Some background...I am a married 50 year old male.  My wife is the same age.  I have been having an affair with a younger women, she is 28.  I have been having unprotected sex roughly weekly with both partners.  My younger partner has had one other partner that I'm aware of as well.  

Timing...on 2/23 my wife let me know she was having yellow/green discharge that was foul smelling, not fishy.  On 3/2 I went in for testing and received negative results for N. GONORRHEA NUC. ACID, C. TRACHOMATIS NUC. ACID, and Trichomoniasis Test along with Hep and HIV, urine and blood.  I did wait 2 hours before the urine test from previous urination.  

I'm sure you can understand my concern.  Do I have legitimate concerns that I passed along an STI to my wife and tested negative?  Are there other STI's or possible reasons for her issues?