Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae -positive Shiga toxin-producing Escherichia coli .

It is remarkable that only using these six genes, EHEC can be clearly identified from read assemblies obtained from in silico mixtures and complex samples such as milk metagenomes. These various combinations of discriminative biomarkers can be implemented as novel marker genes for the unambiguous EHEC characterization from different strains mixtures as well as from raw milk metagenomes.