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They got some parasites in the wild, too and they get infected during importation with some more.
In nature they got much more place to go, so the parasite pressure isn't that high as it is in those little cages we use to keep our chameleons. They seldom reinfect themselves, the parasite burden is kept low and the chameleons often have a balanced host-parasite relationship without clinical symptoms.
The problem in wild caught is that catching and transport means big stress for the chameleon, so the parasites have a good chance to increase and become a problem. And in captivity, they have a very little action range, a high infection pressure, frequently reinfections, massive infestation and stress as well. So we build a relly nice environment for the parasites to get a real problem and it's very important for our chameleons to keep them parasite free.
There's a dissertation about parasites found in wild chameleons on Masoala peninsula, north and east madagascar from Nicolá Lutzmann 2006. That's maybe an interesting paper for you (and be sure, the dissemination of the parasites in chameleons kept in captivity is different).