Etiology and Treatment of Urinary Tract Infections (UTI)

The microbial etiology of urinary tract infections (UTI) has been regarded as well-established and reasonably consistent. There are minor variations in the prevalence of etiological agents based on the settings (community vs. hospital-acquired), age (children vs. adults), and gender (female vs. males).

Bacteria can invade and cause UTI via three major routes: ascending, hematogenous, and lymphatic pathways. Ascending route is the most common course of infection in females. Hematogenous spread accounts for less than 5% of UTIs and rarely occurs with gram-negative bacilli.

Polymicrobial UTI in the absence of underlying anatomic abnormalities, foreign bodies or trauma are rare. The presence of three different organisms even in large quantities suggest a contaminated urine specimen.


Escherichia coli

Escherichia coli is the most common cause of community-acquired symptomatic UTIs, especially cystitis. Uropathogenic E. coli (UPEC) has remained the predominant uropathogen (80%) isolated in acute community-acquired uncomplicated UTIs. Escherichia coli can adhere to the urethral and bladder mucosa via pili.

Staphylococcus aureus

Staphylococcus aureus can cause pyelonephritis (infection of the renal parenchyma). In the case of bacteremic patients, S. aureus reaches the kidney via hematogenous spread or the descending route.

Staphylococcus saprophyticus 

It is common in young women. Approximately 10% to 15% of cases of UTIs in women of reproductive age groups are caused by S. saprophyticus.


Mycobacteria can cause UTI in HIV-positive patients.

Pseudomonas aeruginosa

Pseudomonas aeruginosa can cause urinary tract infections, most common in patients staying in healthcare settings for longer. Patients with anatomic or neurologic abnormalities affecting their urinary tract or heavily antibiotic-experienced patients are also predisposed to UTIs from Pseudomonas aeruginosa.


Infrequently cause uncomplicated cystitis and pyelonephritis.

Other bacteria

Other bacteria commonly isolated from patients with UTIs are Klebsiella spp., Proteus spp. Enterobacter spp. Acinetobacter, Citrobacter, beta-hemolytic streptococci etc.


Candida species can cause UTI in patients with extensive prior antibiotic use and indwelling Foley catheters. Other high-risk patients are diabetic, immunocompromised, and immunosuppressive therapy patients.


Viruses rarely cause UTIs. Adenovirus, BK virus, and cytomegalovirus can cause hemorrhagic cystitis. These viruses almost exclusively cause cystitis in immunocompromised hosts such as those who have undergone stem cell transplants.

Factors affecting prevalence of Etiological Agents

The etiology of UTI is also affected by underlying host factors that complicate UTI, such as

  1. Age: The most common organisms isolated in children with uncomplicated UTI are Enterobacteriaceae. Gram-positive organisms are common, and polymicrobial infections account for up to 1 in 3 infections in the elderly.
  2. Gender: Women are affected more often than men (about 40 to 50 times) because of the shorter female urethra (4 cm) compared with the male urethra (20 cm) i.e., infectious agents reach the bladder more easily in females.
  3. Diabetes: Etiologic pathogens associated with UTI among patients with diabetes include Klebsiella spp., Group B streptococci, and Enterococcus spp., as well as E. coli.
  4. Spinal cord injury or urinary catheterization: Patients with spinal cord injuries commonly have E. coli infections.

Complicated vs. Uncomplicated UTI:

Complicated UTI has a more diverse etiology than uncomplicated UTI, and organisms that rarely cause disease in healthy patients can cause significant disease in hosts with anatomic, metabolic, or immunologic underlying diseases.

Treatment of Urinary Tract Infections

Choice of the antibiotics for the treatment of any infections depends on patients’ specific factors (age, underlying diseases/abnormalities) local resistance patterns of the etiological agents, and cost & availability of the drugs).

There are several national and international guidelines that help to choose an empiric regimen for UTIs. You can refer to 2010 IDSA/ESCMID guidelines (they preferred nitrofurantoin, trimethoprim-sulfamethoxazole, fosfomycin, and pivmecillinam for uncomplicated cystitis in women) or local guidelines of your country/hospital regarding the choice of antibiotics for the treatment of UTI.

Drugs used for the empiric treatment of uncomplicated UTIs are:  

  1. Ciprofloxacin:
    1. Avoid fluoroquinolones for uncomplicated UTIs when alternative antibiotics are possible.
    2. Fluoroquinolones should not be used if the local prevalence of resistance of the uropathogen exceeds 10%.
  2. Nitrofurantoin:
    1. In patients with reduced renal function, nitrofurantoin should only be used if local resistance data suggests a high resistance to alternative agents.
    2. Due to lower drug levels in the renal parenchyma, nitrofurantoin and fosfomycin should be avoided in cases of suspected pyelonephritis.
  3. Trimethoprim-sulfamethoxazole (co-trimoxazole): should not be used if the local prevalence of resistance of uropathogen (E.coli) exceeds 20%.

In the cases of suspected pyelonephritis (loin pain and fever), suspected UTI in men, recurrent UTI, pregnancy, and failed antibiotics treatment or persistent symptoms, urine should be sent for the culture.

Read here: Specimen Collection for the diagnosis of Urinary Tract Infection (UTI)


  1. Minardi, D., d’Anzeo, G., Cantoro, D., Conti, A., & Muzzonigro, G. (2011). Urinary tract infections in women: etiology and treatment options. International journal of general medicine, 4, 333–343. 
  2. Chu, C. M., & Lowder, J. L. (2018). Diagnosis and treatment of urinary tract infections across age groups. American journal of obstetrics and gynecology, 219(1), 40–51. 
  3. Kaur, R., & Kaur, R. (2021). Symptoms, risk factors, diagnosis and treatment of urinary tract infections. Postgraduate medical journal, 97(1154), 803–812.  

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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