This was my thought. The author does mention a combination of drugs that his doctor put him on, which is probably the "triple therapy" of antibiotics and a proton-pump inhibitor.
After this part of the story, incidentally, is when he starts getting better. Maybe it was the lack of coffee, but the antibiotics were probably helpful too.
Author is not talking about that, but from what I know testing for H. Pylori and E. Coli is part of any endoscopy. Stomach ulcers may and do appear even if there is no harmful bacteria in a stomach.
