Evaluation of the EntericBio multiplex polymerase chain reaction system as a routine method for the detection of stool pathogens and screening of carbapenemase-producing Enterobacterales.

Acute infectious gastroenteritis is a major contributor to morbidity and mortality globally. Currently, traditional laboratory diagnostic methods, mainly microscopy and culture, are the mainstay of detecting faecal pathogens in most low- and middle-income countries (LMICs). These methods are time-consuming, laborious, have long turnaround times and poor sensitivity. Carbapenemase-producing Enterobacterales (CPE) have become pathogens of global public health concern. Due to their niche within the human body, CPE can be detected using faecal sampling. Many laboratories use culture-based methods for the detection of CPE with similar limitations as conventional stool culture. Increasingly, laboratories are using molecular methods to detect stool pathogens and CPE due to their higher sensitivities, short turnaround times, ease of use and their ability to detect multiple pathogens or enzyme types from a single stool sample. Owing to the high cost of these assays, there is a paucity of data on the use of these assays in LMICs. This study evaluated the performance of the EntericBio Dx, VP3 and CPE Panels for the routine detection of stool pathogens and CPE in an academic laboratory in Pretoria, South Africa. Impact of the implementation of the EntericBio system on turnaround time of results and media usage was also assessed. A total of 314 prospective clinical stool specimens and rectal swabs were tested in parallel using the standard-of-care and the respective EntericBio assay. Also tested on the EntericBio system were 158 retrospective stored samples previously characterised. All discordant results were resolved using independent referee methods. The EntericBio Dx and CPE panels had sensitivities of 100% each and specificities of 100% and 99%, respectively. The VP3 panel performed well for the detection of rotavirus and adenovirus, with high sensitivities for both targets. The evaluation of the VP3 panel for other targets was limited by a lack of isolates for those targets. There was a significant reduction in turnaround time with the implementation of the EntericBio assay and an estimated ten-fold reduction in media usage. Implementation of the EntericBio system will have a positive impact on patient management, timely institution of infection prevention and control measures, and antimicrobial stewardship efforts.