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PF starts & develops an "inner mass" of infection. No one knows the cause(s) yet. The body's immune system sees this as "foreign" & begins attacking. In order for the immune system to "get this foreign intruder" out, it signals the body to create fistula (tube-like structures) in order for the infection to drain out of the body. Nobody has yet to find the cause of infection & much research has been done by various veterinary universities throughout the world. The infection NEVER abates with use of any antibiotics so the process continues on & on with the inner mass getting larger & larger. The body's immune system continues to attack in this way & does not "turn off".
We ONLY see the fistula & NOT the inner mass which is the source. All fistula are connected to this inner mass. It is this mass growing larger which causes the elimination symptoms & irritation (ie licking, scooting, etc). Think of a plant which grows from a bulb.....bulb (inner mass) is under the ground (skin) & shoots upward from the ground & then sends branches of leaves etc above the ground but still underneath, where you do not see, it grows a root system (fistula). Or if anyone has ever really seen a plantar wart that would be a good analogy.
It is well to remember that we are only seeing "the tip of the iceburg" & never the source so when a PF dog calms down with licking, pacing & obvious signs of irritation we can be sure that whatever treatment we are using is working toward shrinking the source. To be sure, periodic digital exams are done at your vet's office (without sedation.....finger up butt to feel the mass) & will further confirm that treatment is working to shrink the mass while healing the damaged tissue that we do see. For topical treatment users especially, it is important for your vet to indicate to you just where she/he feels that inner mass so you can concentrate your applications in that area along with massaging in the ointment ALL about the surrounding anal tissue & in the nooks & crannies of the damaged skin. Q tips are great for getting in those bumpy areas of tissue.