Extended Data Fig. 2: Antimicrobial Resistance Gene Expression By BAL Cluster. | Nature Medicine

Extended Data Fig. 2: Antimicrobial Resistance Gene Expression By BAL Cluster.

From: Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation

Extended Data Fig. 2

Antimicrobial resistance gene (AMR) expression was derived from human-subtracted sequencing files processed using the. CZID Antimicrobial Resistance (AMR) Gene Pipeline v0.2.4-beta, which leverages the Resistance Gene Identifier (RGI) v6.0.0 to generate read k-mer alignments (KMA) against the Comprehensive Antibiotic Resistance Database (CARD) v3.2.3 and WILDCARD v3.1.0. AMR transcripts were summed across all AMR genes and normalized to sample ERCC reads (left) and additionally to total BAL mass of bacteria (right) and varied by cluster (Kruskal-Wallis p < 0.001 and p < 0.001, respectively). n = 127, 74, 45, and 32 for Clusters 1-4, respectively. For all box-whisker plots: boxes indicate the median and interquartile range and whiskers extend to the largest value above the 75th percentile (or smallest value below the 25th percentile) that is within 1.5 times the IQR.

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