Natural Remedies to Treat Pneumonia

I have had pneumonia for 3 1/2 months now. They have tried 3 courses of antibiotics to cure it, but nothing seems to help. It has been mild, they term it walking pneumonia, but it just won't cure. I am really wondering if water kefir (which I believe is awesome btw!) may have caused this accidentally, but my Dr was immediately dismissive of the idea. I make homemade water kefir so it is really rich in bacteria and about 2 weeks before I started noticing the breathing pain I accidentally inhaled some water kefir when drinking it, it was a good amount because I really choked on it. I never thought a whole lot about the pain I started having in my back when taking deep breaths because I never had any other symptoms, thought it was a pulled muscle (my doctor thought the same thing when I went in 6 weeks later). Eventually the pneumonia was found on a CT scan and it had become a somewhat larger case because it had been there so long I guess. Anyhow, I am wondering if this may be an opportunistic infection of "good bacteria" simply because it ended up in the wrong place and maybe that's why the antibiotics they keep giving me aren't working because they are aimed at the "bad bacteria". Any information would be greatly appreciated!!!