PCR-Based Versus Conventional Stool Testing in Hospitalized Patients with Diarrhea: Diagnostic Yield, Clinical Impact, and Stewardship Implications

Accurate and timely identification of enteric pathogens is crucial for guiding treatment in hospitalized patients with acute diarrhea. Conventional stool testing often lacks sensitivity, whereas multiplex PCR diagnostics offer rapid, comprehensive pathogen detection. This retrospective multicenter study included 267 adult inpatients with acute diarrhea from two hospitals. Patients underwent either traditional stool diagnostics (<i>n</i> = 146) or multiplex PCR testing combined with stool culture (<i>n</i> = 121). Clinical data, diagnostic yields, antibiotic use, and clinical outcomes were analyzed. The multiplex PCR group demonstrated a significantly higher diagnostic yield than traditional testing (77.7% vs. 41.1%, <i>p</i> < 0.001), detecting more mixed infections (34.7%) and a broader range of pathogens, including <i>Campylobacter</i>, viruses, and parasites. PCR positivity correlated independently with bloody diarrhea (OR 16.5; 95% CI: 1.81-150.26) and dehydration (OR 7.05; 95% CI: 1.40-35.45). PCR testing reduced inappropriate antibiotic use (OR 0.30; <i>p</i> < 0.001), shortened antibiotic duration post-result (median 5 vs. 7 days; <i>p</i> < 0.0001), and increased antibiotic adjustments (42.1% vs. 27.4%; <i>p</i> = 0.011) and discontinuation (12.4% vs. 3.7%; <i>p</i> = 0.033). The PCR group had more ICU admissions (20.7% vs. 7.1%, <i>p</i> = 0.001) and longer hospital stays (median 10 vs. 6 days, <i>p</i> < 0.0001), reflecting more severe illness. Liver cirrhosis, comorbidity burden, and systemic inflammation predicted worse outcomes. Multiplex PCR enhances pathogen detection and promotes antibiotic stewardship in hospitalized patients with diarrhea. Rapid results support earlier, targeted clinical decisions, particularly in patients with complex comorbidities or severe presentations.