A retracted stoma (sometimes called a ‘flush’ stoma) sits below the skin. A normal stoma protrudes past the skin level.
There are many things that can cause stoma retraction, including complications of the surgery, weight gain, etc.
The biggest nuisance with a retracted stoma is they can make securing a pouch very difficult. The protrusion of a normal stoma helps make a proper seal, so without this protrusion, the stoma output can go between the skin and the barrier, compromising the seal.
There are ways to prevent leakage with a retracted stoma. First, there are barriers, pouches, and inserts with convexity that helps prevent leakage for retracted stomas. There are also a number of pastes and adhesives to keep leaks from occurring.
Here is a great summary on the Silicon Valley Ostomy support group site.
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