Burning sensation in urethra. Issue?

Hi I am having pain and burning sensation in urinary tube. Pain & burning is only in the penile tube. Got Urine Routine, Urine Culture and Ultrasound scans done and report said pus cells 15-20hpf, culture report said e coli uti and sensitive to all antibiotics, Ultrasound scan said thickened bladder wall and non obstructive stone measuring 3.5mm in right kidney. I am taking Nitrofuratoin antibiotic everyday along with urispas tablet. Now I have completed 5 days of medication but still pain n burning sensation in penile tube isn't going away. Also from past few days I am urinating minimum 15 times a day. I am worried wat to do. Can stone be stuck in penile tube and not cause any pain. I am worried abt my situation. Pls advise what might be causing this issue