Microbiological diagnosis of urinary tract infections

"The main infections of the urinary tract are bacterial and fungal, although there are also viral and parasitic infections".


The most frequent infections in men are those of the urinary tract. They are produced by a variety of microorganisms: bacteria, viruses, parasites and fungi.

The presence of bacteria in urine is called bacteriuria. This is not always indicative of infection. A bacterial count greater than 100,000 CFU's (colony forming units)/ml, accompanied by an inflammatory response, is indicative of urinary infection.

In general, contamination by urethral microbiota due to poor sample collection correlates with a count of less than 100,000 CFU/ml.

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When is the microbiological diagnosis of urinary infections performed?

There are situations, where it is possible to diagnose urinary tract infection with counts below 100,000 CFU/ml.

These include:

  • Children with vesicourethral reflux (kidney damage).
  • Pregnant women (risk of asymptomatic UTI and fetal damage).
  • Invasive procedures in the urinary tract.
  • Catheterized patients.
  • Acute urethral syndrome.
  • Patients with previous antibiotic treatment.
  • High fluid intake.
  • Patients with urinary obstruction.
  • Acute pyelonephritis.

Most frequent indications of this test:

  • Cystitis (pain, burning and urinary frequency).
  • Pyelonephritis (lateral pain, fever, systemic symptoms).
  • Prostatitis.
  • Intrarenal abscesses.

Do you suspect you have a urinary infection?

Microbiological diagnostic tests may be required

How is the diagnosis of a urinary infection made?

The urine sample can be collected in different ways:

  • Middle portion of urination (this is the most common way): to avoid contamination, certain precautions should be taken, such as washing the external genitalia and nearby areas with soap and water; women, separate the labia with their hands and, after discarding the first portion of urine, collect the middle portion in a sterile wide-mouth container.

    It is advisable to collect the sample first thing in the morning. The collection of urine in infants and young children is more complicated. Special bags are used that are attached to the perineum of girls or around the penis of boys.

    If the sample has not been collected within one hour or the bag becomes dirty, it must be replaced, since contamination with fecal microbes is a fairly frequent problem.
  • Suprapubic puncture: the area to be punctured is disinfected with an iodophor, the sample is taken by transcutaneous puncture with a syringe directly from the bladder
  • Bladder catheter: urine is obtained by puncture through the catheter that has been previously disinfected. Catheterization can be used to obtain a ureteral sample.

In cases of prostatitis, there is a protocol for taking a sample, but due to its complexity, two urine samples are taken (medium urination), before and after a prostatic massage has been performed.

The sample must be sent to the laboratory quickly to avoid overgrowth of microorganisms. If this is not possible, it should be kept at 4º C.

Microscopic examination:
The microscopic examination of the urine allows to appreciate the cytology of the urine (red blood cells, leukocytes, epithelial cells) and bacteria. The visualization of red blood cells, leukocytes and cylinders in a significant number is a pathological finding. Most urinary tract infections are accompanied by more than 10 leukocytes/mm.3.
A count of more than 10 desquamatory cells/mm.3. indicates poor sample collection.

Diagnosis of UTIs of bacterial etiology
1-10 ml. of urine is sown in appropriate culture media. After 24 hours of incubation under suitable conditions, generally at 35ºC, the count and identification of the developed colonies is carried out.

The identification of the bacteria is based on:

Stains: bacterial morphology and dyeing behaviour.
Biochemical tests.

Once the bacteria have been identified, an antibiogram is carried out to determine the sensitivity to different antibiotics and to choose the most appropriate treatment.

Diagnosis of UTIs of fungal etiology:
Once the urine has been centrifuged, the sediment is sown in specific media for the isolation of fungi and/or yeasts.

The identification is also based on biochemical tests, and the sensitivity to different antifungal agents is also determined.

Diagnosis of renal tuberculosis:
Within the mycobacteria the most important species is Mycobacterium tuberculosis. For the isolation of this bacterial genus, more specific means and longer incubation times are required.

It takes 2-3 weeks to observe Mycobacterium tuberculosis colonies, although cultures are not discarded as negative until after 8 weeks.

Identification and sensitivity tests should also be performed in this case.

Diagnosis of ITUs of parasitic origin
The most common parasite in this type of infection is Trichomonas vaginalis. A microscopic examination of the urine sediment collected during 24 hours or, failing that, the first portion of the urine is done to visualize the parasite.

Other parasites (Schistosoma haematobium) can cause infections, although they are rare in our environment.

Diagnosis of UTIs of viral etiology
Viral causes are rare, although it is possible to recover certain viruses from the urine in the absence of disease of the urinary tract.

Where do we do it?


The Infectious Diseases Service
of the Clínica Universidad de Navarra

This area works on the diagnosis and treatment of diseases produced by an infectious agent, which can be bacteria, virus, fungus and protozoa. Infections affect people by causing very different processes that can be located in any tissue of the human body, so it requires a specific approach.

This area carries out its activity on three fronts: care work, focused on the diagnosis and treatment of infectious diseases; teaching, with training of medical students, resident doctors and nurses; and research vocation, through the development of clinical and laboratory studies.

Organized in care units

  • Infections associated with biomaterials.
  • Nosocomial infections (multi-resistance).
  • Infections in immunosuppressed patients.
  • Community infection.
  • Traveler's medicine.
  • Prudent use and optimization program of anti-infective therapy.
  • Control of infection by multi-resistant microorganisms.
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Why at the Clinica?

  • We perform the traveler's assessment and analytical tests in less than 24 hours.
  • Second opinion consultation when the infection has not yet been resolved.
  • We ensure the prudent use of antibiotics.