Fig. 1.

Study overview and analysis workflow. A Enrollment flow diagram for the critically ill adult cohort with acute respiratory illnesses that was studied. B Metagenomic next-generation sequencing (mNGS) approach and analysis workflow. The primary analysis assessed the performance of metagenomic next-generation sequencing (mNGS) antimicrobial resistance (AMR) prediction in 27 subjects with LRTI due to 32 culture-confirmed bacterial pathogens. Secondary analyses included mNGS epidemiological assessment of hospital exposure and AMR gene burden in the airway microbiome, and proof of concept assessment of CRISPR/Cas9 targeted mNGS using Illumina and real-time nanopore sequencing