AbstractTracking artificially seeded foodborne pathogens in foods with high background microbiota is challenging. Wheat flour and its subsidiary products are known to carry a high native microbial load, which could interfere with tracking and enumeration of target organisms in such matrices. Shiga toxin‐producing Escherichia coli (STEC) serogroups O26, O121, and O157:H7 were transformed with the pGFPuv plasmid encoding ampicillin resistance (+Amp) and green fluorescent protein and were additionally conferred resistance to streptomycin (+Amp + Strep) through exposure to incremental concentrations of the antibiotic. Growth characteristics of these antibiotic‐resistant strains were compared to those of the nonresistant native strains (NR). The supplementation of ampicillin and ampicillin + streptomycin in growth media was evaluated for its ability to suppress growth of the native microbial load of three different commercial cake mixes. Antibiotic supplementation in growth media was successful in suppressing the native microbiota of the cake mixes, while the growth characteristics of the +Amp + Strep variants of the three STEC strains did not differ significantly from the NR strains (p > .05). These results indicate that STEC strains with ampicillin and streptomycin resistance markers have improved trackability over their wild‐type counterparts when isolated from food matrices with high background microbiota. These strains would be advantageous for use in laboratory experiments on STEC survival in wheat and wheat derived products as their detection and enumeration can occur without interference from native microbial load.