Fig. 3: BAL pathogen detection.

a, Left: dot plots of common community-transmitted respiratory viruses (left), herpesviruses (middle) and all other viruses (right) detected in the cohort, plotted according to microbial mass (x axis) and microbiome dominance (y axis). Right: bar chart comparing viral detection across the four BAL clusters according to hospital tests and metagenomic sequencing. b, Left: all H. influenzae, S. aureus and S. pneumoniae detected in the cohort were plotted, with the dashed lines indicating the cutoffs of mass ≥10 pg and bacterial dominance ≥20%. Taxa above these cutoffs are shown in the upper-right quadrant (shaded in yellow) to indicate outliers within the cohort. Right: bar chart comparing potentially pathogenic bacteria detected across the four BAL clusters according to hospital tests and metagenomic sequencing. c, Left: all microorganisms detected in the BAL of three patients are shown, with the arrows indicating fungi present in high quantities. Right: bar chart comparing potentially pathogenic eukaryotes detected across the four BAL clusters according to hospital tests and metagenomic sequencing.