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Over 10% of Crohn’s disease (CD) patients initially present with perianal lesions. While some patients exhibit concomitant intestinal involvement at diagnosis, the majority develop luminal manifestations during follow-up, with approximately 5% never developing luminal lesions. Diagnostic clinical features include fistula characteristics, such as complex fistula, inter-organ communication, recurrent fistula, persistent inflammatory wounds refractory to surgical drainage, multiple internal/external fistula openings, as well as the presence of ulcerations, anal stenosis, and inflamed skin tags. Additional risk factors can guide the diagnosis of CD, notably young age, family history of CD, rheumatological and autoimmune manifestations, or association with hidradenitis suppurativa. A comprehensive diagnostic approach necessitates multidisciplinary consultation and a thorough etiological assessment, including blood tests, fecal calprotectin dosage, endoscopic assessment with biopsies, capsule endoscopy, as well as bacteriological and histological samples taken during fistula surgery. This facilitates luminal involvement detection and eliminating different diagnoses like tuberculosis and actinomycosis. The TOpCLASS consortium (Treatment Optimization and CLASSification of Perineal Crohn’s disease) has proposed major and minor criteria for diagnosing isolated ano-perineal Crohn’s disease in the absence of histological proof, providing a framework for therapeutic management. Careful management is crucial, as undertreatment can compromise patient outcomes. These patients frequently exhibit a refractory phenotype, often necessitating therapeutic escalation, with the therapeutic response serving as additional diagnostic validation.