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Background Enteric Infections (EI) may cause a flare of inflammatory bowel disease (IBD). It is important to differentiate a worsening induced by EI from an inflammatory flare, as this affects treatment decisions. Multiplex polymerase chain reaction (m-PCR) enables simultaneous identification of multiple organisms in stool samples, thereby aiding the diagnosis of EI-induced flares. We performed a systematic review to ascertain the clinical utility of pathogen detection by m-PCR in patients with IBD.Methods Electronic databases (PubMed, Embase, Scopus) were searched on 1st June 2025. We selected all studies that reported m-PCR in subjects with IBD (ulcerative colitis or Crohn’s disease). We extracted data on pathogen detection, comparative diagnostic performance relative to standard-of-care diagnostic practices, and impact on treatment decisions. We assessed the risk of bias using the Joanna Briggs Institute checklist. A random-effects meta-analysis was performed to estimate the pooled prevalence and odds ratios (ORs) with 95% confidence intervals (CIs).Results Twenty studies (18 cohorts) with 5,273 IBD subjects were included ( IDDF2026-ABS-0093 Figure 1. PRISMA flowchart). The pooled prevalence of a positive m-PCR amongst subjects with IBD (IDDF2026-ABS-0093 Figure 2. Pooled prevalence of a positive m-PCR amongst subjects with IBD) was 0.30 (95% CI 0.21 to 0.40). The pooled OR of finding a positive stool m-PCR in IBD subjects (IDDF2026-ABS-0093 Figure 3. Pooled OR of finding a positive stool m-PCR in IBD subjects compared to healthy subjects and non-IBD diseased controls) was 3.38 (95% CI 1.69 to 6.75) compared to healthy subjects, and 0.92 (95% CI 0.73 to 1.17) when compared to diseased controls with non-IBD illnesses. The pooled OR of detecting an EI with m-PCR versus standard-of-care diagnostics was 4.31 (95% CI 1.49 to 12.50). The prevalence of an EI during flare was 0.49 (95% CI 0.34 to 0.64). The use of stool m-PCR decreased the odds of IBD therapy upgradation (IDDF2026-ABS-0093 Figure 4. Pooled odds of IBD therapy upgradation) compared to standard-of-care diagnostics (pooled OR, 0.35; 95% CI 0.24-0.51). Conclusions Stool multiplex PCR is a useful tool for differentiating EI-induced versus inflammatory flares of IBD. Its use can prevent unnecessary upgradation of anti-inflammatory therapy in IBD.Abstract IDDF2026-ABS-0093 Figure 1Abstract IDDF2026-ABS-0093 Figure 2Abstract IDDF2026-ABS-0093 Figure 3Abstract IDDF2026-ABS-0093 Figure 4