The rapid identifi cation of and “fi ngerprinting” bacterial pathogens is an essential component of epidemiological surveillance and investigating the outbreak of a foodborne infection in order to improve food safety. Foodborne outbreaks are increasingly common. In the last two years the CDC has performed at least 25 multistate foodborne outbreak investigations (https://www.cdc.gov/foodsafety/outbreaks/multistate-outbreaks/ outbreaks-list.html). During the last two decades, molecular methods of bacterial strain identifi cation have replaced phenotypic assays, increasing the discriminatory ability of identifying and typing the pathogenic bacterial strains. They have transformed the way an outbreak investigation is conducted. Standard bacterial phenotyping uses the morphology of bacterial colonies on culture media, as well as serological and biochemical assays, and antibiotic susceptibilities, to distinguish pathogenic microorganisms and identify different strains (Arbeit 1995). However, these traditional methods lack the ability to distinguish between two closely related bacterial strains sensitively. Further limitations of this approach include poor reproducibility,
need for specialized reagents and the lack of applicability to a wide range of bacterial pathogens. Molecular analysis differentiates between bacterial strains on the basis of their genetic profi le. However, these approaches can be costly and time-intensive and require standardization (Field et al. 2004).