Foodborne illness caused by Enterohemorrhagic E. coli (EHEC) and Shigella remain a public health issue in developed countries. The current microbiological methods for detecting EHEC and Shigella typically involve an enrichment step that aims to amplify the pathogenic organisms relative to the background bacteria flora present in foods. Following enrichment, there is a screening step to identify pathogens based on presence of virulence genes (ex. stx and eae for EHEC). False-positive detection of EHEC can occur if virulence targets are present within the population of bacteria found in foods, but not in any single organism. In this study, a Multiplexed Single Intact Cell ddPCR (MuSIC ddPCR) was developed to reduce the false-positives in the EHEC method. During enrichment, EHEC and Shigella are often outcompeted by non-target bacteria. The role of microbial antagonism of non-target bacteria in preventing growth of EHEC and Shigella in enrichment culture was also investigated.