Clinical Evaluation and Cost Analysis of Great Basin Shiga Toxin Direct Molecular Assay for Detection of Shiga Toxin-Producing Escherichia coli in Diarrheal Stool Specimens

The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxin-producingEscherichia coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin (stx 1 andstx 2 ), as well as theE. coli serotype O:157-specific markerrfbE , are simultaneously detected within 2 h. ST Direct was evaluated using 1,084 prospectively collected preserved stool specimens across five clinical centers. An additional 55 retrospectively collected, frozen specimens were included to increase the number of positive specimens evaluated. Results were compared to results from routine culture and an enzyme immunoassay (EIA) specific for the recovery and identification of STEC. ST Direct was found to be 93.2% sensitive and 99.3% specific for detection ofstx 1 andstx 2 and 95.7% sensitive and 99.3% specific for detection ofE. coli serotype O:157. All specimens with false-positive results were found to containstx 1 orstx 2 or were found to be positive for serotype O:157 when analyzed using alternative molecular methods. All 4 false-negativestx 1 orstx 2 results were reported for frozen, retrospectively tested specimens. In all cases, the specimens tested positive forstx by an alternative FDA-cleared nucleic acid amplification test (NAAT) but were negative forstx 1 andstx 2 following nucleic acid sequence analysis. Based on these data, culture and EIA-based methods for detection of STEC are only 33% sensitive compared to molecular tests. A retrospective cost analysis demonstrated 59% of the cost of routine stool culture to be attributable to the identification of STEC. Taken together, these data suggest that ST Direct may provide a cost-effective, rapid molecular alternative to routine culture for the identification of STEC in preserved stool specimens.