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Chronic Vaginal/Cervical inflammation
I tried to look through what's already been posted, but I decided to post anyway while I was going through the stack.

For about a year and a half, I've been dealing with what appears to be a chronic vaginal problem.  It's to the point that I don't know what's normal.  Long Hx, sorry.  Tried to keep it brief...

July 2009 - went in for an annual and mentioned heavy discharge, diagnosed with BV.  Normal Pap.  Treated with Doxycycline (10d) and Flagyl (7d, oral).  Was in long term monogamous relationship at that point, he was neg for STDs and he was my first.  It's likely I had the infection for quite a while, because the heavy discharge seemed 'normal' to me.  Tested negative for G/C by PCR.

July 2009 - developed oral thrush from Abx, oral nystatin for 2 weeks.

Early Sept 2009 - developed classic BV symptoms - fishy grey discharge, the whole deal.  Treated with Metrogel and doxy, fixed.  Tested negative for G/C by PCR.

Jan 2010 - New partner (who was HSV2 positive), return of heavy yellowish discharge from summer, sometimes stringy, slight sour smell.  Some pain with intercourse  Doc saw 'clue cells' and white blood cells, inflammation of cervix.  Tindamax (oral) and metrogel.  Negative PCR.

End of Jan 2010 - Discharge, irritation, vaginal dryness (slight variation of symptoms). Doc had prescribed 1 refill of Metrogel, so self-administered as directed. Negative HSV antibody test.

End of Feb 2010 -  Not sexually active. Return of heavy yellow discharge, cervical inflammation, WBCs in discharge.  Doxy/metrogel.  Negative PCR.  Negative HSV (antibody specific test)

April 2010 - Sexually active once more with partner number 1, monogamous.  Return of heavy yellow discharge and vaginal irritation, WBCs in discharge.  Went back to a different clinic, doc saw yeast and bacteria. prescribed 1 course of metrogel and 1 diflucan (last day)  Negative PCR.

June 2010 - @ primary care physician for unrelated symptoms.  Normal thyroid tests, normal electrolyte tests.  Because of my past partner, requested full STD panel.  All Negative - HSV2, HIV, Syphilis.

End of July 2010 - Back for annual.  Normal pap, but still have heavy yellow discharge, slight sour smell, lots of white blood cells, inflammation.  Doc decides to screen for everything (Gonnorrhea, Chlamydia, Trich, and several others I can't remember - basically, she said she was testing for everything she could test for).  All negative.  HSV negative (6 month mark).  Prescribed Doxy/Metrogel.  Same relationship, make a point to shower before and after sex (both of us)

Sept 1 2010 - Notice profuse white discharge, some discomfort during sex.  Tried RePhresh, vag felt irritated.  Discharge persisted and turned yellowish with a slight sour odor, like the discharge I experienced before. Home tested vaginal pH and it came up normal (4.5, lowest the test strip could see).  Back to first Doc who sees WBCs in discharge.  Prescribed oral flagyl. Discharge seemed normal, abstained from sex as I had before and decided to do so until I had a follow up appt.
Developed Oral thrush on last day of flagyl (Sept 7), went to clinic and was given nystatin (oral suspension).  Nystatin course overlapped with period (sept 11-18), was careful to use pads - used tampons 3x, kept in for no more than 4 hours.  3 days post period experienced some vaginal dryness, clear discharge.  4th day post period (today), return of cramping, heavy yellow discharge, but odorless.

So basically, I have a recurring yellow discharge that's often thick or stringy.  Typically it begins as odorless, but may have a slightly sour smell.  I don't notice other odors.  I keep getting diagnosed with BV and am given Abx, and all the tests come back negative.  With one exception, I do not have the classic symptoms of BV.  Based on all those little 'what does this discharge mean' charts, the symptoms might be closest to chlamydia, but that test comes back negative and my monogamous partner does not have G or C.  

My sexual history includes 2 partners, the second one HSV2 postive; however, full STD tests 6 months post-second-partner show negative tests for HSV2, HIV, etc.  I've never had a positive test for G, C, or Trich.  My first and current partner is STD-free.

In terms of general healthy, I am a 29 y/o female with no allergies, very active lifestyle (exercise 4-5x/week).  I use unscented soaps and detergents, wear cotton underwear, and clean after exercise.  I have a normal period, though I've noticed the cycle length has increased over the last year to approx 32 days.  No recent fluctuations in weight or other health, normal BMI.  I eat yogurt and have started taking oral probiotics with some regularity, including FemDophilus, during and after antibiotics treatment - even tried taking FemD 2x/day toward the end of this last period (obviously did not work).  My diet could be improved, but is relatively healthy.

I already had a doctor's appointment for a few days from now, to see if the Oral Flagyl resolved the symptoms (hence, why I've abstained from sex since the course of Abx).  I need to ask some questions, and was hoping to get more from any feedback or advice people might have.

1) is it possible my vaginal flora haven't repopulated properly?  Is there any way to test the makeup of the flora?
2) could this be physiological?
3) is it possible an estrogen imbalance could predispose me to infection? (I am not taking any birth control, we use condoms)
4) Would douching or vinegar sitz baths be appropriate if there is no evidence of infection? (I've never done either, because I know they're typically associated with BV)
5) should I go on the pill (since its a method of BC that supposedly does not disrupt flora and maintains estrogen levels)?
6) Should I try regularly using a product like Rephresh? (only tried it once)  Or try vaginal delivery of probiotics?

I have no idea what this could be or why I keep coming up as infected, when everything tests negative.  I haven't had any kind of intimacy in weeks, due to the diagnosed BV and then the oral thrush.  My partner is understanding, but it aggravates me.  My insurance is no longer covering some tests because I've exceeded the limit, and with the copays and medicine this is getting expensive.  And mostly, I just feel unwell - if not because of the discharge, then because of the antibiotics.  I love to swim, and I haven't in months because I worry I'm going to disrupt my vaginal flora because of the water or the bathing suit.  Depending on what happens with the appt coming up, I'll try to see a new doctor, but I don't know what they're going to do that's different.  
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