Introduction: Among several factors, prior treatment with antibiotics may obscure the BAL culture result. We explored the possible gain of supplementary BAL microbiome analysis.

Methods: BAL specimens obtained at our institution (1.1.2021-31.12.2021) were analysed using combined 16S /18S rDNA gene amplicon based microbiome analysis to evaluate the presence of species-specific sequences. We compared with culture results. Clinical information included timing of antibiotic treatment, underlying disease, comorbidity, biochemistry and microbiology results.

Results: We collected 67 BAL samples from 65 patients; median age 67 (range 22-89). Patients were immunosuppressed in 9 cases (14%), antibiotics administered 72 hours before BAL in 20 cases (32%), intensive care unit (ICU) treatment in 2 cases (3%), active cancer diagnosis in 6 cases (10%), and an active haematological disease in 16 cases (25%).

BAL culture was positive in 40 cases (63%), 16S positive in 26 (39%), 18S positive in 7 (11%). In 3 cases (5%), normal pharyngeal flora DNA result was deemed not clinically significant. No parasitic DNA was found.

Negative culture with a positive 16S was found in 11 cases (16%), and with a positive 18S in 1 case (2%).

Among 40 patients with positive cultures, 21 (53%) had a negative 16S and 5 (13%) had a negative 18S; 15 (38%) had a positive 16S and 2 (5%) had a positive 18S. Agreement on an identified pathogen was found in 11 of 15 cases (65%). Differing pathogens were identified in 4 cases (24%).

Among cases with both a positive culture and a positive 16S/18S, additional pathogens were found on either technique in 3 cases (18%).

Conclusion: Microbiome analysis on BAL added clinically important results to standard cultures