Mapping the respiratory microbiome in intubated children over time

Area of Science:

• Pediatric critical care medicine
• Microbiology and infectious diseases
• Genomics and bioinformatics

Background:

• Critically ill children requiring intubation frequently receive empirical antibiotics.
• This practice contributes to antibiotic overuse and challenges antimicrobial stewardship.
• Opportunistic pathogens are often present in airways, complicating treatment decisions.

Purpose of the Study:

• To investigate if prior lung disease increases opportunistic pathogens in children's airways.
• To prospectively profile tracheal aspirate (TA) microbiome in intubated children.
• To compare microbiome composition between children with and without prior lung disease.

Main Methods:

• Longitudinal tracheal aspirate (TA) samples collected from 13 pediatric intensive care unit patients.
• Analysis using 16S rDNA sequencing and conventional cultures.
• Correlation with patient demographics and clinical data from electronic medical records.

Main Results:

• Identified 98 bacterial genera, with Pseudomonas and Streptococcus dominating.
• Significant inter-patient variation in TA microbiome structure observed.
• Patient identity, not clinical category or time since intubation, was a key determinant of microbiome variation.

Conclusions:

• Substantial inter-patient variability in airway microbiome limits the impact of clinical factors.
• Discrepancies noted between culture and sequencing for certain bacteria (e.g., Streptococcus).
• Future large-scale studies should consider antibiotic exposure and host factors for targeted pediatric respiratory infection management.