Fig. 2

A AMR genes detected in the lower respiratory microbiome of critically ill patients. Composite results of DNA and RNA mNGS. AMR genes are listed in rows and are grouped by antimicrobial class. Each column represents a patient respiratory sample and is grouped by LRTI status. B AMR gene burden in the respiratory tract, measured by averaging sequencing depth across the AMR allele per million reads sequenced (dpM) in the respiratory microbiome did not differ between LRTI-positive patients and those with non-infectious acute respiratory illnesses. C The burden of AMR genes detected in the lower respiratory tract microbiome was greater in patients with hospital-onset LRTI versus those with either community-onset LRTI or no evidence of LRTI. Legend: depth = average sequencing depth across each AMR gene allele normalized per million reads sequenced. Legend: Bla = beta lactam; AGly = aminoglycoside; Fos = Fosfomycin; Flq = fluoroquinolone; Gly = glycopeptide; Mac/Lin/Str = macrolide, lincosamide, streptogramin; Phe = phenicol; Tet = tetracycline; Tmp-Sul = trimethoprim/sulfamethoxazole; depth = average sequencing depth across each AMR gene allele normalized per million reads sequenced. The horizontal bars in panels B and C indicate mean values