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VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

Fig 3

Examples of variant-phenotype relationships determined by the association models.

(A) K18768.0 indicates blaKPC, the K. pneumoniae carbapenemase. The presence of blaKPC is associated with resistance to ceftazidime in K. pneumoniae as shown. The numbers in the plots represent the frequency of certain MIC (minimal inhibitory concentration) values. Numbers in the plot represent total number of isolates with the given MIC value. (B) K18093.13 is oprD, an imipenem/basic amino acid-specific outer membrane pore; absence of oprD is associated with resistance to imipenem in P. aeruginosa. (C) K18790.0 represents blaOXA-1, the beta-lactamase class D OXA-1. Its presence is associated with resistance to cefepime in E. coli. (D) K19278.0 is aac6-lb gene. The presence of this variant is associated with amikacin resistance in A. baumannii. The “+” and “-”sign in the X-axis represent whether the wild-type gene exists or not. The red horizontal lines mark the mean and standard error of the groupwise MIC measurements. Each gray dot represents an MIC value. P-values are calculated based on Fisher’s exact test. MIC: minimal inhibitory concentration.

Fig 3