Extended Data Fig. 6: RNA-Seq and NanoString data reveal differential gene expression that distinguishes susceptible from resistant clinical isolates for S. aureus + levofloxacin and P. aeruginosa + ciprofloxacin.
(a) RNA-Seq data from two susceptible or two resistant clinical isolates of each species treated with the indicated fluoroquinolone at 1 mg/L for 60 minutes are presented as MA plots. Statistical significance was determined by a two-sided Wald test with the Benjamini-Hochberg correction for multiple hypothesis testing, using the DESeq2 package28. (b) Heatmaps of normalized, log-transformed fold-induction of antibiotic-responsive transcripts from 24 independent clinical isolates of each species treated with the indicated fluoroquinolone at 1 mg/L for 60 minutes. For each species, NanoString data from all candidate transcripts are shown at left, and top the 10 transcripts selected from Phase 1 testing are shown at right. (c) GoPhAST-R predictions of probability of resistance from a random forest model trained on Phase 1 NanoString data from the derivation cohort and tested on the validation cohort (y-axis) compared with standard CLSI classification based on broth microdilution MIC (x-axis). Horizontal dashed lines indicate 50% probability of resistance. Vertical dashed lines indicate the CLSI breakpoint between susceptible and not susceptible (that is intermediate/resistant). Numbers in each quadrant indicate concordant and discordant classifications between GoPhAST-R and broth microdilution.
