Pyelonephritis and Perinephric Abscess

Pyelonephritis is infection affecting the renal pelvis and the renal parenchyma. This condition arises mostly as a complication of bladder infection that ascends to the upper urinary tract. Pyelonephritis can be acute or chronic (which results from persistent or chronic infections). Typical acute symptoms are flank pain, fever, and nausea with vomiting. The chronic type depends on the underlying pathology. The diagnosis is established via clinical presentation, supported by laboratory findings (in blood and urine). Imaging studies are performed if severe illness is noted or there is no response to initial treatment (antibiotics). CT is the study of choice, given its ability to detect renal abnormalities associated with the infection, including the extent of the disease. Perinephric abscess is an infection involving the perinephric space between the kidney and Gerota’s fascia. Perinephric abscess can be an extension from pyelonephritis or from hematogenous spread of a systemic infection. The diagnosis is established via CT scan. The treatment includes antibiotics, with abscess drainage (which is both diagnostic and therapeutic).

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  • Pyelonephritis is infection of the kidney (pelvis and parenchyma) or the upper urinary tract and is considered a complicated urinary tract infection (UTI).
  • Perinephric abscess is an infection characterized by suppurative material (liquefaction) between Gerota’s fascia and the renal capsule.
    • Can extend into the psoas and transversalis muscles
    • Can extend into the peritoneal cavity
UTI ascending and hematogenous

Ascending hematogenous urinary tract infection

Image by Lecturio. License: CC BY-NC-SA 4.0

Types of pyelonephritis

Acute pyelonephritis is the sudden-onset infectious process and inflammation of the kidney(s) from ascending infection or hematogenous spread of systemic infections.

  • Uncomplicated pyelonephritis: infection with typical presentation and without the risk factors listed for the complicated type.
  • Complicated pyelonephritis:
    • Associated with pregnancy
    • Uncontrolled diabetes
    • Kidney transplantations
    • Urinary anatomical abnormalities
    • Acute or chronic kidney failure
    • Hospital-acquired infection
    • Immunocompromised state 
  • Chronic pyelonephritis emerges from recurrent or continuing UTIs, often associated with major anatomic abnormalities.


  • Acute pyelonephritis:
    • More common in females than in males
    • 15–17 cases per 10,000 females 
    • 3–4 cases per 10,000 males
  • Chronic pyelonephritis: 
    • Common in children
    • Associated with vesicoureteral reflux (VUR) disease, which is noted in 30%–40% of children with UTIs
    • More common in females
  • Perinephric abscess: 
    • Rare; accounts for approximately 0.02% of hospital admissions 
    • Approximately 75% due to complications of UTIs
    • 20%–60% associated with renal calculi



  • Gram-negative bacteria
    • Escherichia coli (most common):
      • Adheres to urinary tract
      • Has P fimbriae that interacts with the uroepithelial cells
    • Proteus mirabilis
    • Klebsiella spp.
    • Citrobacter spp.
    • Pseudomonas aeruginosa (seen in individuals who underwent procedures or had health care exposure)
  • Gram-positive bacteria
    • Staphylococci
    • Enterococci
    • Group B streptococci
  • In some cases, fungi (e.g., Candida) and viruses (adenovirus) cause UTIs.

Risk factors for urinary tract infections

Associated with the development of pyelonephritis and perinephric abscess:

  • Stasis and obstruction caused by: 
    • Benign prostatic hyperplasia (BPH) 
    • VUR
    • Medications that promote incomplete emptying of the bladder
    • Urethral stricture
    • Cystocele
    • Neurogenic bladder
  • Foreign body: 
    • Introduces pathogen, or 
    • Acts as a nidus of infection (e.g., catheter, instrumentation)
  • Conditions that cause decreased resistance to organisms, such as:
    • Diabetes mellitus
    • Malignancy
    • Immunosuppression
    • Spermicide use
    • Estrogen depletion
    • Antimicrobial use
  • Other:
    • Trauma
    • Anatomic abnormalities
    • Female (urethra is shorter and the anal and genital regions are close)
    • Sexual activity
    • Menopause
    • Fecal incontinence
    • Chronic constipation in toddlers


Acute pyelonephritis

  • Initial process:
    • Starts when the vaginal introitus or urethral meatus is colonized by pathogens, often the fecal flora
    • These microorganisms ascend into the bladder, and acute pyelonephritis develops when the infection reaches the kidney(s).
      • Ascending infection introduces the microorganism to the upper urinary tract.
      • Instrumentation also predisposes to ascending infection. 
    • Infection also can come from bacteremia, when seeding of the kidneys takes place (seen in staphylococci). 
  • Histopathologic findings: 
    • Necrosis or abscess formation is noted within the parenchyma.
    •  Renal tissue infiltration by neutrophils, macrophages, and plasma cells
  • Complications:
    • Renal abscess, a walled-off cavity of infection, with large lesions (> 2 cm) seen in individuals with a delayed diagnosis of diabetes
    • Perinephric abscess
    • Renal failure
    • Sepsis

Chronic pyelonephritis

  • Chronic pyelonephritis can occur when infection is persistent or recurrent. 
  • Affected kidney marked by inflammation and scarring:
    • Dilated, blunted calyces
    • Tubular thyroidization (tubules filled with colloid casts, like thyroid tissue)
    • Fibrosis and inflammatory infiltrates in interstitium
  • Predominant risk factors include:
    • Genitourinary tract anomalies 
    • Urinary tract obstruction (such as enlarged prostate or renal calculus)
    • VUR:
      • Primary: most common form of reflux, arising from incompetent or inadequate closure of the ureterovesical junction (UVJ)
      • Secondary: abnormally high voiding pressure does not close the UVJ (such as in posterior urethral valves)
  • Xanthogranulomatous pyelonephritis:
    • A variant of chronic pyelonephritis
    • Characterized by renal destruction by granulomatous tissue, which is believed to be from aberrant inflammation
    • Usual setting is obstruction due to infected renal stones.
    • Commonly associated with Proteus mirabilis and E. coli
    • Histopathologic changes show infiltration by lipid-laden macrophages.

Perinephric abscess

  • Also begins either from local infection or hematogenous spread
    • When the organism initially invades the kidney, there can be outward spread to the perirenal fat (usually in gram-negative organisms). 
    • Perinephric abscess also can form from a ruptured renal abscess.
    • The organism can come from the circulation (seen in staphylococcal infections) and seed the peritoneal fat and, in most cases, may not affect the kidney.
  • Risk factors include:
    • Diabetes
    • Pregnancy
    • Urinary tract abnormalities

Clinical Presentation

Clinical features of pyelonephritis

  • Acute pyelonephritis:
    • Classic triad of symptoms:
      • Fever
      • Costovertebral tenderness
      • Nausea/vomiting
    • Can be associated with symptoms of cystitis (but not always seen): 
      • Frequency
      • Urgency
      • Dysuria 
      • Suprapubic tenderness
    • Pediatric symptoms:
      • Poor feeding 
      • Failure to thrive
    • Geriatric symptoms: 
      • Altered mental status 
      • Disorientation
  • Chronic pyelonephritis is associated with: 
    • History of acute pyelonephritis 
    • Recurrent episodes of fever, lethargy, flank pain, and nausea

Clinical features of perinephric abscess

  • Insidious onset of:
    • Fever
    • Vague lumboabdominal pain
    • Fatigue, sweats, and weight loss
  • Can have a palpable flank mass
  • Symptoms of a lower UTI are not typical.



  • Findings suspicious for pyelonephritis: fever, flank pain, nausea/vomiting
  • Blood tests:
    • Possible ↑ serum creatinine 
    • Leukocytosis (CBC)
  • Urine studies:
    • Urinalysis:
      • Pyuria 
      • Bacteriuria
      • Hematuria
      • WBC casts (suggestive of renal origin of pyuria)
      • Nitrite: reflects + Enterobacteriaceae (e.g., E. coli)
    • Urine culture: growth supports diagnosis of infection and identifies etiologic organism
    • Pregnancy test, because pregnancy affects management choices
  • Imaging studies are often pursued if the infection is associated with severe illness or does not improve:
    • Ultrasonography (acute pyelonephritis):
      • Kidney may be diffusely or focally enlarged
      • Areas with edema are hypoechoic.
      • If hemorrhage is present, the area affected is hyperechoic.
      • Can be normal
    • Ultrasonography (chronic pyelonephritis):
      • Renal scarring, atrophy, and/or cortical thinning
      • Retraction of the papilla from overlying scar leads to calyceal clubbing
      • Thickened and dilated calyceal system
      • Asymmetric kidneys
    • CT (method of choice):
      • Detects an obstruction (e.g., stones causing hydroureter, hydronephrosis)
      • Identifies urinary tract anomalies 
      • Hypodense renal lesions due to ischemia can be seen.
    • MRI is an option if it is necessary to avoid use of contrast or radiation.
    • Other imaging studies:
      • Voiding cystourethrography: establishes presence and degree of VUR  
      • IV pyelography/urography: checks for anomalies and obstruction

Perinephric abscess

  • Findings of:
    • Fever, costovertebral tenderness
    • No response to treatment for pyelonephritis
    • Unexplained peritonitis, pelvic abscess, and empyema
  • Blood tests:
    • ↑ WBC
    • Elevated inflammatory markers
    • ↑ Creatinine and ↓ GFR 
    • Blood culture 
  • Urine studies: 
    • Urinalysis: 
      • Pyuria
      • WBC casts
      • Bacteriuria
      • May be negative if the abscess does not communicate with the collecting system
    • Urine culture: identifies the offending organism
  • Imaging: 
    • If presentation is nonspecific, plain radiography can be the initial test. Radiography may occasionally reveal suspicious findings.
      • Scoliosis with the concavity toward the affected kidney
      • Abdominal mass 
      • Kidney enlargement with indistinct outlines or undefined renal shadow 
      • Loss of psoas margin
      • Radiopaque calculus/calculi
    • Ultrasonography: can show a thick-walled perinephric abscess (hypoechoic or mixed echogenicity)
    • Abdominal CT with contrast:
      • Best imaging 
      • Shows an abscess in the perinephric space (attenuation of soft tissue or fluid)
      • Gas pockets may also be seen. 
      • Allows visualization of extension to adjacent structures
Axial CT image

Axial CT image through the upper pole of the right kidney showing perinephric abscess reaching posteriorly to the inferior vena cava.

Image: “Axial CT image through the upper pole of the right kidney showing perinephric abscess reaching posterior to IVC.” by Wani NA. License: CC BY 2.0


Acute pyelonephritis

Management depends on the severity of the clinical presentation and risk factors for drug resistance:

  • Uncomplicated pyelonephritis (mild course or with hemodynamic stability):
    • Empiric treatment:
      • 1st choice: oral fluoroquinolones such as ciprofloxacin or levofloxacin (not for children)
      • Alternative: cephalosporins (such as ceftibuten or cefpodoxime) or trimethoprim–sulfamethoxazole
    • Most cases can be managed on an outpatient basis.
    • Hospitalization is necessary if an affected individual is unable to maintain hydration or is severely ill.
  •  Complicated pyelonephritis or severe uncomplicated pyelonephritis: 
    • Hospitalization:
      • IV therapy
      • After clinical improvement → oral therapy
    • Empiric therapy options (no risk of multidrug resistance):
      • Ceftriaxone
      • Piperacillin–tazobactam
      • Ciprofloxacin or levofloxacin
    • Empiric therapy options (with risk for multidrug resistance):
      • Piperacillin–tazobactam
      • Meropenem, imipenem, or doripenem
      • If urine shows gram-positive cocci: vancomycin, daptomycin, or linezolid
    • For critically ill individuals (requiring intensive care): vancomycin + antipseudomonal carbapenem

Chronic pyelonephritis

  • Treatment of underlying cause (e.g., urology consult for obstruction)
  • For recurrent infections, long-term antibiotic therapy is an option.
  • Xanthogranulomatous pyelonephritis is treated with nephrectomy (partial or full) after initial antibiotic treatment.

Perinephric abscess

  • Antibiotics (choice depends on the suspected pathogenesis):
    • If associated with pyelonephritis, therapy targets Enterobacteriaceae.
    • If associated with staphylococcal systemic infection, therapy targets this etiologic agent.
  • Drainage:
    • If abscess is small (e.g., < 3 cm), antibiotic may be enough (especially if other specimens provide sufficient information regarding etiology)
    • Percutaneous drainage is done for diagnostic (especially if other specimens are not available) and therapeutic purposes.
    • Larger abscesses and/or failures to resolve with antibiotics require surgical intervention.

Differential Diagnosis

  • Acute appendicitis: inflammation of the vermiform appendix. Acute appendicitis can also present with fever and pyuria. The pain of appendicitis is typically localized in the RLQ, not the costophrenic angle. Diagnosis can be confirmed with imaging (CT scan).  
  • Acute cholecystitis: like pyelonephritis, acute cholecystitis is more common in women and may present with fever and abdominal pain. However, in acute cholecystitis, the pain is localized in the RUQ, not the costophrenic angle. Also, urinalysis in the case of pyelonephritis shows bacteriuria, which can help differentiate it from cholecystitis. 
  • Pancreatitis: can present with fever and abdominal pain, but the pain is localized in the epigastrium, not the costophrenic angle. Laboratory studies help distinguish these conditions: the urinalysis in pyelonephritis shows abnormalities such as bacteriuria and pyuria,  and pancreatitis is associated with elevated amylase and lipase. 
  • Lower UTI: can coexist with pyelonephritis. Lower UTIs usually are not associated with flank pain and are generally shorter in duration. Similar organisms lead to lower and upper UTIs; thus, antibiotics targeting these etiologic agents cover both lower UTI  and pyelonephritis. 
  • Renal abscess: collection of suppurative material within the renal parenchyma. Renal abscess is usually associated with VUR and urinary tract obstruction from a stone. Differentiation from perinephric abscess is achieved with imaging studies (e.g., CT scan).
  • Urinoma: mass or encapsulated collection of extravasated urine. Urinoma arises from urinary tract injury or from spontaneous rupture secondary to urinary obstruction.  Urinoma can be differentiated from perinephric abscess by imaging studies, which include ultrasonography, CT, and MRI.


  1. Barshak M, Kasper DL. (2018). Intraabdominal infections and abscesses. Chapter 127 of Jameson J, Fauci AS, Kasper DL, Hauser SL, Longo DL, Loscalzo J (Eds.), Harrison’s Principles of Internal Medicine, 20th ed. McGraw-Hill.
  2. Belyayeva M, Jeong JM. (2021). Acute pyelonephritis. StatPearls.
  3. Hooton T, Gupta K. (2021). Acute complicated urinary tract infection (including pyelonephritis) in adults. UpToDate. Retrieved July 25, 2021, from
  4. Lohr, J. (2019). Chronic pyelonephritis. Medscape. Retrieved July 25, 2021, from
  5. Meyrier, A. (2021). Renal and perinephric abscess. UpToDate. Retrieved July 25, 2021, from 
  6. Okafor CN, Onyeaso E.E. (2020). Perinephric abscess. StatPearls. Retrieved July 28, 2021,

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