Was the infection treated? Prilosec is not made to be taken without stopping for a couple of weeks and then re-starting it again. I would stop it for a few days and see if the diarrhea stops, if not then contact your GI about this. If you had an infection your doctor should have made sure it cleared up, and exactly what caused it. It sounds like he is guessing with the acid reflux, when there may be more to it. Always better to make your doctor aware of new symptoms that arise right away. Look at what you're eating and see if you've been eating something new that may be causing the diarrhea. Keep yourself well hydrated with water, Gatorade and orange juice. If you stop the Prilosec keep some tums handy in case the acid reflux acts up and if the diarrhea continues call your GI. Take care and let us know how you are doing.
Read the side effects to the prilosec, I know Nexium and others can have side effects that include diarrhea.