Faecal multiplex PCR testing and its clinical utility in inflammatory bowel disease: a systematic review and meta-analysis

Abstract

Gastrointestinal infections can mimic flares of inflammatory bowel disease (IBD). We performed a systematic review to study the clinical utility of pathogen detection using stool multiplex PCR (MPCR) testing in patients with IBD. We systematically searched PubMed, Embase and Scopus on 1 June 2025 for studies reporting MPCR testing in IBD. Data on pathogen detection, comparative diagnostic performance with standard of care and clinical outcomes were extracted. A random-effects meta-analysis was performed to estimate the pooled prevalence and ORs. Risk of bias was assessed using the Joanna Briggs Institute checklist. 20 studies (18 cohorts), comprising 5273 patients, were included. The pooled prevalence of enteric pathogens was 0.30 (95% CI 0.21 to 0.40; I²=95.4%). Among patients presenting with IBD flares, the prevalence of infection detected by MPCR was 0.49 (95% CI 0.34 to 0.64; I²=92.5%) and was higher compared with conventional diagnostic methods (pooled OR 4.31; 95% CI 1.49 to 12.5). Three studies assessing management changes showed that PCR testing significantly reduced the need for therapy escalation (pooled OR 0.35, 95% CI 0.24 to 0.51; I²=0%). PCR positivity was associated with increased antibiotic use but did not seem to influence hospitalisation, emergency visits or surgery. Stool MPCR improves detection of enteric pathogens in IBD flares and may reduce unnecessary escalation of immunosuppressive therapy in the short term. The results are based largely on retrospective, heterogeneous studies and may be subject to residual confounding. Future randomized controlled trials are needed to confirm these findings and address long-term implications of MPCR testing.