Abstract
Infectious gastroenteritis is a global health problem associated with high morbidity and mortality rates. Rapid and accurate diagnosis is crucial to allow appropriate and timely treatment. Current laboratory stool testing has a long turnaround time (TAT) and demands highly qualified personnel and multiple techniques. The need for high throughput and the number of possible enteric pathogens compels the implementation of a molecular approach which uses multiplex technology, without compromising performance requirements. In this work we evaluated the feasibility of the NanoCHIP® Gastrointestinal Panel (GIP) (Savyon Diagnostics, Ashdod, IL), a molecular microarray-based screening test, to be used in the routine workflow of our laboratory, a big outpatient microbiology laboratory. The NanoCHIP® GIP test provides simultaneous detection of nine major enteric bacteria and parasites: Campylobacter spp., Salmonella spp., Shigella spp., Giardia sp., Cryptosporidium spp., Entamoeba histolytica, Entamoeba dispar, Dientamoeba fragilis, and Blastocystis spp. The required high-throughput was obtained by the NanoCHIP® detection system together with the MagNA Pure 96 DNA purification system (Roche Diagnostics Ltd., Switzerland). This combined system has demonstrated a higher sensitivity and detection yield compared to the conventional methods in both, retrospective and prospective samples. The identification of multiple parasites and bacteria in a single test also enabled increased efficiency of detecting mixed infections, as well as reduced hands-on time and work load. In conclusion, the combination of these two automated systems is a proper response to the laboratory needs in terms of improving laboratory workflow, turn-around-time, minimizing human errors and can be efficiently integrated in the routine work of the laboratory.
Highlights
This evaluation was performed as a part of the efforts to present a valid alternative to the currently used non-molecular detection methods, in view of the wellknown advantages of using molecular methodologies for the concomitant detection of different enteric pathogens in human stool, advantages that have been demonstrated in numerous publications [14, 18, 35, 36]. For this purpose two types of studies were performed, a retrospective and prospective study. In both cases the results of the NanoCHIP1 Gastrointestinal Panel (GIP) were first compared to the routine conventional methods and discrepant results were further tested by qPCR and/or sequencing
The combined results in the retrospective study clearly demonstrated a higher diagnostic yield achieved by the NanoCHIP1 GIP in Salmonella spp, Shigella spp, Campylobacter spp, Giardia sp., Dientamoeba fragilis and Blastocystis spp. when compared to the conventional methods
There were pathogens that were detected only by the NanoCHIP1 GIP and these results were defined as false positive, the negative agreement values remained above 95%
Summary
The objective of the current study was to evaluate the use of a novel automated multiplex PCR system, the NanoCHIP1 GIP, a molecular electronic microarray system that is intended to simultaneously identify parasites and bacterial gastrointestinal pathogens in clinical faecal specimens [26]. The aim of our study was to compare the NanoCHIP1 performance to conventional methods routinely used in our laboratory, including the Blastocystis spp.and Dientamoeba fragilis, which were not included at the time of evaluation in any molecular panel. The purpose of the current study was to evaluate the NanoCHIP1 GIP test as a molecularbased diagnostic system for routine detection of enteric bacterial and parasitic pathogens in a rather big outpatient laboratory
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