A new laboratory workflow for the diagnosis of gastroenteritis in pediatric patients by using FilmArray® Gastrointestinal Panel

Introduction. Pathogen-induced acute gastroenteritis is one of the leading cause of childhood morbidity and mortality worldwide. Conventional diagnostic methods for routine detection of enteric pathogens are time consuming, labor-intensive, often lack sensitivity and specificity, and leave undiagnosed cases. More recently, the introduction of the syndromic multiplex PCR systems has allowed to simultaneously detecting a wider range of enteric pathogens. This study represents a 2-year picture of the epidemiology of enteric pathogens in children suffering from gastroenteritis using the FilmArray® Gastrointestinal Panel (FA-GP), a multiplex molecular assay that allows to simultaneously detecting a large panel of pathogens independently of the etiological suspicion. Materials and Methods. A total of 2128 stool samples, collected from children with clinical suspicion of bacterial and/or viral gastroenteritis attending the University Hospital of Parma, was submitted to the FA-GP and, when an adequate aliquot was available, to electron microscopy (n = 1494) for virus detection and to an enterovirus-targeting real-time PCR (n = 2110). Specimens with positive results for Salmonella, Yersinia enterocolitica, Vibrio, diarrheagenic Escherichia coli/Shigella, Campylobacter, Plesiomonas shigelloides by the FA-GP were also submitted to conventional diagnostic methods. When a parasite was detected by the FA-GP, the same sample and/or additional samples up to three per patient were submitted to conventional assays as confirmed. Results. The FA-GP gave positive results in 1171 (55%) cases: 801 (68.4%) contained a single agent and 370 (31.6%) multiple agents, for a total of 1660 pathogens. Enteropathogenic E. coli, rotavirus, norovirus, toxigenic Clostridioides difficile, and sapovirus were the most commonly detected pathogens. A total of 970 additional agents (424 of which as single pathogen) was detected by the FA-GP and not included in the clinical suspicion. The overall recovery rate of the conventional methods from stools that resulted positive by the FA-GP was 39% for bacteria, 35.7% and 82.9% for Giardia intestinalis and Cryptosporidium, respectively, and ranged from 3.2% to 62.8% for viruses, if excluding all electron microscopy-negative astroviruses. Enterovirus, an agent not targeted by the FA-GP, was revealed in 9.2% (194/2110) of the examined samples, and in 73 cases it was the only agent detected. Discussion and Conclusions. The results of this study allowed to extend the range of detectable pathogens independently of the clinical suspicion, to detect co-infections in almost one third of children positive for at least one agent and to show that conventional methods would have missed more than half of the enteric agents detected by the FA-GP.