Objective: To compare the diagnostic effectiveness, including sensitivity and specificity, of multiplex Polymerase Chain Reaction (PCR) panels against commonly used immunochromatographic Rapid Diagnostic Tests (RDTs) for the etiological diagnosis of acute intestinal infections (AII). Methods: A prospective, cross-sectional study was conducted involving 350 patients (180 children, 170 adults) presenting with symptoms of AII at a tertiary care infectious diseases hospital between January 2024 and September 2024. Stool samples were collected from each patient and processed in parallel. All samples were analyzed using a commercial multiplex PCR panel targeting 22 common enteric pathogens (viruses, bacteria, parasites) and a panel of standard RDTs (for Rotavirus/Adenovirus, Campylobacter spp., and Clostridioides difficile toxin A/B). The multiplex PCR results, supplemented by culture confirmation for bacterial pathogens, were used as the reference standard to calculate the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the RDTs. Results: The multiplex PCR panel identified at least one pathogen in 72.0% (252/350) of patients, compared to 41.7% (146/350) by the RDT panel. Co-infections were detected in 18.3% (46/252) of PCR-positive samples. The most common pathogens identified by PCR were Norovirus GII (22.0%), Enteropathogenic E. coli (EPEC) (15.4%), and Rotavirus A (14.0%). Compared to the PCR reference standard, the Rotavirus RDT demonstrated high sensitivity (93.9%) and specificity (98.7%). The Campylobacter RDT showed moderate sensitivity (76.5%) but high specificity (99.1%). The C. difficile toxin RDT exhibited the lowest sensitivity (68.2%) but excellent specificity (99.4%). A significant portion of diagnoses made by PCR (e.g., Norovirus, EPEC, Shigella) were not covered by the RDTs used. Conclusion: Multiplex PCR panels provide a significantly higher diagnostic yield and broader pathogen coverage for the etiological diagnosis of AII compared to a standard panel of RDTs. While RDTs, particularly for Rotavirus, remain valuable for rapid screening in specific contexts, their moderate sensitivity for key bacterial pathogens and limited scope can result in missed diagnoses. The comprehensive results from PCR panels are superior for guiding targeted therapy, antimicrobial stewardship, and outbreak investigation.

Acute intestinal infections (AII), etiological diagnosis, PCR, multiplex PCR, molecular diagnostics, rapid diagnostic test (RDT), immunochromatography, sensitivity, specificity, comparative effectiveness.

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