I Have A 53 Yr Old Son Thought He Had

I have a 53 yr old son thought he had flu, fever,, rash sore throat for about 6wks before seeing dr/ Dr. put him on antibiotic, prednisone, cough syrup /codine after 10 days got a refill then still no better sent him to chest specialist. More blood work, xrays said either walking puemonia or valley fever He has been on the antibiotic now for 6 weeks He is feeling better and the really bad cough is better . He lost weight and has been in bed all this time. Dr says he needs to stay on the medicine longer. Isnt being on antibiotic this long a bad thing?