I don't think ducks should pose any problems to your pregnancy. You don't really need to touch them to take care of them, and if you're still concerned I'd say just wash your hands. Also you could talk to your doctor if its still a huge concern. I wouldn't worry about it though.
I think of it this way, hundreds of years ago pregnant women did farming and took care of all sorts of animals, and still had healthy happy children. Just wash your hands and everything should be fine.
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