Culture-independent analysis of pediatric bronchoalveolar lavage specimens

Philip Zachariah, Chanelle Ryan, Sruti Nadimpalli, Gina Coscia, Michelle Kolb, Hannah Smith, Marc Foca, Lisa Saiman, Paul J. Planet

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Rationale: The clinical utility of culture-independent testing of pediatric BAL specimens is unknown. In addition, the variability of the pediatric pulmonary microbiome with patient characteristics is not well understood. Objectives: To compare testing with 16S rRNA gene–based sequencing to conventional cultures of BAL specimens in children Methods: Study subjects were not more than 22 years old and underwent BAL from May 2013 to August 2015 as part of clinical care. DNA extracted from BAL specimens was used for 16S rRNA gene–based analysis, and results were compared with routine cultures from the same samples. Indices of microbial diversity and relative taxon abundances were compared on the basis of subject characteristics (diagnosis and antibiotic use). Results: From 81 participants (male, 51%; median age, 9 yr), 89 samples were collected. The 16S rRNA genes of 77 samples (86.5%) from 70 subjects were successfully analyzed. These 70 subjects included 23 with cystic fibrosis, 19 who were immunocompromised, and 28 who were nonimmunocompromised. Of 68 organisms identified in culture, 16S rRNA gene–based analyses detected corresponding taxa in 66 (97.1%) and also identified potentially clinically significant organisms missed by cultures (e.g., Staphylococcus, Legionella, and Pseudomonas). Taxa that varied significantly with diagnosis and antibiotic use included Veillonella, Corynebacterium, Haemophilus, and Streptococcus. The microbiota of cystic fibrosis samples was less diverse. A “core” group of 15 taxa present in all three diagnosis groups was identified. Conclusions: Culture-independent analysis was concordant with routine cultures and showed the potential to detect noncultured pathogens. Although culture-independent testing identified relative changes in organism abundance associated with clinical characteristics, distinct microbiome profiles associated with disease states were not identified.

Original languageEnglish (US)
Pages (from-to)1047-1056
Number of pages10
JournalAnnals of the American Thoracic Society
Issue number9
StatePublished - Sep 2018
Externally publishedYes


  • Bronchoalveolar lavage
  • Children
  • Microbiome

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine


Dive into the research topics of 'Culture-independent analysis of pediatric bronchoalveolar lavage specimens'. Together they form a unique fingerprint.

Cite this