Comparison of several Real-Time PCR Kits versus a Culture-dependent Algorithm to Identify Enteropathogens in Stool Samples

Abstract

This study aims to validate the current diagnostic method for the clinical detection of gastroenteritis. We analyzed 400 stool samples to detect three of the most common enteropathogens: Salmonella spp., Campylobacter spp., and Yersinia enterocolitica. All specimens were tested with a routine clinical diagnosis algorithm and with five real-time PCR assays. A total of 98 specimens (24.5%) were positive for enteropathogens. We found 24 samples positive for Salmonella enterica, 71 positive for Campylobacter spp., and 4 positive for Yersinia enterocolitica. All evaluated methods exhibited a good performance in identifying Salmonella and Yersinia enterocolitica, being the highest positive percent agreement (PPA) value of 95.8% and 100%, respectively. The clinical algorithm showed the highest ppA value identifying Salmonella, due to the enrichment in selenite broth. However, the evaluated methods showed notable differences in the identification of Campylobacter species, obtaining a wide range of PPA values: 59.2%-100%. The clinical algorithm showed the lowest PPA value since it was only able to detect Campylobacter jejuni and Campylobacter coli species. This study revealed the importance of implementing the real-time PCR technique in a clinical algorithm: it improved the accuracy of the diagnosis and provided results in a shorter time compared to routine clinical methods. Acute gastroenteritis is a leading cause of morbidity and mortality worldwide 1 , particularly in at-risk populations, such as children, older individuals, and immunocompromised patients. We included three bacteria in this study: Salmonella spp., Campylobacter spp., and Yersinia enterocolitica, which are among the most common enteropathogens that cause gastrointestinal infections. Thus, their rapid, accurate identification is crucial for infection control, and in selected cases, for determining the most suitable therapy. According to the Centers for Disease Control and Prevention, during 2016, the Foodborne Active Surveillance Network identified 24,029 cases of foodborne infections, which led to 5,512 hospitalizations (22.9%) and 98 deaths (0.4%). Some of these cases were detected by culture, but others were detected with culture-independent diagnostic tests (CIDTs). Current CIDTs mainly comprise two types: antigen-based and nucleic acid-based assays. In 2016, one study showed that many infections were identified with a CIDT and without a culture confirmation; most frequently, Campylobacter (32%) and Yersinia (32%); but also Shiga toxin-producing E.coli (STEC) (24%), Shigella (23%), Vibrio (13%), and Salmonella (8%) 2. That study revealed the consequences of the current change in diagnostic trends. The implementation of CIDTs in clinical laboratories has led to more exhaustive diagnoses. Most of these tests are ordered by clinicians, because CIDTs are easier to perform and they return results faster than traditional culture techniques. Moreover, samples are subjected to deep screening when multiplex panels are used; consequently, the number of reporte...

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