Step 1: The phrase flask-shaped ulcer is a buzzword pointing to invasive intestinal amoebiasis, whose agent is Entamoeba histolytica.
Step 2: The trophozoite adheres to the colonic epithelium and releases lytic enzymes that dissolve cell membranes and proteins, allowing it to burrow through the mucosa.
Step 3: Because invasion is widest below a small mucosal opening, the resulting ulcer looks like a flask - narrow neck, wide base.
Step 4: Confirmation in stool comes from seeing trophozoites containing ingested red cells (erythrophagocytosis). Giardia (malabsorption), pinworm and H. pylori do not produce this lesion.
\[\boxed{\text{Entamoeba histolytica}}\]