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Background The diagnosis of intestinal TB (ITB) is challenging because of its overlapping features with Crohn's disease. This outcome-based study evaluated the combination of colonoscopy, histopathology, Xpert MTB/RIF and TB culture for best sensitivity and specificity. Method This was a four-year retrospective, observational study of 426 clinically suspected patients who underwent colonoscopy with biopsies for histopathology, Xpert MTB/RIF and TB culture. ITB was diagnosed using the composite reference standard (CRS), which comprised either histological features or culture or Xpert MTB/RIF positivity, and positive response to anti-tuberculous treatment on follow up. Results 35 (8.2%) patients were diagnosed with ITB. Histopathology had the highest sensitivity (91.4%) and negative predictive value (99.2%), MTB/RIF had the highest specificity (100%) and positive predictive value (100%). A combinatorial approach with Xpert MTB/RIF and histopathology had optimal diagnostic value (97%), approaching 100% sensitivity with culture. 40% of cases were diagnosed within 12 hours with Xpert MTB/RIF and 97% cases within three days. Conclusion This combinatorial diagnostic model provides rapid and reliable diagnosis of ITB which may be useful in endemic areas.

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