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Jul 28, 2018 · Getting Off of Omeprazole in Digestive Health

For six months in 2017 I complained of acid and was popping Gaviscon like candy. GP said to keep taking it if I needed it.
September 2017 I was very sick with the flu for 2 weeks, went to the walk in clinic and chest xray showed 'pneumonia' . 3 courses of antibiotics and 2 months being bed ridden and no change in the chest xray. The coughing was out of control.
I forced myself out of bed and started to get better.
Referral to a respirologist found Micobacterium Letiflavim in my lungs through sputum tests. TB clinic doctor said the amount was so minute that it wasn't the problem and it is not unheard of to have this in the general population as it is found in water.
Puffers were prescribed but they made me cough worse.
Burning became so unbearable I mentioned it to the respirologist and he sent me for Barium swallow. The radiologist said reflux was the worst she has ever seen. Tip me backwards and stomach acids flow right out.
I was put on PPI. I have had both endoscopy and bronchoscopy. They found hiatus hernia but were happy that there has been no damage from the acid in my GI tract.
My CT scans (x3) continue to see on 50% clearing in my lungs. Respirologist is stumped and doesn't understand why it has not cleared up. (they are guessing that all of my acid, while I was bed ridden, was leaking into my lungs and have done damage). His only suggestion is to do a lung biopsy which I have refused so far. They aren't looking for anything specific but rather searching for anything at all to answer the question of what is left in the lungs that they are seeing and can't identify. I said if the lungs have cleared up 50% since the PPI meds, let's wait and see if there continues to be improvement.
Now I am severely deficient in vitamins D and B12 to the point of being critical but GP just said to take supplements and get rechecked in 2 months.
I was the one that brought up the suggestion of the PPI causing the D and B12 deficiency and the GP agreed it could be the reason.
So here I am feeling like crap, still coughing and short of breath. Now my energy level has bottomed out and my bones are stiff and sore.
They have put me on a waiting list to be tested for surgery on the stomach sphincter to see if I am a candidate but I don't know enough about that surgery or if I should even have it. The Gastro specialist says it isn't a one time fix and I may have to have it again in the future.
Is there a specialist that looks at all things combined? My specialists are all looking at their own fields of expertise but I am feeling like someone needs to be looking at the whole picture and combining treatment. Right now it seems like the left hand doesn't know what the right hand is doing.
They are treating me like an anomaly but I'm feeling like and finding from posts that my situation isn't so unique.
Any thoughts?