I have a good friend who was diagnosed with a bacterial infection in his lung and it has made him quite sick with no energy. he looked into treatment and he was told that it is very difficult to treat and he had to live with it. he wouldn't accept that and did some research and saw more specialists. he was told that the only place where he could have treatment was the Jewish hospital in Denver. he has since been there and had tests for 10 days. They were able to identify 2 separate bacterial infections and he is now on several antibiotics for weeks to kill the first infection. After that is cured he will be on intravenous injections for a year to kill the other bug.
I don't know if this is the same problem that you are talking about but this information might help somebody . Hopefully your Mother just has acid reflux but it sounds odd about the lung bacteria.
Good luck

I have bronchiectasis and MAC disease in my lung so I am required to send sputum samples in regularly. That’s when they are able to detect it.