Metagenomic Sequencing of Matched Tracheal Aspirate and Mini-BAL Specimens

Accurate and informative microbiologic testing is essential for guiding diagnosis and management of pneumonia in critically ill patients. Sampling of tracheal aspirate (TA) is less invasive compared to mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach, despite concerns of inferiority due to increased potential for oropharyngeal contamination. Advancements in metagenomic next generation sequencing (mNGS) now permit assessment of airway microbiota at a resolution previously unachievable using culture-based methods. Here we leverage mNGS to quantitatively assess microbial composition in paired mBAL and TA specimens and find moderate differences that resolve in the setting of bacterial pneumonia.