Acute pyelonephritis is an infection of one or both of the kidneys. It occurs as a result of an ascending urinary tract infection (UTI) which has spread from the bladder up towards the kidneys. It is usually caused by bacteria entering the urinary tract through the urethra.

Whilst lower UTIs are very common, pyelonephritis is much rarer. However, it is an important diagnosis to make because if left untreated it can lead to serious complications and irreversible kidney damage.


  • Incidence: 100.00 cases per 100,000 person-years
  • Peak incidence: 40-50 years
  • Sex ratio: more common in females 3:1
Condition Relative
Urinary tract infection (lower) in adults35.00
Acute pyelonephritis1
Ruptured abdominal aortic aneurysm0.10
<1 1-5 6+ 16+ 30+ 40+ 50+ 60+ 70+ 80+


Many organisms can cause acute pyelonephritis however the most common are gram negative bacteria:

  • Escherichia coli (80%)
  • Klebsiella species
  • Proteus mirabilis
  • Pseudomonas species (more common in hospital acquired infections)
  • Enterobacter species

In rare cases, fungi (most commonly Candida species) can cause pyelonephritis. This is usually seen in patients with nephrostomy tubes, patients who are immunocompromised, etc.

A number of factors increase the risk of infection:

  • Female sex
    • Women’s urethras are shorter than men’s, so it’s easier for bacteria to enter
  • Factors that reduce the flow of urine (if urine cannot flow properly, it becomes stagnant allowing bacteria to multiply rapidly)
    • Stones, BPH, tract abnormalities
    • Spinal cord injuries leading to a neuropathic bladder
  • Retrograde ascent of bacteria
    • Vesico-ureteric reflux- a condition where urine from the bladder flows backwards into the ureters and kidneys
  • Catheter use
  • Pregnancy
  • Immunosuppression
    • Diabetes mellitus, corticosteroid use, cancer, HIV, etc


Bacteria entering the urinary tract through the urethra can cause symptoms of a lower urinary tract infection (cystitis/urethritis).
  • If these bacteria travel up to the kidneys, pyelonephritis can occur.

  • A much rarer mechanism is the bacteria reaching the kidney through the blood stream.
    • This can occur in patients with infective endocarditis.

Clinical features

Symptoms of pyelonephritis typically develop quickly; usually over a couple of days.

Most commonly:

Other symptoms include:
  • Haematuria
    • This may require further investigation as it could be a sign of cancer- bladder, renal or prostate cancer in men.
    • Consider a 2-week wait referral for urological cancers
  • Foul-smelling urine
  • Malaise
  • Diarrhoea
  • Confusion

Clinical findings-
  • Tenderness over the loin area
  • Signs of shock
    • Urosepsis is a life-threatening complication of pyelonephritis and can lead to septic shock. Signs include hypotension tachypnoea, skin changes, oliguria

It is important to note that the presentation can differ between age groups:
  • Young children may have non-specific symptoms such as a fever, irritability and poor feeding
  • Elderly patients may present with increased confusion or new incontinence.


Pyelonephritis is diagnosed by taking a medical history and by physical examination. Investigations can help exclude other causes of a patient's symptoms and as an aid to make the diagnosis.

NICE 2019 guidelines advise that a definitive diagnosis can be made in patients with loin pain and/or fever if a UTI is confirmed by culturing a urinary pathogen from the urine and other causes of loin pain and/or fever have been excluded.

The following investigations are recommended in all patients-
  • Mid-stream urine (MSU)/ catheter specimen urine (CSU)
    • These samples should be taken before starting empirical drug treatment
    • Urine cultures are positive in around 90% of patients
    • Negative cultures do not exclude the diagnosis

Other investigations to consider include-
  • Urinalysis
    • This should not delay starting antibiotics
    • Not to be used in patients with long term catheters or aged over 65
  • Blood tests including blood cultures
    • Inflammatory markers may be elevated
    • Blood cultures are positive in around 20% of patients

Imaging is not routinely performed in all patients. It is recommended in men and children and for patients with recurrent pyelonephritis.

  • Ultrasound (US)
    • Useful in children as it is quick and there is no risk of radiation
    • May identify obstruction or stones
    • May identify complications such as perinephric collections and hydronephrosis
  • CT (non contrast)
    • CT scan of the kidneys, ureters and bladder (CT KUB)
    • More sensitive than US
  • MRI
    • Can be used in pregnant woman

Differential diagnosis

There are a wide range of differentials that need to be considered before a diagnosis of pyelonephritis can be made. These include the following-

  • Simple UTI (lower urinary tract infected)
    • Suprapubic pain, frequency and dysuria are more common in a simple infection, pain is less severe
    • Fevers usually more pronounced in pyelonephritis
    • Systemic systems such a malaise are more common in pyelonephritis
  • Causes of an acute abdomen
    • Examples include appendicitis, diverticulitis, acute pancreatitis
    • Costovertebral/flank pain more likely in pyelonephritis
    • Guarding not usually a feature of pyelonephritis
    • Nausea and vomiting can be a feature of both
  • Abdominal aortic aneurysm (AAA)
    • Can also present with back pain
    • Pulsatile abdominal mass may be felt in an AAA
    • Ultrasound can be used for initial assessment to detect an AAA
  • Gynaecological causes
    • Ectopic pregnancy, endometritis
    • Ensure all relevant patients have a pregnancy test and take a detailed gynae history if appropriate
  • Costovertebral angle pain less common
  • Lower lobe pneumonia
    • Consider if respiratory symptoms are present


The mainstay of treatment of acute pyelonephritis is antibiotics. Empirical antibiotics should be started after urine cultures have been taken. These can later be tailored once the sensitivities are available.

  • Other treatments to consider:
    • IV fluids
    • Analgesia
    • Antiemetics if required

  • NICE offers guidelines for the use of catheters in patients with symptoms of pyelonephritis-
    • Remove if possible
    • Ensure catheters are correctly positioned, drain correctly and are not blocked.
    • Catheter change in patients with a long term catheter if it has been in place for more than 7 days

Patients can often be managed with oral antibiotics (7-10 day course usually required) in the community but hospital admission should be considered in the following circumstances-

  • Pregnant woman
  • Patients who are not improving in the community despite 48 hours of treatment
  • Severe pain
  • Patients with signs of severe illness
    • Tachycardia, hypotension, reduced urine output, tachypnoea, confusion, etc
  • Patients who are unable to tolerate oral fluids/medicines
  • Patients at risk of developing complications
    • Those with underlying diseases such as diabetes mellitus
    • All babies under 3 months
    • 65 years old +
    • Patients with a known abnormalities of the of the genitourinary tract

Hospital treatment may be required so that intravenous antibiotics can be given.

Rarely, surgery may be required to drain a renal abscess. Recurrent pyelonephritis can be caused by structural problems and surgery may be required to correct abnormalities to reduce the risk of further infections.

In very severe infection, a nephrectomy may be required.


If treated appropriately complications can often be avoided however they can occur. The main ones to be aware of include:

  • Acute kidney injury
  • Urosepsis
    • If the bacteria enter the bloodstream, sepsis can occur
  • Perinephric/renal abscess
  • Premature labour in pregnancy

  • Chronic pyelonephritis
    • Characterised by scarring on the kidney which occurs after recurrent or persistent infections
    • Can be asymptomatic