Distribution of viral, bacterial, and parasitic agents in patients with gastroenteritis

In this study, viral, bacterial, and parasitic agents were assessed in stool samples of patients with a preliminary diagnosis of gastroenteritis using culture, microscopic native Lugol, immunochromatographic tests, and syndromic PCR methods. And the frequencies of these agents were determined and the methods were compared. 100 stool samples from patients diagnosed with gastroenteritis were examined between September 2024-May 2025 at the Medical Microbiology Laboratory of Dursun Odabaş Medical Center, Van Yüzüncü Yıl University. After examining the physical characteristics of the stools, such as color, consistency, and odor, the stools were microscopically examined for parasitic agents. The stool samples were analysed chromatographically for Entamoeba histolytica, Giardia lamblia, and Cryptosporidium antigens, as well as for Adenovirus and Rotavirus. For culture, stool samples were inoculated on Eosin Methylene Blue, Salmonella Shigella Agar, 5% Sheep Blood Agar, and Campylobacter Selective Media with 10% Sheep Blood. The media were incubated at 37°C for 24-48 hours, and for Campylobacter at 42°C for 2 weeks. The Multiplex Bio Speedy® Gastroenteritis RT-qPCR MX-24 Panel was used for nucleic acid detection of gastroenteritis agents. Of the 100 samples included in the study, 52 (52%) were obtained from female patients and 48 (48%) from male patients. 46 (46%) of the patients were pediatric and 54 (54%) were adult. A total of 79 agents were detected in the multiplex panel, including 55 bacterial (35 E. coli pathotypes, 6 Campylobacter, 10 C. difficile Toxin, 2 Shigella and 2 Salmonella), 19 viral (10 Rotavirus, 3 each Astrovirus, Sapovirus, Adenovirus) and 5 parasitic agents (3 Giardia and 2 E. histolytica). As a result of the syndromic test, while 9 of 10 rotavirus-positive samples and 1 of 3 adenovirus-positive samples were also found positive by chromatographic test, 2 of 87 rotavirus-negative samples and 1 of 95 adenovirus-negative samples were found positive by chromatographic test. A high level of concordance was found between the cassette test and PCR for rotavirus. No positivity was detected in any of the 100 samples in the rapid cassette test for Entamoeba, Giardia, and Cryptosporidium antigens. Two of the four samples with Salmonella detected in culture, one of the two Shigella positive samples, and one Campylobacter positive sample were also positive with the syndromic test. Five samples without Campylobacter detected in culture were also positive with the syndromic test. Regarding bacterial pathogens, very good agreement was observed between culture and PCR for Salmonella and Shigella (Kappa=0.795; p<0.001), while moderate agreement was observed for Campylobacter (Kappa=0.273; p<0.001). Syndromic multiplex PCR was found to have higher sensitivity compared to conventional methods such as microscopy, immunochromatography, and culture. Therefore, its use in conjunction with conventional methods in clinical practice is important for both confirming results and obtaining antibiogram data. Routine use of syndromic testing, particularly in the pediatric age group, can contribute to the prevention of outbreaks by ensuring accurate diagnosis and protecting public health. However, further studies with larger sample sizes are needed to increase the reliability of the findings. Keywords: Gastroenteritis, multiplex syndromic, PCR, stool, infectious diarrhea