Fig. 4: Susceptible (MIC < EUCAST breakpoint) and resistant (MIC > EUCAST breakpoint) E. coli isolates can be differentiated by the fraction of cells called resistant by the model.

a The fraction of cells in the sample called resistant by the susceptible-resistant classifier (Resistant Fraction) is plotted against the MIC of the strain (mg/L) on a logarithmic scale, with each biological replicate represented as a circle. The test dataset is composed of holdout images, previously unseen by the classifier, from each clinical isolate. The EUCAST breakpoint (0.5 mg/L, green) and the treatment condition (10 mg/L, blue) are shown with shaded vertical lines. All strains with an MIC below the EUCAST breakpoint have a resistant fraction less than or equal to 0.2, whereas the fraction classified resistant is nearly 1.00 for the strains with an MIC above the EUCAST breakpoint. Representative, correctly classified images of ribosome phenotypes from each of the clinical isolates are shown for each point. Scale bar, 2 μm. b The confusion matrix for the ciprofloxacin-resistant and ciprofloxacin-susceptible classifier trained on 6 strains on a holdout, unseen dataset of those 6 strains.The testing dataset is composed of 28,448 images from unseen biological replicates. See Accuracy Metrics for details on Accuracy, Sensitivity, Specificity, PPV, and NPV. c The number of cells necessary to classify a sample as coming from a population of susceptible or resistant bacteria with 99% confidence. Simulated samples of different susceptible:resistant ratios (S:R) were transformed through the sensitivity and specificity of the susceptible-resistant classifier to determine the minimum number of cells necessary to differentiate them. Here, we plot the mean Resistant Fraction and 99% confidence interval after 1000 trials with samples ranging from 1 to 40 cells sampled (N) for susceptible:resistant ratios of 0:100 (purple triangles), 50:50 (blue circles), and 100:0 (green diamonds). As the number of cells sampled increases, the confidence interval of the Resistant Fraction narrows. Susceptible samples can be differentiated from resistant samples with a sample of 2 cells (purple dotted line). A mixed sample can be differentiated from a resistant sample with 7 cells (blue dotted line) or from a susceptible sample with 12 cells (green dotted line). The confidence interval for resistant cells is narrower than that of susceptible cells because the classifier is more sensitive than it is specific.