Urethritis not fully treated or resistant to initial antibiotics: The patient's symptoms persist despite completing a course of doxycycline and metronidazole, which are commonly used to treat urethritis caused by chlamydia and gonorrhea. This suggests the infection may not have been fully eradicated or is resistant to the antibiotics used.

Urinary Tract Infection (UTI): The symptoms of penile swelling, redness, and painful urination could be indicative of a UTI that has not been adequately treated by the antibiotics prescribed for urethritis.
Prostatitis: Inflammation of the prostate gland can cause painful urination, and if the prostate is involved, the initial antibiotic treatment might not have been sufficient.
Epididymitis: Inflammation of the epididymis, which stores sperm behind each testicle, can cause pain and swelling in the testicular area and might be related to the urinary symptoms if the infection has spread.

Testicular Torsion: Although less likely given the context of recent antibiotic treatment, testicular torsion is a medical emergency that can present with sudden severe pain and swelling. It requires immediate surgical intervention to save the testicle.
Fournier's Gangrene: A severe and potentially life-threatening condition characterized by necrotizing fasciitis of the genitalia. It's crucial to consider this diagnosis in cases of severe pain, swelling, and redness, especially if there are signs of systemic infection.

Behçet's Disease: A rare condition that can cause genital ulcers and might be associated with urinary symptoms due to its systemic nature, affecting blood vessels throughout the body.
Reiter's Syndrome (Reactive Arthritis): A form of arthritis that occurs as a reaction to an infection elsewhere in the body, often in the gastrointestinal tract or the urethra. It can cause symptoms including urethritis, conjunctivitis, and arthritis, and might be considered if other explanations for the symptoms are ruled out.