Evaluation of the performance of direct stool and rectal swabs for molecular diagnostics of infective gastroenteritis by the highly multiplexed Stat-Dx gastrointestinal system


Infective gastroenteritis (GE) remains a leading cause of global morbidity and mortality especially in childhood. One of the barriers to diagnosing GE is the difficulty and time delays in obtaining and transporting a bulk stool specimen. The use of rectal swab specimens for testings may overcome this barrier. Bulk stool may contain more inhibitory material for molecular diagnostics than do flocked swab samples. Rectal swabs may offer additional advantages as they are designed to sample an area just proximal to the surgical anus, the anatomical location of many of the bacterial and some of the protozoal pathogens of diagnostic interest. Conversely, bulk stool samples contain more contents derived largely from the small intestine, which may in fact dilute the cellular material of interest contained in the colonic mucosal surface.


The DiagCORE GE assay (DC-GE) is a cartridge based, qualitative multiplex molecular test assay, configured for use with the DiagCORE® Analyzer for automated, integrated nucleic acid (NA) extraction and multiplex rtPCR. It tests for the presence or absence of of viral or bacterial NA of 23 gastrointestinal pathogens. The cartridge can be loaded with liquid stool in UTM specimen or with a direct ´dry´ swab, through its respective dedicated sampling ports. After loading through either of these sampling ports, the sample is identically processed within the fully contained cartridge.

An observational, prospective-retrospective study was designed to compare the clinical performance of 3 sample types, bulk stool in liquid media (LSM), dry direct stool swabs (DSS) and dry direct rectal swabs (DRS). All samples were tested according instructions for use and protocol conditions.


All groups of DC-GE pathogens were represented in the study. Direct swab samples showed similar detection rate for most pathogens, while a higher yield for several bacterial targets was observed. In general, for these pahogens 1-4 better CT values were found in dry swab samples.


The combination of rapid sample acquisition, such as rectal swabs, with sensitive rapid detection methods,such as PCR, may allow for targeted treatment and the potential for significantly improved outcomes for this common and, in many places, deadly infection.

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