I had C.diff last year and my doctor started me on Flagyl but it was awful... terrible taste in my mouth, dizziness, etc. Since oral Vancomycin is not absorbed into the bloodstream, it has a lot less side effects than Flagyl, so I asked my doctor to switch me and he did. It worked well for me, in combination with Florastor (S.boulardi supplement, a dietary yeast probiotic that crowds out the bad guys in your gut). You will probably much prefer the Vanco to the Flagyl, so be happy!
Doctors usually prescribe Flagyl for C.diff first because it's cheaper, but in the long run Vancomycin is usually more effective from the research I have done on it. You may need to taper on and off at the end to catch as many spores as you can. Make sure you take it on schedule like clockwork, dont' miss a dose or be late! Works better that way.
Most people recover from C.diff after just one or two courses of antibiotics, and most likely you will be fine, too! Just remember that C.diff is tricky to completely eradicate once you are infected because it hibernates in virtually indestructible spores. You will need to be extra careful down the road if you ever need to take antibiotics for any reason, and after colonoscopy prep, because that can put you at risk of a C.diff relapse.
Please be very careful and use good hygiene because as you probably already know, C.diff is extremely contagious. You could infect your entire family or reinfect yourself. Hand sanitizers (Purell) and most cleansers are ineffective at killing it in spore form. Wash your hands vigorously and with lots of soap and water, and use bleach every day to clean the bathroom.
You can find much more good information at the following support group:
http://www.cdiffsupport.com/phpBB/
I have long wondered if C.diff can cause Crohn's, or if we're just more susceptible to it. Studies have shown that people taking antacids or acid-suppressing medicines (Pepcid, Prilosec, etc.) are more prone to contracting C.diff, as are people taking ibuprofen (Advil, Motrin, etc.) I took both for many years before being diagnosed with C.diff and Crohn's.
I also often wonder how many people here are suffering from C.diff and don't know it. Tests for it are notoriously unreliable with something like a 60-75% false negative rate. Some people get tested once and it is negative and their doctor never considers it again. Most doctors who are knowlegable about C.diff know it take at least 3 negative tests to be pretty confident of a true negative result.
I'm so glad you got an accurate test result and are getting treatment. You will feel much better soon.