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

Abstract

BackgroundEndotracheal aspirates (ETAs) are widely used for microbiological studies of the respiratory tract in intubated patients but involve sampling through an established endotracheal tube using suction catheters, both of which can acquire biofilms that may confound results. Research questionDoes standard clinical ETA in intubated patients accurately reflect the authentic lower airway bacterial microbiome? Study design and methodsWe applied comprehensive quantitative bacterial profiling using 16S rRNA V1V2 gene sequencing to compare bacterial populations captured by standard clinical ETA with contemporaneous “gold standard” samples acquired directly from the lower airways through a freshly-placed sterile tracheostomy tube in 13 patients undergoing percutaneous tracheostomy following prolonged (median 15 days) intubation. Metrics of bacterial composition, diversity and relative quantification were applied to samples. ResultsPre-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 demonstrates that standard clinical endotracheal aspirate sampling has good concordance with the authentic lower airway microbiome in intubated patients.