A Comparative Evaluation of the GENE-Up Assay for the Detection of Escherichia coli O157:H7

Introduction: Shiga-toxigenic Escherichia coli O157:H7 (STEC O157) remains one of the major food-borne public health threats since it was first identified as a pathogen in 1982. In the US, per year, the CDC estimates ca. 95,000 STEC O157 infections, among which ca. 3700 are lab confirmed cases. STEC O157 contaminated beef and beef products are now considered adulterated by the FSIS. The current PCR systems remain inherently burdened with cumbersome sample preparation, especially for complex matrices such as beef and beef products, along with complex instrumentation and interpretation tools.   The GENE-UP^™ E. coli O157:H7 (ECO) is a Fluorescence Resonance Energy Transfer (FRET) based real-time PCR that utilizes probe-melt peak analysis to detect STEC O157 while simultaneously differentiating between E.coli O157:H7 and O157:non H7. 

Purpose: To perform a comparative evaluation of ECO methods against the USDA/FSIS MLG 5.09  and 5A.04. 

Methods: In total, 451 mTSB enriched beef and beef products samples were processed through MLG and ECO. All positive results were confirmed using culture-based isolation of STEC O157. Any discrepant results were retested for confirmation. 

Results: Comparative sensitivity, specificity, false positive rate, and false negative rate against culture between MLG and ECO were 91 vs 92, 91 vs 99%, 9 vs 0.76%, and 8.5 vs 8.3%, respectively. Positive predictive value, negative predictive value and the overall accuracy were found to be 54 vs 95, 99 vs 99%, and 91 vs 99%, for MLG and ECO, respectively.   

Significance: These data demonstrate that the ECO assay provides a highly sensitive detection of Escherichia coli O157:H7  that is comparable to USDA/FSIS MLG. The convenient sample preparation along with a user friendly instrumentation and software interface, makes the GENE-UP^™ E. coli O157:H7 a viable alternative for Escherichia coli O157:H7 detection.