• John E McGinniss, Jevon Graham-Wooten, Samantha A Whiteside, Ayannah S Fitzgerald, Layla A Khatib, Kevin C Ma, David M DiBardino, Andrew R Haas, Fredric D Bushman, Barry D Fuchs, and Ronald G Collman.
• Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.
• Chest. 2024 Jun 1; 165 (6): 141514201415-1420.

BackgroundEndotracheal 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 QuestionDoes standard clinical ETA in intubated patients accurately reflect the authentic lower airway bacterial microbiome?Study Design And MethodsComprehensive 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.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.InterpretationUnbiased molecular profiling shows that standard clinical ETA sampling has good concordance with the authentic lower airway microbiome in intubated patients.Copyright © 2024 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

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