to, the upper respiratory tract microbiome.
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
authors.forename: Sabine M P J
authors.identifier: 0000-0002-4927-5692
authors.initials: SM
authors.lastname: Prevaes
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.|Both authors contributed equally.
authors.forename: Wouter A A
authors.initials: WA
authors.lastname: de Steenhuijsen Piters
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.|Both authors contributed equally.
authors.forename: Karin M
authors.initials: KM
authors.lastname: de Winter-de Groot
authors.affiliation: Dept of Paediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Centre, Rotterdam, The Netherlands.
authors.forename: Hettie M
authors.initials: HM
authors.lastname: Janssens
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
authors.forename: Gerdien A
authors.initials: GA
authors.lastname: Tramper-Stranders
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
authors.forename: Mei Ling J N
authors.initials: ML
authors.lastname: Chu
authors.affiliation: Dept of Paediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Centre, Rotterdam, The Netherlands.
authors.forename: Harm A
authors.initials: HA
authors.lastname: Tiddens
authors.affiliation: Dept of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands.
authors.forename: Mireille
authors.initials: M
authors.lastname: van Westreenen
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
authors.forename: Cornelis K
authors.initials: CK
authors.lastname: van der Ent
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.
authors.forename: Elisabeth A M
authors.initials: EA
authors.lastname: Sanders
authors.affiliation: Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands d.bogaert@umcutrecht.nl.
authors.forename: Debby
authors.initials: D
authors.lastname: Bogaert
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D001424:Bacterial Infections / Q000382:microbiology*; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology; D003550:Cystic Fibrosis / Q000382:microbiology*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D064307:Microbiota; D009426:Netherlands; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012137:Respiratory System / Q000382:microbiology; D012141:Respiratory Tract Infections / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S