Microbiome Profiling of Endotracheal Tube Aspirates Versus Direct Lower Airway Sampling in Intubated Patients

Endotracheal aspirates are commonly used for microbiological studies of the respiratory tract in intubated patients and involve sampling through established endotracheal tubes using in-line suction catheters. These catheters can develop biofilms that may confound results. Sequence-based microbiome profiling enables comprehensive, quantitative enumeration of microbial communities. We applied bacterial 16S rRNA gene sequencing to airway bacterial communities sampled through standard Endotracheal aspirates. A Gold standard sample was acquired through a fresh tracheostomy tube in long-term Intubated patients scheduled to undergo percutaneous bedside tracheostomy. We then interrogated the endotracheal tube and suction catheter biofilm which were collected antecedent to the tracheostomy. We also acquired a series of new endotracheal aspirates that we collected at various timepoints following the tracheostomy. We found that endotracheal aspirates through established endotracheal tubes closely resembled the airway microbiome sampled through freshly placed tracheostomies. Endotracheal tube and suction catheter biofilms also closely resembled cognate ETA and fresh trach communities. Our study provides molecular evidence supporting the use of ETAs for microbiology of the lower respiratory tract in intubated patients and, furthermore, suggests reciprocal relationships between respiratory device biofilms and the airway microbiome.