brand logo

Am Fam Physician. 2020;102(3):173-180

Patient information: A handout on this topic is available at

This clinical content conforms to AAFP criteria for CME.

Author disclosure: No relevant financial affiliations.

Acute pyelonephritis is a bacterial infection of the kidney and renal pelvis and should be suspected in patients with flank pain and laboratory evidence of urinary tract infection. Urine culture with antimicrobial susceptibility testing should be performed in all patients and used to direct therapy. Imaging, blood cultures, and measurement of serum inflammatory markers should not be performed in uncomplicated cases. Outpatient management is appropriate in patients who have uncomplicated disease and can tolerate oral therapy. Extended emergency department or observation unit stays are an appropriate option for patients who initially warrant intravenous therapy. Fluoroquinolones and trimethoprim/sulfamethoxazole are effective oral antibiotics in most cases, but increasing resistance makes empiric use problematic. When local resistance to a chosen oral antibiotic likely exceeds 10%, one dose of a long-acting broad-spectrum parenteral antibiotic should also be given while awaiting susceptibility data. Patients admitted to the hospital should receive parenteral antibiotic therapy, and those with sepsis or risk of infection with a multidrug-resistant organism should receive antibiotics with activity against extended-spectrum beta-lactamase–producing organisms. Most patients respond to appropriate management within 48 to 72 hours, and those who do not should be evaluated with imaging and repeat cultures while alternative diagnoses are considered. In cases of concurrent urinary tract obstruction, referral for urgent decompression should be pursued. Pregnant patients with pyelonephritis are at significantly elevated risk of severe complications and should be admitted and treated initially with parenteral therapy.

Acute pyelonephritis, a serious and relatively common bacterial infection of the kidney and renal pelvis, accounts for approximately 250,000 office visits and 200,000 hospital admissions annually in the United States.13



As of 2014, Escherichia coli resistance to trimethoprim/sulfamethoxazole and fluoroquinolones in the United States exceeded 35% and 10%, respectively.

A systematic review of 8 randomized controlled trials (N = 2,515) demonstrated equivalent clinical success rates in treating uncomplicated acute pyelonephritis with a 5- to 7-day course of fluoroquinolones compared with a 14-day course.

In the male subgroup of a 2017 randomized controlled trial, a 7-day course of ciprofloxacin was inferior to a 14-day course with respect to short-term cure rates with no differences in long-term outcomes.

Clinical recommendationEvidence ratingComments
Urine culture and antimicrobial susceptibility testing should be performed in patients with suspected acute pyelonephritis and used to direct antibiotic therapy.7 CExpert consensus guideline in the absence of clinical trials
Initial imaging should not be performed in uncomplicated cases of acute pyelonephritis. Contrast-enhanced computed tomography of the abdomen and pelvis is indicated in septic patients, when urinary obstruction is suspected, or when patients do not respond to appropriate therapy within 48 to 72 hours.23 CExpert consensus guideline based on low-quality observational evidence
Fluoroquinolones (e.g., ciprofloxacin for 7 days or levofloxacin [Levaquin] for 5 days) and trimethoprim/sulfamethoxazole for 14 days are appropriate first-line oral antibiotic therapies for uncomplicated acute pyelonephritis in women when the causative organism is susceptible.7,30 AExpert consensus based on consistent evidence from randomized controlled trials demonstrating effectiveness
In locations where Escherichia coli resistance to empiric oral therapy is likely greater than 10%, an initial broad-spectrum, long-acting parenteral antibiotic such as ceftriaxone, ertapenem (Invanz), or an aminoglycoside should be given concurrently.7 BExpert consensus based on lower quality clinical trials demonstrating benefit when combined with beta-lactams
Patients at increased risk of infection with multidrug-resistant organisms and those with sepsis should be treated with parenteral antibiotics that have activity against extended-spectrum beta-lactamase–producing organisms until susceptibility data are available.7 CExpert consensus guideline in the absence of clinical trials

Epidemiology and Microbiology

  • The highest incidence is among otherwise healthy women 15 to 29 years of age.3

  • Escherichia coli accounts for approximately 90% of uncomplicated pyelonephritis cases4,5; factors that define complicated pyelonephritis are listed in Table 1.6,7

  • Other causative organisms are more prevalent in complicated cases, but E. coli remains predominant4,5 (eTable A).

  • As of 2014, E. coli resistance to trimethoprim/sulfamethoxazole and fluoroquinolones in the United States exceeded 35% and 10%, respectively.5

  • Extended-spectrum beta-lactamase–producing uropathogenic organisms demonstrate resistance to third- and fourth-generation cephalosporins and are increasingly prevalent in the United States and globally.5

  • Risk factors for infection with multidrug-resistant organisms are listed in Table 2.5,7

Abnormal urinary tract anatomy or function; obstruction
Chronic catheterization or recent urinary tract instrumentation
Increased risk of multidrug-resistant organisms (Table 2)
Male sex*
Older age, frailty
Significant comorbidities (e.g., diabetes mellitus, organ transplant, sickle cell disease)
UropathogenTotal (n = 521)Uncomplicated (n = 286)Complicated* (n = 235)
Escherichia coli86.9%95.1%77.0%
Klebsiella pneumoniae4.8%1.4%8.9%
Staphylococcus aureus0.8%0%1.7%
Group B streptococcus0.4%0.3%0.4%
Staphylococcus saprophyticus0.4%0.7%0%
Antimicrobial use within the past 3 months (particularly fluoroquinolones and antipseudomonal penicillins)
History of multidrug-resistant urinary isolate (e.g., extended-spectrum beta-lactamase–producing organisms)
Hospitalization or institutionalization within the past 3 months
Indwelling urinary catheters
Travel outside the United States within the past 30 days
Urologic abnormalities


  • Flank pain and tenderness in the presence of pyuria are highly suggestive of pyelonephritis and differentiate it from other urinary tract infections.4,6,8,9

  • Fever is typically present but is not a universal symptom. Lower urinary tract symptoms (e.g., frequency, urgency, dysuria) may be absent in as many as 20% of patients.4,6,8,9

  • Other potential signs and symptoms of pyelonephritis include the following 4,6,8,9:

    – Constitutional symptoms (e.g., fever, chills, malaise)

    – Nausea, vomiting, and abdominal pain

    – Abdominal or suprapubic tenderness

    – Tachycardia or hypotension


  • Urine culture with antimicrobial susceptibility testing should be performed in all patients; when clinically reasonable, urine culture should be performed before the patient receives antibiotics.7

  • Several studies demonstrate no reduction in contamination rates with preparatory cleansing or midstream catch; catheterization is not necessary for specimen collection.1013

  • A basic metabolic profile and complete blood count help evaluate severity and can identify complications, particularly renal failure.9,14

  • Serum inflammatory markers have not been shown to assist in the diagnosis or treatment of pyelonephritis.1418

  • Blood cultures should be considered only in diagnostically ambiguous situations, when patients fail to improve within 48 to 72 hours, or when urine culture is unlikely to grow a predominant organism (e.g., indwelling catheterization, patients already taking antibiotics). Blood cultures are positive in 10% to 40% of patients with acute pyelonephritis, but the presence of bacteremia rarely affects therapy.8,1922

  • Initial imaging is not recommended in uncomplicated cases of acute pyelonephritis.23

  • Diagnostic imaging to identify obstruction or structural abnormalities should be considered in the following circumstances23,24:

    – Sepsis

    – Concern for urolithiasis

    – New renal insufficiency with glomerular filtration rate less than or equal to 40 mL per minute per 1.73 m2

    – Known urologic abnormalities

    – Failure to respond to appropriate therapy within 48 to 72 hours

  • When diagnostic imaging is indicated, contrast-enhanced computed tomography of the abdomen and pelvis is the preferred modality.23,25

  • When contrast or radiation is contraindicated, such as during pregnancy, ultrasonography and magnetic resonance imaging may be used.23

Already a member/subscriber?  Log In


From $145
  • Immediate, unlimited access to all AFP content
  • More than 130 CME credits/year
  • AAFP app access
  • Print delivery available

Issue Access

  • Immediate, unlimited access to this issue's content
  • CME credits
  • AAFP app access
  • Print delivery available

Article Only

  • Immediate, unlimited access to just this article
  • CME credits
  • AAFP app access
  • Print delivery available
Purchase Access:  Learn More

Continue Reading

More in AFP

Copyright © 2020 by the American Academy of Family Physicians.

This content is owned by the AAFP. A person viewing it online may make one printout of the material and may use that printout only for his or her personal, non-commercial reference. This material may not otherwise be downloaded, copied, printed, stored, transmitted or reproduced in any medium, whether now known or later invented, except as authorized in writing by the AAFP.  See for copyright questions and/or permission requests.