Evaluation of the Copan Fecal Swab and Seegene Allplex Gastrointestinal multiplex panels for Accurate Molecular Detection of Stool Pathogens with Operational Efficiency for Implementation in a High Volume Laboratory Setting

Background
Traditional diagnostic methodologies for the detection of pathogens in stool have relied on microscopy for ova/parasites (O/P) or culture for pathogenic bacteria. Microscopy is highly subjective and reliant on technologist expertise. Culture based identification of bacterial pathogens requires plating for growth on various selective media followed by biochemical/phenotypic testing for confirmation. Dynacare Microbiology laboratories in Ontario, Canada receive approximately 200 specimens per day for independent diagnosis of O/P and bacterial pathogens. An accurate diagnostic method with efficient workflow was sought for high volume diagnostic testing for O/P and bacterial pathogens in stool specimens.

Methods
The Seegene Allplex Gastrointestinal (GI) multiplex PCR panels for Parasites, and Bacteria (I, II) were evaluated against positive and negative specimens both prospectively with “fresh” stool specimens (n=88) and retrospectively with archived specimens (n=115). All specimens underwent diagnostic testing as per current standard operating protocols accredited by CAP and IQMH: (i) detection of O/P was performed on stool collected in sodium acetate formalin fixative via microscopic examination of wet mount and stained smears and (ii) detection of bacterial pathogens was performed on stool collected in Enteric Transport Media. For bacterial detection, stool was plated onto individual selective media for the isolation of Yersinia enterocolitica, E. coli O157 and Campylobacter jejuni/coli. Stool was also inoculated into Selenite broth for enrichment prior to plating for isolation of Salmonella sp and Shigella sp. Antibiotic susceptibility testing was performed for Salmonella and Shigella isolates. Serotyping was performed for presumptive identification of O157 strains amongst non-sorbitol fermenting E. coli isolates. In addition the limit of detection for bacterial targets was compared in triplicate using “spiked” specimens prepared in Enteric Transport Media and Copan Fecal Swabs. The complete value chain of activities was assessed starting with the pre-analytical phase (specimen collection, transportation, set up for DNA extraction and PCR plates), analytical phase (PCR, reflex test setup for culture and antibiotic susceptibility testing) and post-analytical phase (reporting, referral for confirmatory testing).

Results
The Seegene Allplex GI tests provided superior sensitivity and specificity compared to conventional methods. The limit of detection for bacterial pathogens (Salmonella sp, Shigella sp, Campylobacter jejuni/coli, Yersinia enterocolitica and E. coli O157) was 10-100 fold improved in Copan Fecal Swab specimens compared to Enteric Transport media. Copan Fecal Swab specimens can be loaded directly onto the Nimbus or Starlet platforms for greater operational efficiency and audit trail during automated DNA extraction and PCR plate setup.

Conclusions
The combination of test performance characteristics, operational parameters (throughput, ease of use) highlight Seegene Allplex GI panels and the Startlet/Nimbus instruments as an attractive testing suite for high-volume diagnostic enteric testing of bacterial and parasitic stool pathogens.