Microbiome Profiling Demonstrates Concordance of Endotracheal Tube Aspirates With Direct Lower Airway Sampling in Intubated Patients

Abstract

Background: Endotracheal aspirates (ETAs) are widely used for microbiologic studies of the respiratory tract in intubated patients. However, they involve sampling through an established endotracheal tube using suction catheters, both of which can acquire biofilms that may confound results.

Research question: Does standard clinical ETA in intubated patients accurately reflect the authentic lower airway bacterial microbiome?

Study design and methods: Comprehensive quantitative bacterial profiling using 16S rRNA V1-V2 gene sequencing was applied to compare bacterial populations captured by standard clinical ETA vs contemporaneous gold standard samples acquired directly from the lower airways through a freshly placed sterile tracheostomy tube. The study included 13 patients undergoing percutaneous tracheostomy following prolonged (median, 15 days) intubation. Metrics of bacterial composition, diversity, and relative quantification were applied to samples.

Results: Pre-tracheostomy ETAs closely resembled the gold standard immediate post-tracheostomy airway microbiomes in bacterial composition and community features of diversity and quantification. Endotracheal tube and suction catheter biofilms also resembled cognate ETA and fresh tracheostomy communities.

Interpretation: Unbiased molecular profiling shows that standard clinical ETA sampling has good concordance with the authentic lower airway microbiome in intubated patients.

Keywords: airway sampling; critical illness; endotracheal aspirate; lung microbiome; tracheostomy.