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Due to rapidly falling costs, whole genome sequencing (WGS) is becoming an essential tool in the surveillance of antimicrobial resistance (AMR) in Salmonella enterica. Although there have been many recent works evaluating the accuracy of WGS in predicting AMR from a large number of Salmonella isolates, little attention has been devoted to deciphering the underlying causes of disagreement between the WGS genotype and experimentally determined AMR phenotype. This study analyzed the genomes of six S. enterica isolates previously obtained f