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This situation actually is quite common -- apparently newly appearing chlamydia in a monogamous couple. This response is adapted from my reply to a similar question a month ago.
As should be obvious, the most important thing is that you both need treatment for chlamydia, preferably with doxycycline, not azithromycin -- especially for her. The reasons to prefer doxycycline will become apparent below.
There are several possible explanations for this situation. The first is already on your mind, that your partner has had other sex partner(s) recently and is the source of your infection. (I'm assuming you are being truthful in not having other partners yourself.) You're a far better judge of that possibility than I can be: you're the only one who can judge your relationship, your partner's truthfulness, and so on. In my experience, most people in your situation are pretty good at scoping out the chances: if you are confident in her fidelity and she seems honest and not on the defensive, the odds are good this isn't the explanation.
You can dismiss shared sex toys. This could transmit chlamydia only if previously used immediately (within a few minutes) by an infected person. Dried secretions don't transmit any STI. If you and your partner have not participated in group sex or simultaneous sex by other persons that involved shared sex toys, you can exclude this possibility.
Could either of your tests have been falsely positive? That't unlikely with the current chlamydia tests, and your confirmatory follow-up test rules out that possibility. For sure you both are infected.
Your partner might have been chronically infected despite her past negative test results. It's uncommon for women to be infected and carry chlamydia for more than a year, but it happens. Four years has been documented, and if it can persist 4 years, probably it can go quite a bit longer, so 6 years is possible. This can happen even with negative genital (i.e. vaginal or urethral) testing. The same is probably true in men who have sex with men (but not in straight men, i.e. sex only with female partners). Recent research has revealed a possible explanation: some chlamydial infections can reside harmlessly in the intestine, initially perhaps acquired by oral sex, or by rectal infection that then ascends upward into the intestinal tract. In other words, genital/urine testing can miss infection limited to the rectum or GI tract. And rectal infection with chlamydia doesn't require anal sex: infected vaginal fluids can come in contact with the anus and result in rectal infection. In other words, in women having either genital or rectal chlamydia can cross-contaminate the other. Much of this is quite recent research, and the frequency with which longstanding intestinal infection explains apparently new genital infections isn't known. But probably it happens.
And that comes back to the importance of doxycycline for treatment. CDC recently revised its chlamydia treatment guidelines, with doxycycline as the treatment of choice, and azithromycin to be used only when doxycycline isn't practical or must be avoided (side effects, inability to take the full 7 days of treatment, etc). One reason for the change is the rectal and gastrointestinal issue just discussed: azithromycin is unreliable for rectal or GI infection, but doxycycline is fully effective.
In summary, you both need treatment with doxycycline. (However, you could get azithromycin, which remains nearly 100% effective for urethral infection in strictly heterosexual males.) You may never know for sure when and how chlamydia (re)appeared in your relationship, and perhaps it doesn't much matter. But perhaps these comments will help you sort it out, if you choose to pursue the issue with your partner.
I hope these comments are helpful. Let me know if anything isn't clear.
HHH, MD
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