Commercial RT-PCR Tests Compared to Culture for Bacterial Gastroenteritis

Nucleic acid-based testing (culture-independent diagnostic testing, CIDT) for bacterial gastroenteritis offers three major advantages over culture-based diagnosis: it has better analytical sensitivity, is less labor intensive through automation, and has faster turnaround times.

Multiple commercial nucleic acid test assays (i.e. real-time PCR, RT-PCR) are available, testing at a minimum of four pathogens (Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli (STEC), and Shigella). However, there are many caveats associated with CIDT for bacterial gastroenteritis, and gaps in the evaluation of commercial assays.

Clinical Microbiologists at the University of Calgary (Calgary, AB, Canada) and their colleagues used clinical stool specimens and contrived samples comprising commonly circulating species, serotypes, biovars, and/or toxin subtypes were for a comparison of four commercial RT-PCR tests. The four tests were: RIDAGENE Bacterial Stool Panel and EHEC/EPEC Panel (R-Biopharm AG, Darmstadt, Germany); FTD Bacterial Gastroenteritis assay (Fast Track Diagnostics, Luxembourg); BD MAX Enteric Bacterial Panel and Extended Enteric Bacterial Panel (BD Canada, Mississauga, ON, Canada); Prodesse ProGastr SSCS Assay (Hologic Inc., San Diego, CA, USA).

The four commercial RT-PCR assays were challenged with 67 contrived stool specimens, each spiked with an isolate representing different Campylobacter species, Salmonella serotypes, Shigella species and serotypes, STEC toxin subtypes, Y. enterocolitica serotypes/biotypes, and Yersina spp; these isolates are the common circulating types in Alberta, Canada. All assays gave positive results for C. jejuni, C. coli, Y. enterocolitica, and all species and serotypes of Shigella, but negative results for Y. non-enterocoltica spp. and C. upsaliensis. Most Shiga toxin subtypes were detected by all assays except for stx2f, which was detected by Ridagene.

The performance of the four commercial assays was assessed using 171 clinical fecal specimens collected prospectively, which were initially tested by culture at the frontline diagnostic laboratories. This included feces that were 125 culture-positive or 46 culture-negative for Campylobacter, Salmonella, Shigella, STEC, or Y. enterocolitica. Using culture as a reference standard, the sensitivity for all organisms (excluding Yersinia) was >96% for all four assays and specificity was >90%, except for BD Max (87%).

The authors concluded that their study provided a third-party evaluation of four commercially available RT-PCR assays for bacterial gastroenteritis and demonstrated the assays to be mostly equivalent to each other and culture with a few caveats. Depending on the prevalence of certain stx sub-types, Yersinia species, and Campylobacter species in a laboratory's jurisdiction, without further improvement in culture-independent tests, culture methods remain critical for the detection of these pathogens. The study was published on January 1, 2022 in the International Journal of Infectious Diseases.

Related Links:
University of Calgary
R-Biopharm
Fast Track Diagnostics
BD Canada
Hologic