None of mine have ever gotten Rabies or any other vaccine in their neck... did you watch where the vet injected? I did have one dog get a reaction to a rabies vaccine once that presented as a swollen area at the injection site but it was further down then their neck.
I would get her into the vet tomorrow and see what the swelling is from and they will also be able to tell you whether you can go ahead with the spay or not.
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 Armani & Chloe |