Mostly it’s done by stool culture, which works best before antibiotics are started. C. diff is diagnosed with a different kind of test, but still best without antibiotics. You could try something like the following:
1) I have a combination of symptoms (diarrhea/arthritis/conjunctivitis) that sounds like Reiter’s syndrome/reactive arthritis.
2) It hasn’t responded to Xifaxan (if that’s still true)
3) Can we try a stool culture to look for a specific bacterial cause?
J-pouchers probably have a different bacterial risk profile than folks with colons, but I don’t know if anyone has studied it in detail. Since most of these infections are thought of as occurring in the colon, doctors sometimes assume that J-pouchers can’t get them. This is certainly false for C. diff, and probably false for the others, too.
Phun phact: One of the reasons the term “Reiter’s syndrome” has fallen out of use is that Reiter was a dreadful Nazi.
Here’s more than you probably wanted to know about diagnosis of bacteria in stool: https://cmr.asm.org/content/28/1/3