Fig. 3. Genotypic predictions of antimicrobial resistance.

Distribution of minimum inhibitory concentration (MIC) values (mg L⁻¹) for ciprofloxacin in a collection of S. Typhi isolates with different combinations of genetic mechanisms that are known to confer resistance to this antibiotic. Only combinations observed in at least five genomes are shown. Dashed horizontal lines on the violin plots mark the CLSI clinical breakpoint for ciprofloxacin. Point colors inside violins represent the genotypic AMR prediction by Pathogenwatch on each combination of mechanisms. Barplots on the top show the abundance of genomes with each combination of mechanisms. Bar colors represent the differences between the predicted and the observed SIR (e.g., red for a predicted susceptible mechanism when the observed phenotype is resistant). S susceptible, I intermediate, and R resistant.