Genitourinary Tract Infections
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URINARY TRACT INFECTIONS (Urethritis, Cystitis, Pyelonephritis)

General Goal: To know the major cause(s) of these diseases, how they are transmitted, and the major manifestations of each disease.

Specific Educational Objectives: The student should be able to:

1. recite the common cause(s) of these disease.

2. describe the common means of transmission.

3. describe the major manifestations of this infection.

4. describe how you diagnose, treat and prevent this infection.

Reading: MEDICAL MICROBIOLOGY by P.R. Murray, K.S. Rosenthal, G.S. Kobayashi and M.A. Pfaller, 6th Edition. page number depends on microorganism.

Lecture: Dr. Neal R. Chamberlain


  1. N.R. Chamberlain. The Big Picture Medical Microbiology, 2009. Chapter 34, pg. 341-346 McGraw-Hill
  2. R. ORENSTEIN and E. S. WONG. Urinary Tract Infections in Adults. American Family Physician. March 1, 1999.
  3. Wilson ML, Gaido L. Laboratory diagnosis of urinary tract infections in adult patients. Clin Infect Dis. 2004;38:1150-1158.


UTI’s are defined as a significant bacteriuria in the presence of symptoms. The bacteria most often seen in UTI’s are of fecal origin. These organisms are a subset of the organisms found in the feces. Strict anaerobic bacteria rarely cause UTI’s. More than 90% of acute UTI’s in patients with normal anatomic structure and function are caused by certain strains of E coli. Ten to 20% of acute UTI’s are caused by coagulase-negative Staphylococcus saprophyticus (young sexually active females) and 5% or less are caused by other Enterobacteriaceae or enterococci.

In complicated cases of UTI, such as UTI's resulting from anatomic obstructions, or from catheterization the most common causes of UTI are E. coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus sp., Pseudomonas aeruginosa. In rare cases Candida albicans can cause UTI (e.g., diabetic patients).

Staphylococcus saprophyticus is a common inhabitant of the gastrointestinal tract. Young women are more susceptible than other ages of women. Sexual intercourse promotes colonization and infections are more common in the late summer to fall seasons.  S saprophyticus is the second most common cause of uncomplicated urinary tract infections (UTI) in sexually active young (13-40 years of age) women following E coli.

Causes of UTI's in ALL Patients



Escherichia coli



Coagulase negative Staphylococcus















Staphylococcus aureus



Staphylococcus saprophyticus










Urethritis - Most of the cases of purulent urethritis without cystitis are sexually transmitted and will be discussed later. The inflammation and infection is limited to the urethra. It is usually a sexually transmitted disease. Pathogens such as Chlamydia trachomatis, Neisseria gonorrhoeae, Ureaplasma urealyticum or Trichomonas vaginalis are the common causes of urethritis. The disease is present in men and women. Complaints include discomfort during voiding, but there are usually no symptoms of postvoid suprapubic pain or urinary frequency.

Cystitis - Results from an irritation of the lower urinary tract mucosa. This infection as such is not invasive. Frequently, one will see (symptoms 1-4 are sometimes called irritative voiding symptoms.):

  1. Dysuria (painful urination)
  2. Urgency (the need to urinate without delay)
  3. Increased frequency of urination
  4. Suprapubic tenderness, pelvic discomfort especially pre- and immediately postvoid. Occurs in 20% of women with uncomplicated UTI.
  5. Small volume voiding.
  6. Increased number of white blood cells in the urine (pyuria)

Hemorrhagic cystitis is characterized by large quantities of visible blood in the urine. It can be caused by an infection (bacterial or adenovirus types 1-47) or as a result of radiation, cancer chemotherapy, or immunosuppressive medication. Clinical presentation usually depends on its origin. All causes result in irritative voiding symptoms typically. When infectious in origin, signs and symptoms of infection may also be encountered. Adenovirus is a common cause and is self-limiting in nature. Hemorrhagic cystitis is often confused with glomerulonephritis, but hypertension and abnormal renal function are absent in hemorrhagic cystitis. Hemorrhagic cystitis may develop months after cessation of radiation therapy.

Pyelonephritis - This infection usually results from ascension of the bacteria to the kidney from the lower urinary tract, but also can arise by hematogenous spread (e.g., from lungs in patients with pneumonia). In contrast to cystitis, pyelonephritis is an invasive disease. Blood cultures are positive in up to 20% of women who have this infection. The patient will experience many of the symptoms of cystitis as well as:

  1. Suprapubic tenderness
  2. Urinary urgency and frequency may be present or absent.
  3. Fever
  4. Flank pain and tenderness (back pain)
  5. Costovertebral angle tenderness (CVA tenderness)
  6. Nausea and vomiting
  7. Peripheral leukocytosis
  8. Urine contains white blood cell casts- elongated structures composed of cells that were tightly packed in the tubules and excreted in a proteinaceous matrix.

Complications of pyelonephritis can include:

  1. Sepsis
  2. Septic shock
  3. Death


Risk factors that increase a patient’s chances of getting a UTI include:


Entry is normally by ascent from the urethra. The organisms that cause UTI’s are usually fecal organisms. Blood borne infections are infrequent usually leading to renal abscesses.

Host factors - Host factors important in protection from cystitis include the normal flow of urine and the constant sloughing of the epithelial cells lining the urinary tract. The kidneys are protected due to the presence of the ureterovesical valves that prevent reflux of urine from the bladder, and constant peristalsis of the ureters.

The larger number of UTI's seen in women is due to the much shorter urethra and the much closer association of the urethra to the anus. Sexual intercourse contributes to the increased number of UTI's seen in women. Celibate women have a lower frequency of bacteriuria.

Some women have been shown to have a much higher number of bacterial receptors on their uroepithelial cells leading to recurrent UTI’s. Any anatomic obstruction or neurological disorder leading to failure to completely eliminate urine from the bladder can lead to UTI. Men in their 50's and above have problems with prostate gland enlargement resulting in obstruction of the urethra followed by incomplete elimination of urine from the bladder and UTI's.

Bacterial factors - The ability of an organism to produce fimbriae (Type 1, P, S, and Dr) is important in that it enables the bacteria to attach to the uroepithelial cells and thereby avoid elimination. Uropathogenic strains of E coli can also resist killing by complement.

Human epithelial cells of the bladder and the kidney can internalize E coli cells. The Type 1 fimbriae are important in attachment of the bacteria to the host epithelial cells and in promoting reorganization of the epithelial cell’s intracellular cytoskeleton to then internalize the bacteria. Internalization of the bacterial cells in epithelial cell vacuoles enhances bacterial cell survival by providing protection from host immune defenses and allows the pathogen greater access to deeper tissues. Once internalized the bacteria can grow in the epithelial cell and form pod-like structures. Intracellular E coli can form a reservoir within the bladder mucosa that may serve as a source for recurrent acute infections (20% of all UTI’s).

The Type 1 fimbriae mediated internalization of E coli is rather slow and the rate of internalization can be increased by 10 fold if the bacteria have first been opsonized by complement component C3. Since uropathogenic E coli are resistant to killing by complement they can then use C3 to gain entry into the host epithelial cells. Not much complement is in the urine in normal conditions. However, during infection LPS from E coli may induce the production of cytokines in the kidney that then causes increased amounts of C3 to gain entrance into the bladder. C3 binds to the surface of the bacterial cells. This surface bound C3 then binds to human complement regulatory protein, CD46, on the surface of the epithelial cell. The CD46 protein then mediates internalization of E coli.

Spread to the kidney - Infection of the kidney is due to ascent from the lower urinary tract and so any factor leading to retrograde flow of the urine to the kidney will predispose the host to pyelonephritis. Such factors include:

  1. Cystitis due to a strain of E coli that produces the mannose resistant pili that binds to the receptor for the P blood group found on epithelial cells and red blood cells.
  2. Internalization of E coli in the proximal tubular epithelial cells of the kidney can also occur helping the bacteria avoid the immune response of the host. C3 bound to the surface of E coli cells appears to also be important in internalization of the bacteria in the kidney epithelial cells.
  3. Reflux of urine to the kidney - usually due to incomplete development of ureterovesical valves.
  4. Physiological malfunctions - disorders leading to poor emptying of the bladder. Changes during pregnancy leading to dilatation and decreased peristalsis of the ureters.
  5. Urethral catheters - can serve as a conduit for the bacteria to ascend into the bladder and a source of bacteria for persistent infection.
  6. Urinary tract stones - These stones serve as a place in which bacteria can escape antibiotics and cause further infections. Proteus sp. is an example of an organism, which can cause stone formation. Proteus sp. produce an enzyme called urease that splits urea to ammonia and carbon dioxide. This raises the pH of the urine and facilitates the formation of "struvite" calculi. A high pH in the urine is indicative of a Proteus infection.

Kidney damage is due to the ability of the organism to produce polysaccharide (which inhibits phagocytosis), alpha hemolysin and cytotoxic necrotizing factor 1 (causes tissue damage directly), endotoxin that contributes to inflammation and damage of renal parenchyma and internalization of the bacterial cells in kidney epithelial cells.


The diagnosis of UTI was based on a quantitative urine culture yielding greater than 100,000 colony-forming units (105 CFU) per milliliter of urine, which was termed "significant bacteriuria." This value was chosen because of its high specificity for the diagnosis of true infection, even in asymptomatic persons. However, several studies have established that 30% or more of symptomatic women have CFU counts below this level (low-coliform-count infections). They have also shown that a bacterial count of 100 CFU/ml of urine has a high positive predictive value for cystitis in symptomatic women.

Since very few organisms cause UTI in acute uncomplicated cystitis in young women and since their antibiotic sensitivity is relatively predictable, urine cultures and susceptibility testing add little to the choice of antibiotic. Therefore, urine cultures are no longer advocated as part of the routine work-up of these patients. Instead, these patients should undergo an abbreviated laboratory work-up in which the presence of pyuria is confirmed by traditional urinalysis (wet mount examination of spun urine), the cell-counting chamber technique (looking for more than 8 white blood cells per mm3) or a dipstick test for leukocyte esterase. A positive leukocyte esterase test has a reported sensitivity of 75 to 90% in detecting pyuria associated with a UTI.

Gram stains of urine can be used to detect bacteriuria. In this semiquantitative test, one organism per oil immersion field correlates with 100,000 CFU/ml by culture. Because the procedure is time-consuming and has low sensitivity, it is not routinely performed in most clinical laboratories unless it is specifically requested.

In today's office practice, the dipstick test for nitrite is used as a surrogate marker for bacteriuria. It should be noted that not all uropathogens reduce nitrates to nitrite. For example, Enterococcus, S saprophyticus and Acinetobacter species do not and therefore give false-negative results.

Urinary Tract Infections in Adults


Diagnostic criteria

Principal pathogens

First-line therapy


Acute uncomplicated** cystitis- women

Positive urinalysis for pyuria or bacteriuria (culture not required)

Escherichia coli
Staphylococcus saprophyticus
Proteus mirabilis
Klebsiella pneumoniae

TMP-SMX DS (Bactrim, Septra)
Trimethoprim (Proloprim)
Ciprofloxacin (Cipro)
Ofloxacin (Floxin)

Three-day course is best.
Quinolones may be used in areas of TMP-SMX resistance or in patients who cannot tolerate TMP-SMX.

Acute cystitis in young men

Urine culture with a bacterial count of 1,000 to 10,000 CFU per mL of urine

Same as for acute uncomplicated cystitis

Same as for acute uncomplicated cystitis.

Treat for seven to 10 days.

Acute uncomplicated pyelonephritis

Urine culture with a bacterial count of 10,000 CFU per mL of urine

Same as for acute uncomplicated cystitis

If gram-neg organism, oral fluoroquinolone.
If gram-pos organism, amoxicillin.
If parenteral administration is required, ceftriaxone (Rocephin) or a fluoroquinolone.
If Enterococcus species, add oral or IV amoxicillin

Switch from IV to oral administration when the patient is able to take medication by mouth; complete a 14-day course

Complicated UTI

(women and men)

Urine culture with a bacterial count of 10,000 CFU per mL of urine

Escherichia coli 
Klebsiella pneumoniae
Proteus mirabilis Pseudomonas aeruginosa

Enterococcus species
Frequently multi-drug resistant organisms are present

Gram-negative organism, oral fluoroquinolone
Enterococcus species, ampicillin or amoxicillin with or without gentamicin (Garamycin)

Treat for 10-14 days

Asymptomatic bacteriuria in pregnancy

Urine culture with a bacterial count of more than 10,000 CFU per mL of urine

Same as for acute uncomplicated cystitis

Nitrofurantoin (Macrodantin)
Cephalexin (Keflex)

Avoid tetracyclines and fluoroquinolones.
Treat for three to seven days

Catheter-associated urinary tract infection

Symptoms and a urine culture with a bacterial count of more than 100 CFU per mL of urine

Escherichia coli Proteus, Pseudomonas, Enterobacter, Serratia, Enterococcus, Candida species.

Oftentimes is polymicrobic in long-term indwelling catheter patients.

Gram-negative organism, a fluoroquinolone
Gram-positive organism, ampicillin or amoxicillin plus gentamicin

Candida- remove catheter and no treatment needed if the patient is not high risk (high-risk= neonates and neutropenic patitents) If catheter cannot be removed or the patient is high risk treat with Fluconazole for 14 days

Remove the catheter if possible, and treat for seven to 10 days
Patients with long-term catheters and symptoms, treat for five to seven days

TMP-SMX=trimethoprim-sulfamethoxazole; CFU=colony-forming unit; IV=intravenous.
*--Patient is given a prescription for an antibiotic to take if symptoms develop.

**--Complicated UTI- UTI's that occur due to anatomic, functional or pharmacologic factors and predispose patients to persistent infection, recurrent infection or treatment failure (e.g., anatomic= benign prostate hypertrophy in older males).
Information from Stamm WE, Hooton TM. Management of urinary tract infections in adults. N Engl J Med 1993;329:1328-34.

If culture of the urine is required it must be preformed using a mid-stream catch (clean catch specimen). If the patient can't or won't comply, use percutaneous bladder aspiration or ureter catheterization. Bacteria grow rapidly in urine therefore urine samples should be processed immediately or refrigerated. Cultures refrigerated for more than 2 hours are usually of no value in making the diagnosis.

Diagnosis should also involve the determination of the site of infection (i.e., kidney or bladder-urethra). This may be suggested by the clinical manifestations and preliminary lab tests.

There are a number of tests that may help in establishing the site(s) of infection.

  1. An antibody-coated bacterium in urine test is based upon the principal that bacteria originating in the kidney are coated with specific antibody (detect by fluorescent microscopy following staining with FITC-conjugated, goat anti-human gamma globulin) but those bacteria originating from the bladder are not coated with antibodies. Not always reliable.
  2. Presence of white blood cell casts indicates the patient has pyelonephritis.
  3. Ureteral catheterization under cystoscopic visualization to culture urine directly obtained from each kidney.

If a patient is experiencing recurrent UTI's, the causative organism should be identified by urine culture and then documented to help differentiate between relapse (infection with the same organism) and recurrence (infection with different organisms). Multiple infections caused by the same organism are, by definition, complicated UTIs and require longer courses of antibiotics (e.g., 7 to 10 days) and possibly further diagnostic tests.

Between 10 and 20% of patients who are hospitalized receive an indwelling Foley catheter. Once this catheter is in place, the risk of bacteriuria is approximately 5% per day. With long-term catheterization, bacteriuria is inevitable. Catheter-associated urinary tract infections account for 40% of all nosocomial infections and are the most common source of gram-negative bacteremia in hospitalized patients.

Asymptomatic bacteriuria is defined as the presence of more than 10,000 CFU/ml of voided urine in persons with no symptoms of urinary tract infection. The largest patient population at risk for asymptomatic bacteriuria is the elderly. Up to 40% of elderly men and women may have bacteriuria without symptoms. Aggressively screening elderly persons for asymptomatic bacteriuria and subsequent treatment of the infection has NOT been found to reduce either infectious complications or mortality. Consequently, this approach currently is not recommended.

Three groups of patients with asymptomatic bacteriuria have been shown to benefit from treatment:

Therapy and Prevention

A. The clinical manifestations determine the initial step in therapy.

Afebrile patients experiencing symptoms of lower UTI are treated on an outpatient basis.

Patients experiencing high fever, shaking chills and flank pain, in addition to symptoms of lower UTI, may need to be hospitalized.

B. General guidelines

Underlying uropathies requiring surgical correction are much more common, particularly in males with pyelonephritis, so a more extensive workup is required to prevent reoccurrence.

1. A seven-day course should be considered in pregnant women, diabetic women and women who have had symptoms for more than one week and thus are at higher risk for pyelonephritis because of the delay in treatment.

2. Women who have more than three UTI recurrences documented by urine culture within one year can be managed using one of three preventive strategies:

Long-term studies have shown antibiotic prophylaxis to be effective for up to five years with trimethoprim, trimethoprim-sulfamethoxazole or nitrofurantoin, without the emergence of drug resistance. Antibiotic prophylaxis does not appear to alter the natural history of recurrences since 40 to 60% of these women reestablish their pattern or frequency of UTI's within six months of stopping prophylaxis.

3. Complicated UTI's occur in patients due to anatomic, functional or pharmacologic factors that predispose the patient to persistent infection, recurrent infection or treatment failure. These factors include conditions frequently seen in elderly men, such as enlargement of the prostate gland, blockages and other problems necessitating the placement of indwelling urinary devices, and the presence of bacteria that are resistant to multiple antibiotics. Even though antibiotic-susceptible E coli strains cause more than 80% of uncomplicated UTI's, it accounts for less than 33% of complicated cases. Clinically, the spectrum of complicated UTI's may range from cystitis to urosepsis with septic shock.

If the patient has urinary tract infections urge them to:

A large number of pregnant women develop asymptomatic bacteriuria. Up to 30% of pregnant women with asymptomatic bacteriuria will develop acute pyelonephritis if not treated. Asymptomatic bacteriuria may also have a role in preterm birth, or it may be a marker for low socioeconomic status and thus, low birthweight. Drug treatment of asymptomatic bacteriuria in pregnant women substantially decreases the risk of pyelonephritis. Urine samples should be obtained periodically from pregnant women to determine if they have bacteriuria.

Long-term low dose antibiotic treatment may be necessary in women with frequent reinfections to prevent future UTI’s.

Sexually active women with recurrent UTI’s can prevent recurrences by not using spermicide-containing contraceptives and taking a prophylactic antimicrobial agent around the time of intercourse. Postmenopausal women with recurrent UTI’s can prevent recurrences by taking oral or vaginal estrogen which will shift the vaginal flora from uropathogens to Lactobacillus and will lower the vaginal pH and protect them from an ascending infection.

Send comments and email to Dr. Neal R. Chamberlain,
Revised 6/21/11
©2010 Neal R. Chamberlain, Ph.D., All rights reserved.