You have clearly been treated with many antibiotics, but still have the symptoms. It is possible for an infection to be present and not show up in the urine. There are many other types of bacteria other than gonorrhea or chlamydia that can cause your symptoms.
I would first investigate the prostate. Sometimes prostate infections can be very difficult to treat and may require extended course of antibotics - sometimes as long as 4-12 weeks. I would suggest a referral to a urologist for a thorough digital rectal exam. A transrectal ultrasound can also be obtained to investigate for any abscesses (which won't be treated with antibiotics).
The results from the urethral swab suggests there are no bacteria growing (i.e. this is a negative urethral swab).
It is possible for your partner to obtain a PID from NSU - just because everything is thus far negative does not completely exclude infection.
Regarding the urine sample, it is not uncommon to a few bacteria in it. The WBCs are key, and if negative, it makes a UTI less likely.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.
Kevin, M.D.
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