How long does Xifaxan 550 mg stay in your system?

It depends on the condition for which Xifaxan has been prescribed and on how many times per day you take it, and whether you just started taking it or have been taking it for some time. It also depends on which part of your system you're asking about, since Xifaxan stays mainly in the gut--which is where it is supposed to work--although a small amount does get absorbed into the bloodstream.

You can find some data on this site at https://www.drugs.com/pro/xifaxan.html; look under "Xifaxan - Clinical Pharmacology." In that section under "Elimination", relating to the concentration in blood, it states "The mean half-life of rifaximin in healthy subjects at steady-state was 5.6 hours and was 6 hours in IBS-D patients." This was for patients taking 550 mg 3x per day after two weeks. So, someone with IBS-D on that regimen should expect that more than 90% would be eliminated from the blood after 24 hours.

I have not seen any data on how long a dose may remain active in the gut, but I would expect that it will pass through you at more or less the same rate as everything else.