Comparison of Pairwise Samples of Endotracheal Aspirate and Bronchoalveolar Lavage for Microbial Analysis in Critically ill Patients

Introduction: Bronchoalveolar lavage (BAL) is considered as gold-standard for the characterization of the lung microbiome. The aim of this study was to elucidate the applicability of less-invasive sampling by endotracheal aspirate (ETA) compared with BAL for the analysis of respiratory microorganisms in critically ill patients who required mechanical ventilation. Methods: Pairwise samples of ETA and BAL obtained from mechanically ventilated patients at our intensive care units were collected anonymously for testing the accuracy of ETA compared to BAL. Bacterial community structure was assessed by a metabarcoding approach based on 16S rRNA gene sequencing in ETA and BAL samples. Results: In total, 13 samples of each, BAL and ETA, were collected from 13 critically ill patients. No differences between BAL and ETA were found for alpha diversity based on species richness (p=0.77), Shannon diversity (p = 0.41), Simpson index (p = 0.85) and evenness (p = 0.98). Overall, BAL and ETA samples demonstrated strong taxonomic concordance at the levels of bacterial phyla and genera but differed distinctly at the amplicon sequence variants (ASV) level. Conclusion: In an unselected cohort of mechanically ventilated patients, BAL and ETA samples exhibited profound resemblance at higher taxonomic ranks, with increasing divergence observed at finer taxonomic resolutions. Our findings may facilitate guidance towards the reliability of non-invasive ETA as a valuable approach for clinical studies investigating the lung microbiome.