Distinguishing Intestinal Tuberculosis from Crohn’s Disease: A Review of Integrated Diagnosis and Validation Challenges for New Technologies
Overlapping symptoms in intestinal tuberculosis and Crohn’s disease
Diagnosing intestinal tuberculosis requires interpreting imaging, endoscopy, histopathology, and microbiological test results together. A review published in Diagnostics summarized established tests, emerging diagnostic technologies, and strategies for managing complications, while examining the potential of artificial intelligence and molecular diagnostics and the challenges of validating them. It synthesizes existing studies; it does not directly test the performance of a new integrated diagnostic platform.
Intestinal tuberculosis is an extrapulmonary form of tuberculosis in which Mycobacterium tuberculosis affects the gastrointestinal tract. It commonly occurs in the ileocecal region, where the small and large intestines meet, but can affect other parts of the gut. Abdominal pain, weight loss, fever, and changes in bowel habits overlap with symptoms of Crohn’s disease and gastrointestinal malignancies, making these conditions difficult to distinguish from symptoms alone. Misdiagnosing intestinal tuberculosis as Crohn’s disease and starting immunosuppressive treatment can worsen the infection, so accurate differentiation guides treatment decisions.
Molecular diagnostics and artificial intelligence as complements to established tests
The authors reported searching literature from 2000–2025 and including 78 publications, with findings synthesized narratively. The material reviewed included diagnostic accuracy studies and observational studies, as well as existing reviews and clinical guidelines. The findings should therefore be read as a synthesis of literature with differing study designs and populations.
Computed tomography (CT) is used to assess bowel-wall thickening, lymph-node changes, and complications such as obstruction or perforation. Endoscopy allows clinicians to view mucosal lesions and collect tissue. Transverse ulcers and granulomas with caseous necrosis, which may be seen in intestinal tuberculosis, can help with differentiation, but are not found in every patient. When tissue contains few bacteria, smear microscopy may have difficulty detecting Mycobacterium tuberculosis, and culture can take several weeks.
Molecular tests such as polymerase chain reaction (PCR), GeneXpert MTB/RIF, and GeneXpert MTB/RIF Ultra help detect Mycobacterium tuberculosis DNA in tissue samples. GeneXpert MTB/RIF also provides information about rifampicin resistance. These results need to be interpreted alongside imaging, endoscopic, and histopathological findings; a single test cannot reliably confirm or exclude intestinal tuberculosis in every patient.
The review also described imaging and endoscopy analysis using artificial intelligence (AI), as well as CRISPR-based target enrichment and sequencing. However, the supplement explains that the cited CRISPR study was not specific to tuberculosis, and that research on targeted sequencing in stool focused on pulmonary tuberculosis, with limited data on intestinal tuberculosis. There is insufficient evidence to interpret these approaches as a single, validated non-invasive diagnostic platform for intestinal tuberculosis. AI-based differentiation studies also have limitations, including retrospective designs and data from limited geographic areas, leaving further validation necessary.
Distinguishing the potential to reduce surgery from proven effects
Standard antituberculosis drug therapy is the mainstay of treatment. Even with medication, however, some patients require endoscopic intervention or surgery for complications such as strictures, bowel obstruction, or perforation. The review also discussed endoscopic balloon dilation for selected patients with short fibrotic strictures. It explained that surgery is often performed to manage serious complications rather than the infection itself.
Early differentiation and appropriate treatment are central to managing complications, but this review did not directly establish the diagnostic accuracy of combined CRISPR and AI approaches or demonstrate that they reduce surgery. Research to determine how these technologies perform in patients with intestinal tuberculosis and contribute to clinical care remains a future task. The search databases listed in the abstract and main text differ, and some study descriptions in the supplement are inconsistent; the cited original papers need to be checked when interpreting detailed performance figures.
Sources: Full Diagnostics review, Europe PMC bibliographic record and abstract.
Intestinal tuberculosis (ITB) is a complex form of extrapulmonary tuberculosis characterized by nonspecific gastrointestinal symptoms and substantial overlap with conditions such as Crohn's disease and gastrointestinal malignancies. These similarities frequently lead to diagnostic uncertainty, delayed diagnosis, and inappropriate management. This systematic review summarizes current evidence on the clinical presentation, diagnostic approaches, and therapeutic strategies for ITB, with particular emphasis on emerging diagnostic technologies and their role in reducing surgical interventions. A systematic literature search was conducted using PubMed, Scopus, and Google Scholar following PRISMA guidelines to identify relevant studies published from 2000 to 2025. The review focused on clinical manifestations, imaging findings, endoscopic features, histopathological characteristics, molecular diagnostics, pharmacological therapy, and minimally invasive therapeutic interventions. Accurate diagnosis requires an integrated approach combining clinical assessment with imaging, endoscopic evaluation, and histopathological confirmation. Molecular techniques such as GeneXpert MTB/RIF and GeneXpert MTB/RIF Ultra and multiplex polymerase chain reaction assays improve diagnostic accuracy and shorten detection time. Emerging technologies including artificial intelligence-assisted radiologic interpretation and CRISPR-based stool sequencing platforms show promise for earlier detection. Standard anti-tubercular therapy remains the cornerstone of treatment, while minimally invasive endoscopic and surgical procedures are effective for managing complications such as strictures, obstruction, and perforation. Early and precise diagnosis of intestinal tuberculosis is essential to prevent complications and optimize patient outcomes. Integrating conventional diagnostic approaches with emerging molecular and artificial intelligence-based technologies may enhance diagnostic precision and support i
For patients suspected of having Crohn’s disease who also have a history of tuberculosis or a risk of exposure, symptoms and endoscopic findings alone may not be enough to determine treatment. This review explains why imaging, histopathology, culture, and molecular tests need to be interpreted together in that setting. The clinical context involves considering both the risk of starting immunosuppressive treatment without recognizing possible tuberculosis and the risk of delaying interventions needed for complications. In developing diagnostic technologies, researchers need to establish what information AI or stool-based tests add to existing tests and whether they maintain their performance in patients with intestinal tuberculosis. Non-invasiveness or rapid detection alone does not establish that these tests can replace tissue examination or reduce surgery.