Extended Data Fig. 9: GoPhAST-R accurately classifies AST and detects key resistance elements directly from simulated positive blood culture bottles in < 4 h. | Nature Medicine

Extended Data Fig. 9: GoPhAST-R accurately classifies AST and detects key resistance elements directly from simulated positive blood culture bottles in < 4 h.

From: Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination

Extended Data Fig. 9

(a) Heatmaps of normalized, log-transformed fold-induction NanoString data from the top 10 antibiotic-responsive transcripts directly from 12 simulated positive blood culture bottles for each indicated pathogen-antibiotic combination reveal antibiotic-responsive transcription in susceptible but not resistant isolates. For meropenem, results of carbapenemase / ESBL gene detection are also displayed as a normalized, background-subtracted, log-transformed heatmap above. CLSI classifications of isolates, which were blinded until analysis was complete, are displayed below each heatmap. (b) Probability of resistance from a random forest model trained by leave-one-out cross-validation on NanoString data from (a) (y-axis) compared with standard CLSI classification based on broth microdilution MIC (x-axis) for each isolate. Horizontal dashed lines indicate 50% chance of resistance based on random forest model. Vertical dashed lines indicate CLSI breakpoint between susceptible and resistant. Carbapenemase (square outline) and select ESBL (diamond outline) gene content as detected by GoPhAST-R are also displayed on meropenem plots. See Supplementary Methods for details of spike-in protocol.

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