SabrinaAnn,
It is possible that he had a false negative. When doing the urine test, if the gentleman has urinated within the past two hours or if he cleaned the penis before urinating, the test may not pick up the infection.
Since there is concern that the test may not be correct, have another test done to be sure. Since you had a culture done (swab test), you may wish to have the urine test done this time. Just be sure to follow the instructions carefully.
Whenever there is doubt about the results of a test, the easiest thing to do is just repeat the test for confirmation.
Good luck.