Detection of the agents of GIT infections can be challenging since different technologies are often required to detect bacteria, parasites and viruses. The EasyScreen™ (Genetic Signatures, Australia) assays employ a multiplex real-time PCR which utilize a novel chemistry, 3base™, which universally modifies the nucleic acid sequence of pathogens to improve the efficiency of PCR. Nineteen viral, bacterial and protozoan causes of GIT infetcion may be detected simultaneously.
We investigated the ability of the EasyScreen™ panels to detect common faecal pathogens in comparison with standard methods. Nucleic acid from 390 stool specimens were extracted after an initial heating step using the EZI Virus mini kit v2 sample preparation kits on the EZ1 BioRobot (Qiagen, Australia). Real-time amplification was performed on a CFX96 instrument (BioRad, Australia) using all EasyScreen™ panels simultaneously on each sample. Conventional faecal testing was performed according to clinical request.
Overall, 285 pathogens were detected by either method of which 10 were not confirmed either due to non-availability of a confirmatory test (n=5) or insufficient specimen (n=5). EasyScreen™ assay correctly identified 269 (97.9%) whilst routine testing based upon request by attending Physician detected 202 (73.5%). Additional pathogens detected by EasyScreen™ were further confirmed as positive by routine test or if necessary by independent PCR.
EasyScreen™ assay failed to detect 6 positive samples (Salmonella (n=1), Giardia (n=1) and C. difficile (n=4). There were 6 apparent false positive results; EasyScreen™ assay positive Shigella spp not isolated on culture (n=2) Astrovirus positive (n=2) and C. difficile positive samples (n=2).
The 15-minute universal sample processing step allows a sample tested to give a near complete gastrointestinal screen from sample to result in around 3 hours. These assays are ideally suited for any clinical microbiology laboratory equipped with the basic hardware to perform real-time PCR substantially improving time to patient diagnosis and treatment, increasing sensitivity, and importantly, detecting additional pathogens not requested by the consulting clinician.