What physical examination would you perform?

Mr. Jones is a 54-year-old male who presents to the family practice clinic complaining of sudden urgency to urinate, back pain, frequent urination, and pain with urination. Symptoms began approximately 48 hours ago. He awoke from sleep with urgency and suprapubic discomfort 2 nights ago. His urine now has a strong odor and a cloudy appearance. He has an allergy to Bactrim.

Urine dipstick results: Color, dark yellow, specific gravity 1.035, ph 5.5, protein (-), Ketones (-), Bilirubin (-), Trace blood, Leukoesterase (+), Nitrites (+), Urobilinogen (-)

What are some appropriate questions to ask the patient?
What are three differential diagnoses for the patient?
What physical examination would you perform?
What diagnostics would you include?
Create an evidenced-based plan of care. Include pharmacological and non-pharmacological treatments. Please use references not older than 5 years. Thank you