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Where to Start for Pyelonephritis? Urinalysis, CT, Antibiotics, and Observation?

Roberts, James R. MD

doi: 10.1097/01.EEM.0000544438.37322.8f

Dr. Robertsis a professor of emergency medicine and toxicology at the Drexel University College of Medicine in Philadelphia. Read the Procedural Pause, a blog by Dr. Roberts and his daughter, Martha Roberts, ACNP, PNP, at, and read his past columns at



Kidney infections are not the most interesting or challenging cases in the ED, but they are omnipresent and require the correct diagnosis and treatment. Pyelonephritis can quickly lead to sepsis or septic shock, and the causes and ramifications are varied. A significant medical problem arises once a simple urinary tract infection progresses to the kidney.

A recent article in the New England Journal of Medicine presented a case history and an erudite discussion of acute pyelonephritis in adults. I will discuss only garden-variety, uncomplicated pyelonephritis in the previously healthy adult, but this infection is also present in more complicated patients, such as those with immunocompromise, transplant, and hardware in the urinary tract.

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Acute Pyelonephritis in Adults

Johnson JR, Russo TA

N Engl J Med


The authors reported that an otherwise healthy 35-year-old woman presented with urinary urgency, dysuria, fever, malaise, nausea, and flank pain. She took a fluoroquinolone for diarrhea during a recent trip to India. Her temperature was 38.6°C, pulse was 110 bpm, and blood pressure was 105/50 mm Hg. She had suprapubic and flank tenderness without abdominal tenderness. The white-cell count was 16,500/mm3, and the serum creatinine concentration was 1.4 mg/dL with the most recent measurement before presentation being 0.8 mg/dL. A urinalysis was positive for leukocyte esterase and nitrites.

A few caveats were noted. It is believed that discharge may be possible following initial intravenous antibiotic therapy and fluid resuscitation. Ertapenem or amikacin to cover resistant Escherichia coli was recommended because she had been in another country. These authors suggested no initial ED imaging in this patient.

A 14-day course of trimethoprim-sulfamethoxazole or a seven-day course of fluoroquinolone is sufficient if the patient is deemed stable enough to be discharged. No specific follow-up testing is suggested if the clinical course is without complication, but clinical follow-up within a few days is suggested.

The authors noted that pyelonephritis denotes inflammation of the renal pelvis and kidney, and it typically manifests itself suddenly with signs and symptoms of systemic and bladder inflammation such as fever, chills, malaise, flank pain, urinary urgency, and dysuria. Up to 20 percent of patients lack prior or extant bladder symptoms and present initially with kidney involvement. Flank pain or tenderness is common but not universal. Kidney infection is supported by a urinalysis that indicates bacteria or pyuria, often both, substantiated by a positive urine culture, usually for gram-negative bacilli, most commonly E. coli. Hospitalization is not often required, but it is more likely necessary in young children and the elderly, those clinically toxic, and those with extenuating circumstances. It has been estimated that about 10 percent of cases of septicemia originate from pyelonephritis.



Pyelonephritis can originate from cystitis, but only about three percent of patients with cystitis progress to pyelonephritis, which is more common during pregnancy or with some sort of mechanical obstruction, such as a kidney or ureteral stone or prostate enlargement. Most cases arise from enteric bacteria ascending to the kidneys from the bladder, but rarely bacteremia with Staphylococcus aureus or Candida can seed the kidneys hematogenously.

Most cases resolve within four to five days, but patients who worsen in the first 48 hours raise concerns for potential complications that warrant more urgent intervention. Complications are seen in those with obstruction from stones, tumors, sickle cell disease, diabetes, and perinephric abscess formation. Associated kidney injury usually resolves quickly with treatment, and renal failure is unusual unless there are complications, most commonly obstruction.

Previously young healthy women are the most common patients. The predominant pathogen is E. coli. Men, elderly women, and institutionalized patients are more likely to have non-E. coli gram-negative bacilli and gram-positive pathogens. Microbial resistance of E. coli has become an increasing problem.

Diagnosis: Presumptive diagnosis of pyelonephritis can be made with a urinalysis showing pyuria or bacteriuria, flank pain, and usually a fever. Occasionally, the initial presentation can be confused with cholecystitis, appendicitis, renal vein thrombosis, or PID. Prostatitis is often coexistent or the cause of pyelonephritis in men. Finding 10,000 or more colony-forming units of uropathogens per milliliter of urine confirms infection. Fewer diagnostic labs may be seen if a patient had prior antibiotics or has urinary tract obstruction. Positive blood cultures can occur. Imaging to identify obstruction, abscess, or necrotizing infection is often used, particularly if one suspects urolithiasis, if the urine pH is 7.0 or higher, or a decrease in glomerular infiltration rate, which is suggestive of obstruction, is seen.

Treatment options range from discharge with oral antibiotics to short-term observation with intravenous fluids and intravenous antibiotics to hospital admission. The decision to admit is usually based on clinical acumen, patient characteristics, and the severity of the illness. Intravenous fluids are often administered even to those who will eventually leave the ED.

Antimicrobial Therapy: Antibiotics, the mainstay of therapy, are chosen empirically. Nitrofurantoin is adequate for cystitis, but it should not be used for pyelonephritis. Fluoroquinolones and trimethoprim-sulfamethoxazole are generally highly efficacious. These antibiotics obtain high concentrations in the urine and renal tissues. About 10 percent of E. coli are resistant to these antibiotics, however. Initial treatment with a single antibiotic is not recommended in critically ill or fragile patients.

These authors recommend administration of an initial broad-spectrum intravenous long-acting antibiotic, such as ceftriaxone, gentamycin, amikacin, or ertapenem, for patients who are being discharged. The authors recommend about 18 commonly used antibiotics for treating acute pyelonephritis in adults. A variety of cephalosporins are recommended if fluoroquinolone resistance is a question. Oral therapy with these drugs is best supplemented by an initial dose of intravenous antibiotic given the rising resistance of E. coli to fluoroquinolones and trimethoprim-sulfamethoxazole. Reconsider admission, imaging, and intravenous broad-spectrum antibiotics if no clinical improvement is seen with a day or two of oral antibiotic therapy.

A five- to seven-day course of fluoroquinolone or a 14-day course of trimethoprim-sulfamethoxazole is generally recommended for outpatients. An initial dose of a long-acting IV antibiotic is also suggested.

These authors recommend initial genitourinary imaging in very ill patients and in those with a decrease in GFR, suspected urolithiasis, or urine pH of greater than 7.0. Pyelonephritis is usually associated with an acidic pH of the urine. A urine pH greater than 7.0 is an interesting finding, and should raise the clinician's suspicion for calcium phosphate stones. Imaging for obstruction, abscess, or necrotizing infection is suggested if no improvement is seen in 24-48 hours.



Ultrasound, often done at the bedside, can easily address hydronephrosis, and is the imaging of choice during pregnancy. A contrast-enhanced CT is more sensitive for diagnosing abscess, inflammation, or gas formation, but dye is contraindicated in patients with renal dysfunction. The preferred method for initial evaluation is likely an unenhanced CT. Hydronephrosis should be identified early because it usually involves obstruction or the need for percutaneous drainage.

Special Situations: These authors suggest that any pregnant woman with pyelonephritis should be admitted to the hospital for intravenous antibiotics. Pyelonephritis can progress rapidly and cause life-threatening complications to the mother and fetus. The antibiotic of choice for these patients is a parenteral broad-spectrum beta-lactam, such as ceftriaxone or cefepime. Avoid aminoglycosides, tetracyclines, fluoroquinolones, and trimethoprim-sulfamethoxazole in pregnant women.

Comment: Pyelonephritis is actually a rather in-depth topic, but I will not attempt to cover complicated cases, such as men with prostatitis, those with renal transplant, or those with obstruction or severe immunocompromise. Men with pyelonephritis are a different issue; they often have prostatitis or a stone. I suggest a rectal exam looking for prostatitis and a noncontrast CT in men on the first visit with pyelonephritis.

It goes without saying that all patients with suspected pyelonephritis should have a urinalysis—dipstick and microscopy—and a urine culture with susceptibility testing. Ensure that the urine culture results can be evaluated if the patient is discharged from the ED. The easiest way is to have the patient return to the ED in 48 hours. Blood cultures should be drawn for those who look ill.

It is not always recommended, but a CT without contrast has become a standard radiographic study in all but the most uncomplicated cases. A CT will identify a stone, abscess, obstruction, or a gas-forming infection. Contrast is generally not required in the majority of patients.

I would be in no hurry to discharge a previously healthy woman with pyelonephritis without some period of observation in the ED. It makes sense to admit all but the well-appearing patients to observation to receive IV antibiotics and at least observation for eight to 12 hours. Additional treatments and evaluation can be performed more easily outside the ED.

I'm a fan of giving intravenous antibiotics for those to be discharged. I prefer ceftriaxone or ertapenem, followed by an oral antibiotic, usually trimethoprim-sulfamethoxazole. Be generous with IV fluids, and observe for four to six hours. This has proven effective in most patients. (Ann Emerg Med 1991;20[3]:258.) Despite resistance to fluoroquinolones or trimethoprim-sulfamethoxazole, both are still recommended as reasonable first choices for oral antibiotics.

It seems reasonable to perform a noncontrast CT scan in the ED for those being admitted. Patients with neurogenic bladder, indwelling catheters, or ureteral stents are obviously more complicated and should be admitted and given intravenous antibiotics in the ED with appropriate consultation. Multiple problems have been reported with fluoroquinolone antibiotics, so I prefer to use trimethoprim-sulfamethoxazole as my PO antibiotic of choice for those discharged.

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