Urinary tract infections: Pathology review

Last updated: June 19, 2025

Urinary tract infections: Pathology review

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Development of the renal system
Ureter, bladder and urethra histology
Kidney histology
Renal system anatomy and physiology
Body fluid compartments
Hydration
Movement of water between body compartments
Horseshoe kidney
Renal agenesis
Potter sequence
Posterior urethral valves
Multicystic dysplastic kidney
Polycystic kidney disease
Vesicoureteral reflux
Alport syndrome
Urinary incontinence
Urinary incontinence: Pathology review
Neurogenic bladder
Bladder exstrophy
Antidiuretic hormone
Syndrome of inappropriate antidiuretic hormone secretion (SIADH)
Diabetes insipidus and SIADH: Pathology review
Diabetes insipidus
Nephrotic syndromes: Pathology review
Nephritic and nephrotic syndromes: Clinical
Nephritic syndromes: Pathology review
Minimal change disease
Hydronephrosis
Glomerular filtration
Measuring renal plasma flow and renal blood flow
Renal clearance
TF/Px ratio and TF/Pinulin
Regulation of renal blood flow
Sodium homeostasis
Kidney countercurrent multiplication
Urea recycling
Tubular reabsorption and secretion
Tubular reabsorption and secretion of weak acids and bases
Tubular secretion of PAH
Tubular reabsorption of glucose
Distal convoluted tubule
Loop of Henle
Proximal convoluted tubule
Renin-angiotensin-aldosterone system
Free water clearance
Amyloidosis
IgA nephropathy (NORD)
Poststreptococcal glomerulonephritis
Rapidly progressive glomerulonephritis
Lupus nephritis
Potassium homeostasis
Hypophosphatemia
Hyperphosphatemia
Hypermagnesemia
Hypomagnesemia
Hypocalcemia
Hypercalcemia
Hyperkalemia
Hypokalemia
Hyponatremia
Hypernatremia
Phosphate, calcium and magnesium homeostasis
The role of the kidney in acid-base balance
Acid-base disturbances: Pathology review
Physiologic pH and buffers
Renal tubular acidosis
Renal tubular acidosis: Pathology review
Metabolic acidosis
Metabolic and respiratory acidosis: Clinical
Respiratory acidosis
Metabolic alkalosis
Plasma anion gap
Respiratory alkalosis
Metabolic and respiratory alkalosis: Clinical
Acid-base map and compensatory mechanisms
Ornithine transcarbamylase deficiency
Kidney stones: Pathology review
Nitrogen and urea cycle
Goodpasture syndrome
Erythropoietin
Vitamin D
Kidney stones
ACE inhibitors, ARBs and direct renin inhibitors
Kidney stones: Clinical
Hypokalemia: Clinical
Renal tubular defects: Pathology review
Urinary tract infections: Clinical
Urinary tract infections: Pathology review
Lower urinary tract infection
Proteus mirabilis
Staphylococcus saprophyticus
Enterobacter
Klebsiella pneumoniae
Serratia marcescens
Pseudomonas aeruginosa
Renal artery stenosis
Thiazide and thiazide-like diuretics
Carbonic anhydrase inhibitors
Osmotic diuretics
Loop diuretics
Potassium sparing diuretics
Acute kidney injury: Clinical
Renal azotemia
Postrenal azotemia
Prerenal azotemia
Chronic kidney disease
Acute tubular necrosis
Renal papillary necrosis
Medullary cystic kidney disease
Chronic kidney disease: Clinical
Congenital renal disorders: Pathology review
Medullary sponge kidney
Chronic pyelonephritis
Acute pyelonephritis
Neisseria gonorrhoeae
Chlamydia trachomatis
Urethritis
Prostatitis
Schistosomes
Hemolytic-uremic syndrome
Thrombotic thrombocytopenic purpura
Renal cortical necrosis
Renal cell carcinoma
Angiomyolipoma
WAGR syndrome
Nephroblastoma (Wilms tumor)
Non-urothelial bladder cancers
Transitional cell carcinoma
Electrolyte disturbances: Pathology review
Renal failure: Pathology review
Renal and urinary tract masses: Pathology review
Transplant rejection
Graft-versus-host disease
Non-corticosteroid immunosuppressants and immunotherapies
Hypertension
BK virus (Hemorrhagic cystitis)

Questions

USMLE® Step 1 style questions USMLE

0 of 8 complete

Start
A 23-year-old woman presents to the primary care clinic due to a burning sensation with urination. The symptoms started 3 days ago and now cause the patient to wake up multiple times at night to urinate. Past medical history is unremarkable. The patient is sexually active with their spouse. Physical examination is unremarkable and vital signs are within normal limits. Urinalysis is positive for leukocytes and leukocyte esterase. Urine culture reveals growth of Gram-positive cocci. Which of the following is a feature of the causative organism most likely responsible for this patient’s condition?  

Transcript

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Two people came to the Nephrology ward.

The first one is 25 year old Carmen who recently returned from her honeymoon and now complains of suprapubic pain, dysuria and urinary frequency.

The other one is 35 year old Pamela who has had dysuria, fever, nausea and flank pain for the past 2 days.

On physical exam, she has costovertebral angle tenderness.

CBC and urinalysis were done for both people.

They showed that Carmen had a normal white blood cell count, but on the dipstick test, leukocyte esterase and nitrites were both positive.

For Pamela, the white blood count was high, the dipstick test showed positive leukocyte esterase and nitrites, and on microscopy, there’s white blood cell casts in the urine.

Both Pamela and Carmen have urinary tract infections, or UTIs.

This includes the lower portion of the tract like the bladder and urethra, and the upper portion of the tract like the kidneys and ureters.

UTIs are almost always caused by an ascending infection, where bacteria moves from the rectal area to the urethra and then migrate up the urethra and into the bladder.

Normally, bacteria would be washed away with urination, but in some cases, like with E. Coli, that doesn’t happen.

Instead, E. Coli uses little thread-like extensions called fimbriae to bind the uroepithelial cells and colonize the bladder mucosa, causing cystitis.

From the bladder, the infection can go up the ureter and into the kidney, where they attract neutrophils into the renal interstitium, causing pyelonephritis.

As neutrophils die off, they make their way through the urinary tract and appear in the urine.

The neutrophils and the surrounding inflammatory protein debris is even “casted” into the shape of the tubule, creating white blood cell casts and hyaline casts.

For your exams remember that other factors like sexual intercourse or an indwelling catheter can also let bacteria into the urinary tract.

So remember, in ascending infections bacteria moves from the rectal area to the urethra and then migrate up the urethra and into the bladder.

In most cases, ascending infections are caused by Escherichia coli, but other bacteria like Staphylococcus saprophyticus, Klebsiella pneumoniae or Proteus mirabilis can also cause ascending infections.

Now, descending infections are also possible in rare cases.

This is when the kidneys get infected via hematogenous infection, or spread through the bloodstream.

In this case, acute pyelonephritis can be a consequence of septicemia or bacteremia.

In these situations, the most common organisms are Staphylococcus species and again E. coli.

Okay, let’s talk about cystitis.

There are some risk factors associated with cystitis.

It’s more common in female individuals, because they have a shorter urethra, making it easier for the bacteria to ascend and because the urethra is closer to the rectum, where the primary culprits “live”.

Another risk factor is frequent sexual intercourse, which can lead to “honeymoon cystitis,” especially in younger female individuals.

Remember this type of infection is often caused by Staphylococcus saprophyticus.

Other risk factors include diabetes mellitus, indwelling catheter, and impaired bladder emptying, which can happen when there’s a bladder tumor, for example.

Symptoms include dysuria, which is painful urination, urinary frequency and urgency, and suprapubic pain.

CBC, urinalysis, and urine cultures are done to confirm the diagnosis and find the culprit.

On the CBC, the white blood count is normal.

The appearance of the urine is often cloudy and the dipstick test shows positive leukocyte esterase, which signifies pyuria, or the presence of white blood cell in the urine.

Dipstick also shows positive nitrites, and this is caused by enterobacteriaceae, like E.coli, Proteus and Klebsiella, converting normal urine nitrates into nitrites.

On microscopy, there are more than 10 white blood cells per high power field.

The best way to identify the organism for treatment is to do a urine culture.

Now, sometimes cystitis can be mistaken for urethritis, which is the inflammation of the urethra.

Urethritis can present with the same symptoms as cystitis, but the difference is that urethritis is most commonly caused by Neisseria gonorrhoeae and Chlamydia trachomatis.

Both of these are sexually transmitted infections.

With both, urinalysis shows sterile pyuria, meaning that leukocyte esterase is positive, but when cultures are done, no bacteria are found.

Key Takeaways

Urinary tract infections (UTIs) are common bacterial infections that can occur in any part of the urinary tract, including the kidneys, bladder, ureters, and urethra. They are most commonly caused by bacteria, such as E.coli, Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus saprophyticus.

Symptoms include pain or burning sensation when urinating, frequent urge to urinate, cloudy or strong-smelling urine, pain or pressure in the lower abdomen or back, and in more severe cases, fever or chills.

Risk factors for UTIs include female gender, sex, diabetes mellitus, indwelling catheters, pregnancy, and kidney stones. Complications of untreated or recurrent UTIs can include cystitis, pyelonephritis, and sepsis. Treatment typically involves a course of antibiotics and plenty of fluids to help flush out the bacteria.

Sources

  1. "Robbins Basic Pathology" Elsevier (2017)
  2. "Harrison's Principles of Internal Medicine, Twentieth Edition (Vol.1 & Vol.2)" McGraw-Hill Education / Medical (2018)
  3. "Practical Renal Pathology, A Diagnostic Approach E-Book" Elsevier Health Sciences (2012)
  4. "Diagnosis and management of urinary infections in older people" Clinical Medicine (2011)
  5. "Urinary tract infections in women" European Journal of Obstetrics & Gynecology and Reproductive Biology (2011)
  6. "Uncomplicated Urinary Tract Infection in Adults Including Uncomplicated Pyelonephritis" Urologic Clinics of North America (2008)
  7. "Risk Factors Associated with Acute Pyelonephritis in Healthy Women" Annals of Internal Medicine (2005)
  8. "Diagnosis and Management of Acute Ureterolithiasis" American Journal of Roentgenology (2000)