A. Atopica is a very good drug for allergies, unfortunately it also reduces the immune system and sometimes infections can arise because of that.
She will need antibiotic treatment, it's usually safer to treat for 3 weeks. If she doesn't respond to the antibiotic treatment, a culture and sensitivity needs to be done by taking a urine sample and send it to the lab. Atopica should be discontinued (do not stop it without consulting your vet first) if the infection persists.
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