Brief Answer:
You can have second opinion/get culture of urine done.

Detailed Answer:
Hi Tofeman 632,
Thanks for the query.I have read it &understand your concern.
Yes, you are correct...body does destroy any type of pathological organisms that enters our body.It has got a perfect defence mechanism for that.
White blood cells are the fighters against diseases .The success they get in driving the pathogens out , depends on the immunity status(health) of the person/the gravity of pathogens attack the body.
In this process antibodies are produced to act against the pathogen..in a healthy person the symptoms are totally prevented &person is free from the disease.
In case pathens resist the defence by body, symptoms start appearing, though the battl continues..recovery
from the symptoms indicates that,body conquers /aggravation of symptoms denotes pathogens have success in the attack.
*Here comes the role of antibiotics to help our immune system
**You are in dilema about your status after the unprotected sex. In STDs...most of the times a strong dose of antibiotics for advised days suffices to kill the pathogens &person becomes infection freeThe symptoms totally disappear.
**In case you are still suspicious, please get yourself examined by a urologist to exclude any lesion on external genatalia
-Get repeated routine urine examinations (three days consiquently)
-Get culture &sensitivity examination of urine in case any of the urine reports are positive.
**Personal care : Get your spouce also checked, treated if needful by a doctor.
- Personal genital hygiene maintenance is very important.
-Avoid sex with unknown person...
specially unprotected sex(use condom)
-Drink lot of water
-have nourishing food with proteins,fruits(citrous)&salads.
I hope that helps. Follow up query is welcome.
Thanks

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