We developed a specific, sensitive and highly predictive method of simple selective color-based enumeration of necrotoxigenic E. coli O55 and probiotic E. coli Nissle 1917 strains co-cultured for 24–48 h on modified MacConkey agar. This method enables the integration of E. coli Nissle 1917 into the study of the mechanisms of the pathogenic effects of necrotoxigenic E. coli producing cytotoxic necrotizing factor 2 that have been insufficiently studied in experimental models, and allows for the comparison of its bacterial interference with the effects of other probiotic bacteria, such as lactobacilli and bifidobacteria, in the gnotobiotic piglet model of immunocompromised infants. The cultivation method was verified by the detection of specific bacterial sequences by LNA probes-based PCR detection systems. To our knowledge,
it is the first reported instance of LNA probes being used for bacterial strain discrimination