title: Association of sputum microbiota profiles with severity of community-acquired pneumonia in children.
abstract: Competitive interactions among bacteria in the respiratory tract microbiota influence which species can colonize and potentially contribute to pathogenesis of community-acquired pneumonia (CAP). However, understanding of the role of respiratory tract microbiota in the clinical course of pediatric CAP is limited.
  
  
  
  We sought to compare microbiota profiles in induced sputum and nasopharyngeal/oropharyngeal (NP/OP) samples from children and to identify microbiota profiles associated with CAP severity. We used 16S ribosomal RNA sequencing and several measures of microbiota profiles, including principal component analysis (PCA), to describe the respiratory microbiota in 383 children, 6 months to <18 years, hospitalized with CAP. We examined associations between induced sputum and NP/OP microbiota profiles and CAP severity (hospital length of stay and intensive care unit admission) using logistic regression.
  
  
  
  Relative abundance of bacterial taxa differed in induced sputum and NP/OP samples. In children 6 months to < 5 years, the sputum PCA factor with high relative abundance of Actinomyces, Veillonella, Rothia, and Lactobacillales was associated with decreased odds of length of stay ≥ 4 days [adjusted odds ratio (aOR) 0.69; 95 % confidence interval (CI) 0.48-0.99]. The sputum factor with high relative abundance of Haemophilus and Pasteurellaceae was associated with increased odds of intensive care unit admission [aOR 1.52; 95 % CI 1.02-2.26]. In children 5 to < 18 years, the sputum factor with high relative abundance of Porphyromonadaceae, Bacteriodales, Lactobacillales, and Prevotella was associated with increased odds of length of stay ≥ 4 days [aOR 1.52; 95 % CI 1.02-2.26]. Taxa in NP/OP samples were not associated with CAP severity.
  
  
  
  Certain taxa in the respiratory microbiota, which were detected in induced sputum samples, are associated with the clinical course of CAP.
authors.affiliation: Yale School of Public Health, New Haven, CT, USA. melinda.pettigrew@yale.edu.|Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, LEPH 720, New Haven, CT, 06515, USA. melinda.pettigrew@yale.edu.
authors.forename: Melinda M
authors.initials: MM
authors.lastname: Pettigrew
authors.affiliation: Yale School of Public Health, New Haven, CT, USA.
authors.forename: Janneane F
authors.initials: JF
authors.lastname: Gent
authors.affiliation: Yale School of Medicine, New Haven, CT, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Kong
authors.affiliation: Yale School of Public Health, New Haven, CT, USA.
authors.forename: Martina
authors.initials: M
authors.lastname: Wade
authors.affiliation: St. Jude Children's Research Hospital, Memphis, TN, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Gansebom
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Anna M
authors.initials: AM
authors.lastname: Bramley
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Seema
authors.initials: S
authors.lastname: Jain
authors.affiliation: University of Tennessee Health Science Center, Memphis, TN, USA.
authors.forename: Sandra L R
authors.initials: SL
authors.lastname: Arnold
authors.affiliation: St. Jude Children's Research Hospital, Memphis, TN, USA.|University of Tennessee Health Science Center, Memphis, TN, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: McCullers
mesh_terms: D000293:Adolescent; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D002648:Child; D002675:Child, Preschool; D017714:Community-Acquired Infections / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis; D005260:Female; D006801:Humans; D007223:Infant; D007362:Intensive Care Units / Q000706:statistics & numerical data; D007902:Length of Stay; D016015:Logistic Models; D008297:Male; D064307:Microbiota / Q000235:genetics; D009305:Nasopharynx / Q000382:microbiology; D016017:Odds Ratio; D009960:Oropharynx / Q000382:microbiology; D011014:Pneumonia / Q000382:microbiology*; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D013183:Sputum / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Children; Microbial communities; Microbiota; Pneumonia; Respiratory tract