Several possibilities.
It's possible that your wife contracted chlamydia before she met you and that she's been harboring it all this time. Remember that infections can go undetected for a long time...this is called a dormant stage. Stress, poor nutrition, other illnesses can bring the illnesses out. She's going to have to get examined to make sure that she hasn't been affected by pelvic inflammatory disease, which can leave her infertile.
Of course, she could be lying. You need to deal with the fact that she may have cheated on you.
Contrary to what other people seem to believe, you can't get a disease like this from sitting in hot tubs or toilet seats. That's just silly and a quick perusal of any bona fide scientific journal will tell you that.
By the way...diseases like this are harder to detect in men. Some men may suppress it for longer or may be asymptomatic carriers (which means that they have it, but show no symptoms).
As for anyone who said that you can get diseases from "dirty clinic equipment"...that's just plain ignorance, mixed with paranoia. ANY clinic with "dirty" equipment would be shut down and all the doctor and nurses would lose their licenses.