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Table 1 Comparison of WGS-based genotyping and phenotypic ASTs against the broth microdilution reference. Frequency of isolates assigned to classification groups after phenotypic testing (broth microdilution) and application of interpretive criteria (epidemiological cut-off and clinical breakpoint). Genotype concordance with classification groups is provided for each interpretive criterion. Antimicrobials with ‘-‘values were not assessed due to the absence of established breakpoints or susceptibility test data

From: Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods

Antimicrobial Epidemiological cut-off Clinical breakpoint
Non-Wild Type Wild Type Genotype concordance (%) Resistant Sensitive Genotype Concordance (%)
Ampicillin 57 45 95.10 57 45 95.10
Chloramphenicol 49 53 94.12 49 53 94.12
Ciprofloxacin 27 75 96.08 - - -
Gentamicin 8 94 92.16 7 95 93.14
Nalidixic Acid 28 74 95.10 28 74 95.10
Sulfamethoxazole 69 33 76.47 69 33 76.47
Streptomycin 66 36 89.22 26 76 55.88
Sulfisoxazole 73 29 70.59 - - -
Trimethoprim-Sulfamethoxazole (1:19) 33 69 93.14 30 72 96.08
Tetracycline 57 45 89.22 - - -
Trimethoprim 32 70 96.08 - - -
Overall 499 623 89.75 266 448 86.55