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A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.