Chlamydia

Okay, so, please only serious replies. I don't have time for ugly comments, nor would I appreciate them.
I went for my 36 week check up, which is when they did my group b tests, std testing, etc. a few days later.. Turns out I have Chlamydia. Now, my doctor says that my labs at the beginning of my pregnancy were negative but positive now. How is this possible? Yes I know through sex. BUT I haven't had sex with anyone else other than my SO and he swears time and time again that neither has he. I know, he could be lying, I just truly don't think he is. My labs from the beginning of my pregnancy were done at the hospital. These labs now were done by my doctor. Is it possible that maybe chlamydia wasn't checked in the initial labs? I am just so confused! If anyone has any insight, I would appreciate it! 
Thanks guys