The thing about chlamydia is that you rarely get symptoms! I have wondered about it on numerous occasions, I finally got a test for it and its come up negative so its very possible she is worried for nothing! If she is worried make her go to the doctor, cos the sooner she treats it, the faster itll go away (if she has it) and if she leaves it and she does have it, it can lead to infertility...So id say if shes worried tell her to go to the doctor.
If you havent been with anyone but her id say its impossible for you to have given her chlamydia, normal bacteria in the penis isnt a cause of chlamydia it has to be transmitted.
Depending on how many people shes been with id say it could be in her system for ages without her knowing, so get her to go to the doctor because its very likely she is paranoid about nothing!
Good luck!