Evaluation of 5′-nuclease and hybridization probe assays for the detection of shiga toxin-producing Escherichia coli in human stools

5′-Nuclease and a hybridization probe assays for the detection of shiga toxin-producing Escherichia coli were validated with regard to selectivity, analytical sensitivity, reproducibility and clinical performance. Both assays were capable of detecting the classical stx1 and stx2 genes when challenged with reference strains of E. coli (n = 40), although 1 to 4 minority sequence variants, whose clinical relevance is limited (stx1c, stx1d, and stx2f), were detected less efficiently or not at all by one or both assays. No cross reaction was observed for both assays with 37 strains representing other gastrointestinal pathogens, or normal gastrointestinal flora. Analytical sensitivity ranged from 3.07 to 3.52 log10 and 3.42 to 4.63 log10 CFU/g of stool for 5′-nuclease and hybridization probe assay, respectively. Reproducibility was high with coefficients of variation of ≤ 5% for both inter- and intra-assay variation. Clinical performance was identical with a panel of archived positive specimens (n = 19) and a prospective panel of stools associated with bloody diarrhea (n = 115). In conclusion, both assays proved to be sensitive and reproducible.