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Probably, but it may depend on why you are taking the Ciprofloxacin, in what stage of the infection you currently are (if you still have a high fever, etc.), and what, if any, underlying health or medical conditions you have.
This antibiotic is used to treat bacterial infections. There are no known drug interaction issues between antibiotics and flu vaccinations. The question might be whether your body and immune system, that is actively fighting the bacterial infection can tolerate adding another organism to the mix that will also need your immune system to respond to create antibodies for the flu immunity as well as fight the bacteria. Ask the Doctor Who prescribed the antibiotic if it will be okay before going for the vaccination, or talk to the clinician who will administer the vaccine beforehand so they can evaluate if you should delay the vaccination until the bacterial infection is totally gone.
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