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So does the acanthamoeba get stuck behind the contact and can't get washed away by tears? Or do the contacts cause small abrasions that serve as an entry point? What role is the contact lens playing?
I'm only a student in the field so NotADoctor™ but under normal conditions your tear film layer and blinking keep other liquids out of your eyes. When wearing contacts in water or when cleaning them with tapwater, there is a small amount of the fluid that gets trapped against the eye. If that fluid is fresh water contaminated with acanthamoeba, it provides ample opportunity and time for the acanthamoeba to break through the layer and the contact lens prevents it from being blinked away.