Pyelonephritis: Causes, Symptoms, Diagnosis, Treatment, and Prevention

Pyelonephritis is a severe kidney infection that affects millions of individuals worldwide. It is characterized by inflammation of the renal pelvis and kidney tissue, primarily caused by a bacterial infection. This comprehensive guide will explore the various aspects of pyelonephritis, including its causes, symptoms, diagnosis, treatment options, and preventive measures.

What is Pyelonephritis?

Pyelonephritis is an infection that affects the kidneys, specifically the renal pelvis and the surrounding kidney tissue. It is a type of urinary tract infection (UTI) that involves the upper urinary system. The condition occurs when bacteria, most commonly Escherichia coli (E. coli), enter the urinary tract and ascend from the bladder to the kidneys.


Anatomy and Function of the Kidneys

The kidneys are vital organs of the human body that play a crucial role in maintaining overall health. Here’s an overview of the anatomy and function of the kidneys:


  • Location: The kidneys are two bean-shaped organs on either side of the spine in the lower back, just below the rib cage.
  • Structure: Each kidney is approximately the size of a fist and consists of three central regions: the outer cortex, the inner medulla, and the renal pelvis.
  • Nephrons: The functional units of the kidneys are called nephrons. Each kidney contains millions of nephrons responsible for filtering and processing the blood.
  • Renal Artery and Vein: The kidneys receive their blood supply through the renal artery, and the filtered blood is returned to circulation via the renal vein.


  1. Filtration: The kidneys’ primary function is to filter waste products, excess fluids, and toxins from the blood. Each nephron contains a glomerulus filtering unit, where blood is initially filtered to form a liquid called the filtrate.
  2. Reabsorption: As the filtrate passes through the tubules of the nephron, essential substances such as water, electrolytes (sodium, potassium, calcium, etc.), and glucose are reabsorbed back into the bloodstream. This process helps maintain the body’s balance of fluids and electrolytes.
  3. Secretion: The kidneys also secrete certain substances, such as hydrogen ions, potassium ions, and drugs, into the filtrate to further adjust the body’s acid-base balance and eliminate waste products.
  4. Urine Formation: After filtration, reabsorption, and secretion processes, the remaining fluid in the nephron is converted into urine. The urine is then collected in the renal pelvis and transported to the bladder through tubes called ureters.
  5. Regulation of Fluid and Electrolyte Balance: The kidneys play a crucial role in maintaining the body’s fluid balance by adjusting the amount of water and electrolytes excreted in the urine. This helps regulate blood pressure, osmolarity, and the overall composition of bodily fluids.
  6. Acid-Base Balance: The kidneys help regulate the body’s acid-base balance by reabsorbing bicarbonate ions and excreting hydrogen ions in response to changes in blood pH.
  7. Hormone Production: The kidneys produce essential hormones that regulate various bodily functions. One such hormone is erythropoietin, which stimulates the production of red blood cells in the bone marrow. Another hormone is renin, which plays a role in regulating blood pressure and fluid balance.

Bacterial Pathogens in Pyelonephritis

Pyelonephritis, a kidney infection characterized by inflammation of the renal pelvis and kidney tissue, is primarily caused by bacterial pathogens. The most common causative agent is Escherichia coli (E. coli), responsible for approximately 80-90% of community-acquired cases of pyelonephritis. However, other bacterial species can also contribute to the development of this condition. Understanding the bacterial pathogens involved in pyelonephritis is crucial for appropriate diagnosis, treatment, and preventive strategies.

  1. Escherichia coli (E. coli): E. coli is a Gram-negative bacterium that normally resides in the gastrointestinal tract. However, certain E. coli can ascend from the urethra to the bladder and reach the kidneys, leading to pyelonephritis. Factors such as sexual activity, urinary tract abnormalities, and impaired immune function can increase the risk of E. coli-associated pyelonephritis.
  2. Klebsiella pneumoniae: Klebsiella pneumoniae is another Gram-negative bacterium that can cause pyelonephritis. It is a common pathogen in healthcare-associated infections, especially in individuals with underlying conditions or those who have been hospitalized. Klebsiella pneumoniae is known for its ability to form biofilms and resist antibiotics, making infections more challenging to treat.
  3. Proteus mirabilis: Proteus mirabilis is a Gram-negative bacterium frequently associated with urinary tract infections (UTIs) and pyelonephritis. It possesses unique characteristics, such as swarming motility and the ability to produce urease. The production of urease allows Proteus mirabilis to hydrolyze urea, having ammonia and alkalization of the urine, which can contribute to stone formation and recurrent infections.
  4. Enterococcus faecalis: Enterococcus faecalis is a Gram-positive bacterium that commonly colonizes the gastrointestinal tract and can cause UTIs, including pyelonephritis. It is known for its ability to survive in the urinary tract and resist antibiotic treatment. Enterococcal pyelonephritis may occur in individuals with underlying urinary tract abnormalities, recent instrumentation, or compromised immune systems.
  5. Pseudomonas aeruginosa: Pseudomonas aeruginosa is a Gram-negative bacterium associated with healthcare-associated infections and can cause severe cases of pyelonephritis. It is often seen in individuals with structural abnormalities of the urinary tract, catheter-associated infections, or prolonged hospital stays. Pseudomonas aeruginosa possesses intrinsic resistance mechanisms, making it difficult to treat and leading to increased morbidity and mortality.
  6. Other Bacterial Pathogens: Less commonly, other bacterial species such as Staphylococcus saprophyticusEnterobacter spp., Citrobacter spp., and Morganella morganii can contribute to developing pyelonephritis. These pathogens are typically associated with specific risk factors or unique clinical situations.

Risk Factors for Pyelonephritis

Pyelonephritis, a kidney infection characterized by inflammation of the renal pelvis and kidney tissue, can occur in individuals of all ages. While anyone can develop pyelonephritis, certain risk factors increase the likelihood of experiencing this condition. Understanding these risk factors is essential for identifying individuals who may be more susceptible and implementing preventive strategies. Here are some common risk factors associated with pyelonephritis:

  1. Gender: Females are more prone to pyelonephritis than males due to anatomical differences. The female urethra is shorter, allowing bacteria to travel more easily from the urethra to the bladder and kidneys. Additionally, hormonal changes during pregnancy can affect urinary tract function, increasing the risk of pyelonephritis in pregnant women.
  2. Urinary Tract Abnormalities: Structural abnormalities in the urinary tract, such as kidney stones, vesicoureteral reflux (VUR), urinary tract obstruction, or anatomical defects present at birth, can predispose individuals to pyelonephritis. These abnormalities can disrupt normal urine flow, provide sites for bacterial colonization, and hinder the body’s ability to effectively clear bacteria from the urinary system.
  3. Urinary Tract Obstruction: Any condition that obstructs the flow of urine, such as urinary stones, tumors, enlarged prostate (in males), or urinary catheterization, can increase the risk of pyelonephritis. Obstructions can lead to stagnant urine, creating an environment favorable for bacterial growth and infection.
  4. Compromised Immune System: Individuals with weakened immune systems, such as those with HIV/AIDS, undergoing chemotherapy, or taking immunosuppressive medications, are more susceptible to infections, including pyelonephritis. A compromised immune system impairs the body’s ability to fight off bacterial pathogens effectively, increasing the risk and severity of diseases.
  5. Diabetes: Uncontrolled diabetes can weaken the immune system and impair urinary tract function, making individuals more susceptible to urinary tract infections (UTIs), including pyelonephritis. Elevated blood sugar levels create an environment conducive to bacterial growth and increase the risk of recurrent infections.
  6. Catheter Use: Indwelling urinary catheters are commonly used in healthcare settings, and their presence can introduce bacteria into the urinary tract, increasing the risk of pyelonephritis. Catheter-associated pyelonephritis is a significant concern, especially in hospitalized individuals or those with long-term catheter use.
  7. Recent Urinary Tract Procedures: Recent urological procedures, such as urinary catheter insertion, cystoscopy, or urinary tract surgery, can disrupt normal urinary tract defenses and introduce bacteria, increasing the risk of pyelonephritis. Good sterile techniques during these procedures are crucial to minimize the risk of infection.
  8. Sexual Activity: Engaging in sexual activity can introduce bacteria into the urinary tract, particularly in females. The urethra’s proximity to the anus and the mechanical action during sexual intercourse can facilitate the migration of bacteria to the bladder and kidneys, increasing the risk of pyelonephritis.
  9. Age: Infants and young children may be more susceptible to pyelonephritis due to incomplete bladder emptying, vesicoureteral reflux (VUR), and congenital urinary tract abnormalities. In older adults, age-related changes in the urinary tract weakened immune function, and comorbidities can increase the risk of pyelonephritis.
  10. Personal or Family History: Individuals with a history of UTIs or pyelonephritis may have a higher predisposition to develop the condition. Genetic factors and shared lifestyle habits may contribute to an increased risk of recurrent.

Complications Associated with Pyelonephritis

Pyelonephritis, a severe kidney infection characterized by the renal pelvis and kidney tissue inflammation, can lead to complications if left untreated or inadequately managed. Recognizing and addressing these complications promptly is crucial to prevent long-term consequences. Here are some potential complications associated with pyelonephritis:

  1. Kidney Abscess: One of the most significant complications of pyelonephritis is the formation of kidney abscesses. These are pus-filled pockets that develop within the kidney due to the infection. Kidney abscesses require drainage or surgical intervention to remove the accumulated pus and prevent further damage to the kidney tissue.
  2. Sepsis: Severe cases of pyelonephritis can lead to a condition called sepsis. Sepsis occurs when the infection spreads from the kidneys into the bloodstream, causing a systemic inflammatory response. It can lead to organ dysfunction, low blood pressure, and, in severe cases, life-threatening complications.
  3. Chronic Kidney Disease: Recurrent or severe episodes of pyelonephritis can cause kidney damage over time, leading to chronic kidney disease (CKD). The inflammation and scarring caused by repeated infections can impair kidney function and compromise the organ’s ability to filter waste products from the blood.
  4. Renal Scarring: Prolonged or recurrent pyelonephritis can result in the formation of scar tissue within the kidneys. Renal scarring can affect the normal structure and function of the kidneys, potentially leading to hypertension, proteinuria (excessive protein in the urine), and decreased kidney function.
  5. Septicemia: When the infection spreads from the kidneys to the bloodstream, it can cause septicemia or bloodstream infection. Septicemia can lead to widespread infection throughout the body and may result in severe organ dysfunction and life-threatening complications if not promptly treated.
  6. Pregnancy Complications: Pyelonephritis during pregnancy poses risks to both the mother and the developing fetus. In pregnant women, untreated or inadequately managed pyelonephritis can increase the risk of preterm labor, low birth weight, and maternal complications such as preeclampsia and gestational hypertension.
  7. Acute Kidney Injury: Severe cases of pyelonephritis can lead to acute kidney injury (AKI). AKI is a sudden and significant decrease in kidney function, resulting in the inability of the kidneys to filter waste products and maintain fluid and electrolyte balance properly. It requires immediate medical attention to prevent further kidney damage and restore kidney function.
  8. Urosepsis: Urosepsis is a severe infection that occurs when the urinary tract infection, such as pyelonephritis, progresses to sepsis. Bacteria in the blood characterize it and can lead to systemic complications, multiple organ failure, and a high mortality risk if not treated promptly and aggressively.
  9. Renal Papillary Necrosis: In rare cases, severe or recurrent pyelonephritis can cause renal papillary necrosis. This condition involves the death of the innermost part of the kidney, known as the renal papilla. Renal papillary necrosis can lead to severe pain, blood in the urine, and potentially compromise kidney function.
  10. Long-Term Effects on Quality of Life: Pyelonephritis, especially when it becomes recurrent or leads to chronic kidney disease, can significantly impact an individual’s quality of life. The need for ongoing medical management, dietary restrictions, and potential complications can affect daily activities, overall well-being, and psychological health.

Symptoms and Clinical Presentation

The symptoms and clinical presentation of bacterial infections can vary depending on the specific pathogen involved and the site of infection. However, some common symptoms and signs can be observed in bacterial infections. Here are a few general examples:

  1. Fever: Bacterial infections often cause an elevation in body temperature, resulting in fever. The severity of the fever can vary depending on the type and extent of the infection.
  2. Inflammation: Inflammation is a common response to bacterial infection. It can manifest as redness, swelling, and pain at the site of infection. For example, a skin infection may result in a red, swollen, tender area.
  3. Pain or discomfort: Bacterial infections can cause pain or discomfort depending on the affected area. For instance, a urinary tract infection may cause pain or a burning sensation during urination, while a respiratory infection can cause chest pain and difficulty breathing.
  4. Fatigue and malaise: Bacterial infections can lead to general feelings of tiredness, weakness, and malaise. The immune response to disease can be energy-demanding and cause systemic symptoms.
  5. Specific symptoms based on the site of infection: Different bacterial infections target particular body areas, resulting in site-specific symptoms. For example:
    • Respiratory infections: Cough, shortness of breath, chest pain, and productive cough with colored sputum.
    • Gastrointestinal infections: Diarrhea, abdominal pain, nausea, and vomiting.
    • Urinary tract infections: Increased frequency and urgency of urination, pain or burning during urination, and cloudy or bloody urine.
    • Skin infections: Redness, swelling, warmth, and pus or discharge from the affected area.

Types of Pyelonephritis

Pyelonephritis is generally classified into two main types: acute and chronic. These types differ in duration, presentation, and underlying causes. Here’s a closer look at each type:

Acute Pyelonephritis:

Acute pyelonephritis refers to a sudden and severe infection of the kidneys. It typically develops rapidly and manifests with distinct symptoms. A bacterial infection commonly causes pyelonephritis, primarily Escherichia coli (E. coli), which enters the urinary tract and ascends to the kidneys. Other bacteria, such as Klebsiella, Enterococcus, and Proteus, may also be responsible.

Symptoms of acute pyelonephritis include:
  • High fever
  • Chills and shaking
  • Flank or back pain (typically on one side)
  • Urinary urgency and frequency
  • Pain or burning during urination
  • Cloudy or bloody urine
  • Nausea and vomiting
  • Fatigue or malaise

Chronic Pyelonephritis:

Chronic pyelonephritis is recurrent or persistent kidney infection that causes long-term kidney damage. It is often associated with urinary tract abnormalities, such as kidney stones, urinary tract strictures, or vesicoureteral reflux (a condition where urine flows backward from the bladder to the kidneys). These abnormalities can obstruct or impair the normal flow of urine, leading to repeated infections and kidney damage over time.

Symptoms of chronic pyelonephritis may include:
  • Flank or back pain
  • Frequent urinary tract infections
  • Urinary urgency and frequency
  • Blood in the urine (hematuria)
  • Hypertension (high blood pressure)
  • Swelling (edema) in the legs or face

Differences between Acute and Chronic Pyelonephritis

Understanding the differences between acute and chronic pyelonephritis is important for accurate diagnosis and appropriate management. Here are the key differences between these two types:

Duration and Persistence:

  • Acute Pyelonephritis: Acute pyelonephritis is characterized by a sudden onset of symptoms and a relatively short duration. It typically lasts for a few days to a couple of weeks. Appropriate treatment can resolve the infection, and the kidney function can return to normal.
  • Chronic Pyelonephritis: Chronic pyelonephritis is a long-standing condition that persists for months or even years. It involves recurrent or persistent kidney infections and ongoing inflammation in the kidneys. Chronic pyelonephritis can lead to progressive kidney damage and impaired kidney function.

Symptom Presentation:

  • Acute Pyelonephritis: Symptoms of acute pyelonephritis are often more severe and acute. Patients typically experience a sudden onset of symptoms such as high fever, flank pain, urinary symptoms (urgency, frequency, dysuria), and general malaise. Nausea, vomiting, and abdominal pain may also be present.
  • Chronic Pyelonephritis: Symptoms of chronic pyelonephritis are usually milder and may be more subtle or nonspecific. Patients may experience recurrent urinary tract infections, low-grade fever, mild flank pain, fatigue, and general weakness. Over time, the symptoms may become more pronounced as kidney damage progresses.

Underlying Causes:

  • Acute Pyelonephritis: Acute pyelonephritis is commonly caused by a bacterial infection, most often due to the ascent of bacteria from the lower urinary tract into the kidneys. Escherichia coli (E. coli) is the most common causative organism. Other bacterial pathogens may also be involved, such as Klebsiella pneumoniae, Proteus mirabilis, or Enterococcus faecalis.
  • Chronic Pyelonephritis: Chronic pyelonephritis is typically associated with underlying structural or functional abnormalities of the urinary tract. These abnormalities include vesicoureteral reflux (VUR), kidney stones, urinary tract obstructions, or anatomical defects. Conditions impairing the normal urinary flow and predisposing the kidneys to recurrent infections contribute to developing chronic pyelonephritis.

Long-Term Implications:

  • Acute Pyelonephritis: With prompt diagnosis and appropriate treatment, acute pyelonephritis can generally be resolved without significant long-term consequences. However, if left untreated or inadequately managed, it can lead to complications such as kidney abscesses, sepsis, and acute kidney injury. Recurrent episodes of acute pyelonephritis may increase the risk of developing chronic pyelonephritis.
  • Chronic Pyelonephritis: Chronic pyelonephritis has more significant long-term implications. The ongoing inflammation and kidney damage associated with chronic pyelonephritis can lead to progressive loss of kidney function over time. This can eventually result in chronic kidney disease (CKD) and its complications, such as hypertension, electrolyte imbalances, and renal failure.

Management Approach:

  • Acute Pyelonephritis: Acute pyelonephritis is usually treated with antibiotics to eliminate the infection. Hospitalization may be required for severe cases or individuals with underlying health conditions. Intravenous antibiotics may be administered initially, followed by oral antibiotics for a total treatment duration of 7 to 14 days. Adequate hydration, pain management, and close monitoring of the response to treatment are essential components of acute pyelonephritis management.
  • Chronic Pyelonephritis: The management of chronic pyelonephritis focuses on controlling and minimizing the progression of kidney damage. Treatment aims to prevent further infections, manage underlying urinary tract abnormalities, and preserve kidney function. Antibiotic therapy may be prescribed for recurrent infections. Surgical intervention or other procedures may be necessary to address the underlying issues where structural abnormalities are present. Regular monitoring of kidney function, blood pressure, and urine tests is crucial for assessing disease progression and implementing appropriate interventions.

Diagnosis of Pyelonephritis

Pyelonephritis can be a serious condition if left untreated, so prompt diagnosis and treatment are important. Diagnosing pyelonephritis usually involves a combination of medical history, physical examination, and diagnostic tests.

Here’s an overview of the diagnostic process:

  1. Medical history: The healthcare provider will ask about your symptoms, including any urinary tract infection (UTI) symptoms such as frequent urination, urgency, burning sensation during urination, and back or abdominal pain. They will also inquire about any risk factors you may have, such as a history of kidney stones, urinary catheterization, or other urinary tract abnormalities.
  2. Physical examination: The healthcare provider will perform a physical examination, which may include checking your vital signs, palpating your abdomen and back for tenderness or pain, and listening to your lungs for any signs of infection.
  3. Urinalysis: A urinalysis is a common diagnostic test for pyelonephritis. It involves analyzing a urine sample for bacteria, white blood cells (indicating infection), red blood cells, and other abnormalities. A positive urinalysis showing significant bacteria and white blood cells suggests a urinary tract infection, and if accompanied by symptoms, it may indicate pyelonephritis.
  4. Urine culture and sensitivity: A urine culture may be performed if the urinalysis indicates a possible infection. This test involves growing the bacteria from the urine sample in a laboratory to identify the specific bacteria causing the infection. It also determines the sensitivity of the bacteria to different antibiotics, helping guide appropriate treatment.
  5. Blood tests: Blood tests may be ordered to assess kidney function, check for signs of infection (e.g., elevated white blood cell count), and evaluate overall health. Elevated levels of certain markers, such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), may indicate an inflammatory response associated with pyelonephritis.
  6. Imaging studies: In some cases, imaging studies may be recommended to assess the kidneys and detect abnormalities. Common imaging techniques include ultrasound, which can visualize the kidneys and detect signs of inflammation or obstruction, and computed tomography (CT) scan, which provides detailed images and helps identify complications like abscess formation.
  7. Additional tests: In certain situations, additional tests may be needed. For example, if pyelonephritis is recurrent or associated with urinary tract abnormalities, further investigations like cystoscopy (examining the bladder and urethra using a thin tube with a camera) or a renal scan (evaluating kidney function and drainage) may be required.

Treatment Options for Pyelonephritis A. Antibiotic Therapy B. Hospitalization and Intravenous Treatment C. Surgical Intervention D. Alternative and Complementary Approaches

Prevention and Lifestyle Measures

Pyelonephritis requires prompt medical attention and treatment to prevent complications. The primary goal of treatment is to eliminate the infection, relieve symptoms, and prevent the infection from spreading or recurring. Here are the common treatment options for pyelonephritis:

  1. Antibiotics: The cornerstone of treatment for pyelonephritis is antibiotics. The choice of antibiotic depends on factors such as the severity of the infection, the suspected bacteria causing the infection, and local resistance patterns. Commonly prescribed antibiotics include fluoroquinolones (such as ciprofloxacin or levofloxacin), cephalosporins (such as ceftriaxone or cefuroxime), or trimethoprim-sulfamethoxazole.
  2. Hospitalization: Severe cases of pyelonephritis may require hospitalization, especially if the patient is experiencing high fever, severe pain, vomiting, dehydration, or other complications. Hospital treatment allows for close monitoring, intravenous antibiotics, and supportive care.
  3. Fluids and pain relievers: Adequate hydration is important in managing pyelonephritis. Drinking plenty of water helps flush out the bacteria and promotes healing. Pain relievers like nonsteroidal anti-inflammatory drugs (NSAIDs) like ibuprofen can help alleviate pain and reduce fever.
  4. Urine culture and sensitivity testing: It is essential to obtain a urine sample for culture and sensitivity testing to identify the specific bacteria causing the infection and determine the most effective antibiotic treatment. This helps in tailoring the antibiotic regimen if necessary.
  5. Treatment of underlying conditions: If an underlying condition, such as a kidney stone or urinary tract abnormality, contributed to the development of pyelonephritis, it may need to be addressed. Treatment may involve surgery or other interventions to correct the underlying problem.
  6. Follow-up care: After completing the initial course of antibiotics, follow-up appointments are crucial to ensure the infection has been successfully treated. A repeat urine culture may be done to confirm the eradication of the bacteria. If symptoms persist or recur, further evaluation may be necessary.

Hygiene and Urinary Tract Health

Maintaining good hygiene is essential for overall health, including urinary tract health. The urinary tract consists of various organs, such as the kidneys, ureters, bladder, and urethra, which are crucial in eliminating waste and maintaining the body’s fluid balance. Here are some tips for maintaining good hygiene and promoting urinary tract health:

  1. Drink plenty of water: Staying hydrated helps flush out bacteria and toxins from the urinary tract, reducing the risk of infections.
  2. Practice good genital hygiene: Keep the genital area clean by washing it with mild soap and water regularly. Make sure to wipe from front to back after using the toilet to prevent the spread of bacteria from the anal area to the urethra.
  3. Urinate regularly: Holding urine for extended periods can increase the risk of urinary tract infections (UTIs). Empty your bladder regularly, and don’t delay urination when you feel the urge.
  4. Proper wiping technique: When wiping after using the toilet, always wipe from front to back to avoid introducing bacteria from the anal area to the urethra.
  5. Avoid irritating substances: Some products, such as harsh soaps, douches, powders, and sprays, can irritate the urinary tract. Avoid using these products in the genital area.
  6. Wear breathable underwear: Choose cotton underwear and avoid tight-fitting pants or synthetic fabrics that can trap moisture and create a breeding ground for bacteria.
  7. Practice safe sexual activity: Engage in safe sexual practices to reduce the risk of sexually transmitted infections (STIs) that can affect the urinary tract. Using condoms and practicing good genital hygiene are important preventive measures.
  8. Empty the bladder before and after sexual intercourse: Urinating before and after sexual activity can help flush out any bacteria that may have entered the urethra during intercourse, reducing the risk of UTIs.
  9. Avoid prolonged use of catheters: If you require a urinary catheter, it’s important to follow proper hygiene practices and sterile techniques to reduce the risk of infection. Avoid keeping the catheter in place longer than necessary.
  10. Seek prompt medical attention: If you experience symptoms of a urinary tract infection, such as frequent urination, pain or burning during urination, cloudy or strong-smelling urine, or lower abdominal pain, seek medical attention. Prompt treatment can help prevent complications.


Hooton TM, Gupta K. Acute uncomplicated urinary tract infection in women. UpToDate. Updated October 22, 2021. Accessed November 15, 2021.

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