Enterohemorrhagic E. coli (EHEC) are one of the top bacteria causing foodborne illnesses in Canada. During an outbreak investigation, bacterial clusters associated with high mutators may be missed due to their ability to accumulate mutations. This study compared three approaches for mutation rate estimation: fluctuation assay, mutation accumulation, and a high throughput screening assay based on the fluctuation assay. The screening assay successfully detected a known high-mutator and was then used to screen 100 verotoxigenic strains for high mutation rates. Two high-mutators were successfully detected, indicating that although the phenotype is rare, it is still detectable. Whole-genome sequences of these strains were investigated for genes associated with high mutation rates. The two high-mutators were found to be lacking the mutS gene, known to be associated with hypermutators. Rapid identification of high-mutators would be valuable to inform whole-genome sequencing data and aid in the determination of the scope of a foodborne investigation.