Impact of GI PCR Versus Stool Culture on Clinical Outcomes in Hospitalized Patients: A Retrospective Cohort Study

Gastrointestinal (GI) infections are a common cause of hospitalization, often requiring prompt diagnosis to guide treatment. While traditional stool culture remains widely used, it is limited by long turnaround times and narrow organism detection. Multiplex gastrointestinal PCR (GI PCR) offers broader, faster pathogen identification. This study compares the clinical impact of GI PCR and stool culture in patients admitted with suspected infectious gastroenteritis.

We conducted a retrospective cohort study at a large regional health system, including adult inpatients who had positive stool culture results, GI PCR, or both between January 2019 and September 2024. The primary outcome was hospital length of stay (LOS). Secondary outcomes included targeted antibiotic therapy prescription, antibiotic duration, and inpatient colonoscopy rates. LOS and antibiotic duration were modeled using generalized additive models for location, scale, and shape (GAMLSS); logistic regression was used for targeted antibiotic therapy prescription.

Out of the 408 patients with positive findings, 154 were positive only on stool culture, 153 only on GI PCR, and 101 tested positive on both. GI PCR was associated with a 33.6% reduction in mean LOS compared with stool culture (IRR 0.664, 95% CI: 0.526-0.840, P<0.001). Targeted antibiotic prescription occurred in 59.5% of PCR patients versus 21.4% of those with stool culture alone (OR 5.38, 95% CI: 3.26-8.89, P<0.001). Median antibiotic duration was similar across groups. Colonoscopy was rare (2.0%) and did not differ by test type.

GI PCR significantly improves hospital efficiency and antibiotic targeting in patients with suspected GI infections and should be considered as the primary diagnostic strategy in inpatient settings.