Staph aureus in swab results

Hey there,
So, my first urine culture came back positive for Staphylococcus aureus. I did the whole routine—took Augmentin 1g for seven days and then finished up some nitrofurantoin (like Macrobid) at 50mg twice a day for two weeks... everything seemed fine. But then, about a month later, I start feeling this weird "discomfort"—kind of an itchy sensation? In the meantime, I’ve been intimate with my girlfriend (she isn't showing any symptoms at all), so I went ahead and got another swab. Yep, Staphylococcus aureus is back in the urine, though it didn't show up in my semen test. My doctor basically told me, "There's no inflammation present. Is it just contamination?" What does that even mean? Is she carrying it and passing it back to me during sex? Or could it be related to those hemorrhoids I've been dealing with lately—they bleed sometimes, so could that be a factor? Should I just restart the meds and have her take them too? Any suggestions on how to actually get rid of this annoying Staphylococcus aureus once and for all?
Thanks a ton for the help
Peter

She probably assumed the sample was tainted, thinking it had been 'contaminated' by that specific pathogen after the fact.
It could also be linked to hemorrhoids, especially if there's bleeding involved, since that bacterium originates in the gut.