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

Abstract

The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxinproducing Escherichia coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin (stx 1 and stx 2 ), as well as the E. coli serotype O:157-specific marker rfbE, 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 of stx 1 and stx 2 and 95.7% sensitive and 99.3% specific for detection of E. coli serotype O:157. All specimens with false-positive results were found to contain stx 1 or stx 2 or were found to be positive for serotype O:157 when analyzed using alternative molecular methods. All 4 false-negative stx 1 or stx 2 results were reported for frozen, retrospectively tested specimens. In all cases, the specimens tested positive for stx by an alternative FDA-cleared nucleic acid amplification test (NAAT) but were negative for stx 1 and stx 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 costeffective, rapid molecular alternative to routine culture for the identification of STEC in preserved stool specimens.

Performance of commercial tests for molecular detection of Shiga toxin-producingEscherichia coli(STEC): a systematic review and meta-analysis protocol

“…EIA has suboptimal sensitivity, particularly if a time-consuming enrichment step is not conducted 15–18. Commercial NAATs appear to be more sensitive, but results vary by study and test 19–21. NAATs are more costly than traditional microbiological techniques owing to the equipment and consumables required to perform them.…”

“… 19–21 NAATs are more costly than traditional microbiological techniques owing to the equipment and consumables required to perform them. However, the higher cost may be compensated by increased ascertainment 21 and/or improved patient outcomes. 22 As laboratories consider NAATs, it is crucial to identify the best testing strategy to support time-sensitive, cost-effective treatment decisions.…”

Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness

“…Traditional culture and enzyme-linked immunosorbent assay-based methods for STEC were only 33% sensitive compared with molecular testing. 50 The BioCode GI Pathogen Panel (GPP) was approved in 2018 and tests for 16 enteropathogens. While no available independent studies have been published regarding the assay's clinical utility, reported manufacturer's data suggest that both positive and negative agreements are in line with commercially available reference testing methods.…”