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There is no reason a vet still couldn't run a fecal to see if your silkie has cocci. All you would have to do is take some poop [fresh] to them.
Except that many flat out will not do a fecal. Usually a large animal vet will take the plunge, I know mine has.
Yes, treat the peep for cocci. Unfortunately it falls within that age range that cocci could be the culprit although keeping it with a duck could also be a problem.
Boy thats for sure, I have both and I can't see a duck and a chick living in the same space. Ducks are way to messy.