Acute Pyelonephritis – Causes, Symptoms, Diagnosis, Treatment

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Acute pyelonephritis is a bacterial infection causing inflammation of the kidneys. Pyelonephritis occurs as a complication of an ascending urinary tract infection that spreads from the bladder to the kidneys. Symptoms usually include fever, flank pain, nausea, vomiting, burning with urination, increased frequency, and urgency. This activity outlines the clinical presentation, diagnosis, and management of acute pyelonephritis, and highlights the role of the interprofessional team in caring for patient with the condition.

Acute pyelonephritis is a bacterial infection causing inflammation of the kidneys and is one of the most common diseases of the kidney. Pyelonephritis occurs as a complication of an ascending urinary tract infection (UTI) which spreads from the bladder to the kidneys and their collecting systems. The 2 most common symptoms are usually fever and flank pain. Acute pyelonephritis can be divided into uncomplicated and complicated. Complicated pyelonephritis includes pregnant patients, patients with uncontrolled diabetes, kidney transplants, urinary anatomical abnormalities, acute or chronic kidney failure, as well as immunocompromised patients and those with hospital-acquired bacterial infections. It is important to make a distinction between complicated and uncomplicated pyelonephritis, as patient management and disposition depend on it.

Causes of Acute Pyelonephritis

The main cause of acute pyelonephritis is gram-negative bacteria, the most common being Escherichia coli. Other gram-negative bacteria which cause acute pyelonephritis include Proteus, Klebsiella, and Enterobacter. In most patients, the infecting organism will come from their fecal flora. Bacteria can reach the kidneys in 2 ways: hematogenous spread and through ascending infection from the lower urinary tract. Hematogenous spread is less common and usually occurs in patients with ureteral obstructions or immunocompromised and debilitated patients. Most patients will get acute pyelonephritis through ascending infection. Ascending infection happens through several steps. Bacteria will first attach to urethral mucosal epithelial cells and will then travel to the bladder via the urethra either through either instrumentation or urinary tract infections which occur more frequently in females. UTIs are more common in females than in males due to shorter urethras, hormonal changes, and close distance to the anus. Urinary tract obstruction caused by something such as a kidney stone can also lead to acute pyelonephritis. An outflow obstruction of urine can lead to incomplete emptying and urinary stasis which causes bacteria to multiply without being flushed out. A less common cause of acute pyelonephritis is vesicoureteral reflux, which is a congenital condition where urine flows backward from the bladder into the kidneys.

E. coli is the most common bacteria causing acute pyelonephritis due to its unique ability to adhere to and colonize the urinary tract and kidneys. E.coli has adhesive molecules called P-fimbriae which interact with receptors on the surface of uroepithelial cells. Kidneys infected with E. coli can lead to an acute inflammatory response which can cause scarring of the renal parenchyma. Though the mechanism in which renal scarring occurs is still poorly understood, it has been hypothesized that the adhesion of bacteria to the renal cells disrupts the protective barriers, which lead to localized infection, hypoxia, ischemia, and clotting in an attempt to contain the infection. Inflammatory cytokines, bacterial toxins, and other reactive processes further lead to complete pyelonephritis and in many cases systemic symptoms of sepsis and shock.

  • Mechanical – any structural abnormalities in the urinary tract, vesicoureteral reflux (urine from the bladder flowing back into the ureter), kidney stones, urinary tract catheterization, ureteral stents or drainage procedures (e.g., nephrostomy), pregnancy, neurogenic bladder (e.g., due to spinal cord damage, spina bifida or multiple sclerosis) and prostate disease (e.g., benign prostatic hyperplasia) in men
  • Constitutional – diabetes mellitus, immunocompromised states
  • Behavioral – change in sexual partner within the last year, spermicide use
  • Being female – The urethra is shorter in women than it is in men, which makes it easier for bacteria to travel from outside the body to the bladder. The nearness of the urethra to the vagina and anus also creates more opportunities for bacteria to enter the bladder. Once in the bladder, an infection can spread to the kidneys. Pregnant women are at even higher risk of a kidney infection.
  • Having a urinary tract blockage – This includes anything that slows the flow of urine or reduces your ability to empty your bladder when urinating — including a kidney stone, something abnormal in your urinary tract’s structure or, in men, an enlarged prostate gland.
  • Having a weakened immune system – This includes medical conditions that impair your immune systems, such as diabetes and HIV. Certain medications, such as drugs taken to prevent rejection of transplanted organs, have a similar effect.
  • Having damage to nerves around the bladder – Nerve or spinal cord damage can block the sensations of a bladder infection so that you’re unaware when it’s advancing to a kidney infection.
  • Using a urinary catheter for a time – Urinary catheters are tubes used to drain urine from the bladder. You might have a catheter placed during and after some surgical procedures and diagnostic tests. You might use one continuously if you’re confined to a bed.
  • Having a condition that causes urine to flow the wrong way – In vesicoureteral reflux, small amounts of urine flow from your bladder back up into your ureters and kidneys. People with this condition are at higher risk of kidney infection during childhood and adulthood. Positive family history (close family members with frequent urinary tract infections)
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Symptoms of Acute Pyelonephritis

Symptoms usually appear within two days of infection. Common symptoms include:

  • a fever greater than 102°F (38.9°C)
  • pain in the abdomen, back, side, or groin
  • painful or burning urination
  • cloudy urine
  • pus or blood in the urine
  • urgent or frequent urination
  • fishy-smelling urine
  • shaking or chills
  • nausea – vomiting
  • general aching or ill feeling
  • fatigue
  • moist skin
  • mental confusion
  • Frequent urination
  • Strong, persistent urge to urinate
  • Burning sensation
  • Urine that smells bad or is cloudy

Symptoms may be different in children and older adults than they are in other people. For example, mental confusion is common in older adults and is often their only symptom. People with chronic pyelonephritis may experience only mild symptoms or may even lack noticeable symptoms altogether.

Diagnosis of Acute Pyelonephritis

Histopathology will usually reveal necrosis or putrid abscess formation within the renal parenchyma. The renal tissues are infiltrated with neutrophils, macrophages, and plasma cells. However, the architecture is not completely disorganized.

History and Physical

Acute pyelonephritis will classically present as a triad of fever, flank pain, and nausea or vomiting, but not all symptoms have to be present. Symptoms will usually develop within several hours or over the course of a day. Symptoms of cystitis such as dysuria and hematuria will be present in women usually. In children, common symptoms of acute pyelonephritis can be absent. Symptoms such as failure to thrive, fever, and feeding difficulty are most common in neonates and children under 2 years old. Elderly patients may present with altered mental status, fever, deterioration, and damage to other organ systems. On physical examination, the patient’s general appearance will be variable. Some patients will appear ill and uncomfortable, while others may appear healthy. Patients will usually not appear toxic. When a patient is febrile, fever may be high, often over 103 F. Costovertebral angle tenderness is commonly unilateral over the affected kidney, but in some cases, bilateral costovertebral angle tenderness may be present. Suprapubic tenderness during the abdominal examination will vary from mild to moderate with or without rebound tenderness.

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Lab Test and Imaging

A good history and physical is the mainstay of evaluating acute pyelonephritis, but laboratory and imaging studies can be helpful. A urinary specimen should be obtained for a urinalysis.

  • Blood Test – work such as a complete blood cell count (CBC) is sent to look for an elevation in white blood cells. The complete metabolic panel can be used to search for aberrations in creatinine and BUN to assess kidney function.
  • Urinalysis – For a urinalysis, you will collect a urine sample in a special container at a doctor’s office or at a lab. On urinalysis, one should look for pyuria as it is the most common finding in patients with acute pyelonephritis. Nitrite production will indicate that the causative bacteria is E.coli. Proteinuria and microscopic hematuria may be present as well on urinalysis. If hematuria is present, then other causes may be considered such as kidney stones. All patients with suspected acute pyelonephritis should also have urine cultures sent for proper antibiotic management.  A health care professional will look at the sample under a microscope for bacteria and white blood cells, which the body produces to fight infection. Bacteria also can be found in the urine of healthy people, so a kidney infection is diagnosed based both on your symptoms and a lab test.
  • Urine culture – A health care professional may culture your urine to find out what type of bacteria is causing the infection. A health care professional can see how the bacteria have multiplied, usually in 1 to 3 days, and can then determine the best treatment.
  • Ultrasonography – can be used to detect pyelonephritis, but a negative study does not exclude acute pyelonephritis. Regardless, ultrasound can still be a useful study when evaluating for acute pyelonephritis because it can be done bedside, has no radiation exposure, and may reveal renal abnormalities, which can prompt further testing or definitive treatment.
  • FBC  – this shows elevated white cell count with neutrophilia.
  • Blood cultures – these are positive in approximately 15-30% of cases.


  • X-Ray – Imaging is useful if the clinical picture or biochemical markers are ambivalent, as structural problems are not uncommon. Ultrasonography is usually the first-line investigation. Whether advised for all varies between guidelines. Imaging is normally recommended in men and children; it is mandatory in patients with recurrent pyelonephritis and may help to identify obstruction or stones.
  • CT Scan – The imagining study of choice for acute pyelonephritis is abdominal/pelvic CT with contrast. Imaging studies will usually not be required for the diagnosis of acute pyelonephritis but are indicated for patients with a renal transplant, patients in septic shock, those patients with poorly controlled diabetes, complicated UTIs, immunocompromised patients, or those with toxicity persisting for longer than 72 hours.
  • Dimercaptosuccinic acid (DMSA) scan –  is mainly used for detailed renal cortical views in recurrent cases, to detect scarring.
  • MRI – is also useful in detecting scarring but may require sedation in children. In adults, it is increasingly used where renal infection, masses, and urinary obstruction are suspected but its use is limited by cost and availability.
  • Renal biopsy –  is occasionally employed to exclude papillary necrosis.

Recent studies identified procalcitonin as a biological marker in diagnosing acute pyelonephritis in children, potentially more useful than white cell count or CRP. National Institute for Health and Care Excellence (NICE) guidance advises CRP alone is not useful in differentiating lower UTI from pyelonephritis in children. Cochrane review in 2015 came to the conclusion that although procalcitonin seemed the most helpful, there was not enough evidence to recommend routine use of any of these blood tests in clinical practice at this time.

Treatment of Acute Pyelonephritis

Acute pyelonephritis can be managed as either outpatient or inpatient. Healthy, young, non-pregnant women who present with uncomplicated pyelonephritis can be treated as outpatients. Inpatient treatment is usually required for those who are very young, elderly, immunocompromised, those with poorly controlled diabetes, renal transplant, patients, patients with structural abnormalities of the urinary tract, pregnant patients, or those who cannot tolerate oral intake. The mainstay of treatment of acute pyelonephritis is antibiotics, analgesics, and antipyretics. Nonsteroidal anti-inflammatory drugs (NSAIDs) work well to treat both pain and fever associated with acute pyelonephritis. The initial selection of antibiotics will be empiric and should be based on the local antibiotic resistance. Antibiotic therapy should then be adjusted based on the results of the urine culture. Most uncomplicated cases of acute pyelonephritis will be caused by E. coli for which patients can be treated with oral cephalosporins or TMP-SMX for 14 days. Complicated cases of acute pyelonephritis require intravenous (IV) antibiotic treatment until there are clinical improvements. Examples of IV antibiotics include piperacillin-tazobactam, fluoroquinolones, meropenem, and cefepime. For patients who have allergies to penicillin, vancomycin can be used. Follow-up for non-admitted patients for resolution of symptoms should be in 1 to 2 days. Follow-up urine culture results should be obtained only in patients who had a complicated course and are usually not needed in healthy, non-pregnant women. Any patient that had a complicated UTI should be sent for follow-up imaging to identify any abnormalities that predispose the patient to further infections.

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If left untreated, a kidney infection can lead to potentially serious complications, such as:

  • Kidney scarring – This can lead to chronic kidney disease, high blood pressure, and kidney failure.
  • Blood poisoning (septicemia) – Your kidneys filter waste from your blood and return your filtered blood to the rest of your body. Having a kidney infection can cause the bacteria to spread through your bloodstream.
  • Pregnancy complications – Women who develop a kidney infection during pregnancy may have an increased risk of delivering low birth weight babies.


Reduce your risk of kidney infection by taking steps to prevent urinary tract infections. Women, in particular, may reduce their risk of urinary tract infections if they:

  • Drink fluids, especially water – Fluids can help remove bacteria from your body when you urinate.
  • Urinate as soon as you need to – Avoid delaying urination when you feel the urge to urinate.
  • Empty the bladder after intercourse – Urinating as soon as possible after intercourse helps clear bacteria from the urethra, reducing your risk of infection.
  • Wipe carefully – Wiping from front to back after urinating and after a bowel movement helps prevent bacteria from spreading to the urethra.
  • Avoid using feminine products in the genital area – Using products such as deodorant sprays in your genital area or douches can be irritating.


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