At a glance

Also known as

Urine MCS; urine microscopy & culture; urine culture & sensitivity; C&S

Why get tested?

A urine culture is used to diagnose a urinary tract infection UTI

When to get tested?

If you experience symptoms of a UTI, such as pain during urination

Sample required?

A mid-stream "clean" urine sample; a "in-out" catheter urine sample; a suprapubic aspirate urine sample

What is being tested?

Urine is one of the body’s waste products. It is produced in the kidneys and collected in the bladder until a person urinates. Normally, the urine does not contain significant numbers of any microorganism. However, if bacteria or yeast are introduced into the urinary tract, they can multiply and cause a urinary tract infection, called a UTI. Because urine itself can serve as a culture medium, any bacteria present, including contaminating microorganisms, will multiply rapidly if the urine sample is allowed to stand at room temperature, particularly in the warmer months of the year. This could potentially lead to false-positive or false-negative results. For this reason, urine samples should be processed in the laboratory within 30 minutes of collection. If this is not possible, the specimen must be refrigerated (at about 4°C) immediately: it can then be kept for up to 4-6 hours without any significant changes.

Most UTIs are caused by Escherichia coli (E. coli), one of the most common human bacteria. Other frequently identified bacteria are Proteus, Klebsiella, and Staphylococcus saprophyticus.

How is the sample collected for testing?

A ‘mid-stream’ urine sample is the most common collection necessary for a culture so bacteria present around the urethra and on the hands are not introduced.

The procedure for collecting a clean ‘mid-stream’ includes the following steps:

  • Hands should be washed just before beginning the collection.
  • A soap should be used to clean the penis in males, and females should wash the external genitalia from front to back, holding the labia apart.
  • Do not collect the initial stream of urine since it may be contaminated with skin and urethral bacteria.
  • Midway through the urination process, collect 20-30 millilitres of urine in a sterile screw-top container (hence the name ‘mid-stream’ urine).
  • Tightly cap the container, wash your hands thoroughly and label the container.
  • The sample should be taken to the laboratory as quickly as possible to prevent the further growth of organisms.

Uncontaminated specimens can also be obtained from catheterised patients following the same hygienic procedures for the end of the catheter. Other methods of collection require a health care worker to insert a catheter into the bladder (in-out catheter) or a needle into the bladder (suprapubic aspirate) and are more invasive for the person but may be necessary in people who are unable to collect a mid-stream urine and who do not have a catheter already in place.

How is the sample tested in the laboratory?

A sample of the urine is initially assessed under microscope in a counting chamber or a cell counting instrument and visible cells are counted. The presence of large numbers of white blood cells (‘pus cells’) is strongly indicative of a UTI. Appreciable numbers of squamous epithelial cells (originating from skin) indicate a poorly collected specimen. A small amount of urine (usually 10 microlitres) is then cultured and inoculated plates are placed in an incubator at body temperature for 24 hours. If there is no growth on the agar plates at the end of that time, the culture is usually considered ‘negative’ for significant number of microorganisms that could cause an infection. Occasionally cultures may be prolonged to look for unusual organisms.

If bacteria or yeast are growing, the total number of organisms is counted (colony count), and the organisms are identified by growth characteristics, proteomic testing with MALDI-ToF and/or additional biochemical testing. The number of bacteria present in the sample helps to distinguish between true presence of bacteria in the urine and contamination. The concentration of viable bacteria in a urine sample is usually expressed in colony forming units per litre (CFU/L). If greater than 108 CFU/L of a recognised uropathogen (for example Escherichia coli or Proteus vulgaris) are present in a specimen, this is considered to be reliable evidence of the presence of bacteria in the urinary tract. However, this rule has been validated for uncomplicated urinary tract infections in adult women and clinical reasoning should be employed when interpreting urine culture results from men and symptomatic children.

Further tests determine which antibiotics are likely to be effective in treating the infection.

The Test

How is it used?

The test is used to diagnose a urinary tract infection (UTI).

When is it requested?

The culture may be used when symptoms indicate the possibility of a urinary tract infection, such as pain and burning when urinating and frequent urge to urinate. In addition, it may be used for patients who have a catheter inserted for an extended period of time, even if they do not show obvious symptoms of an infection, since there is a risk of bacteria being introduced by the catheter. Pregnant women in the first trimester (first 3 months of pregnancy), even without any symptoms should be screened for bacteria in their urine which could harm the baby.

What does the test result mean?

A negative culture usually means that there is no laboratory evidence of infection. However, a culture may be repeated if the symptoms persist. In a specimen with large numbers of pus cells but no bacterial growth (‘sterile pyuria’), this is often due to antibiotics taken before the sample is collected which has killed off the bacteria previously present. Another situation is the presence of an organism that is not able to be cultured on standard laboratory methods, the commonest of which is Chlamydia. A different test is required to check for this. Less commonly, difficult-to-grow organisms such as Actinotignum, Gonorrhoea or tuberculosis of the urinary tract may also show a ‘sterile pyuria’. There may be a non-infectious cause of sterile pyruria such as renal disease.

With the symptoms of a UTI, the presence of pus cells and bacteria, as indicated by a positive culture, suggests an infection. Any bacterial infection may be serious and can spread to other areas of the body if not treated. Since pain is often the first indicator of an infection, prompt treatment, usually with antibiotics, will help to alleviate the pain.

When there are no symptoms of a UTI but there is evidence of bacteria in the urine sample, this is termed ‘asymptomatic bacteriuria’. In adults, treatment is generally not recommended unless the person is pregnant. This is because studies have shown that although patients with asymptomatic bacteriuria have a higher chance of getting subsequent symptomatic UTIs, treatment of asymptomatic bacteriuria does not reduce the frequency of getting future UTIs. The unnecessary use of antibiotics will also make the person more likely to get infections that are resistant to antibiotics. Thus, screening for a UTI in asymptomatic adults is not recommended.

However pregnant women especially in the first trimester, are treated for asymptomatic bacteriuria to reduce the risk of an infection affecting the baby.

Is there anything else I should know?

Females get UTIs more often than males. For males with a culture-proven UTI, the doctor may order further tests to rule out the presence of a kidney stone or a structural abnormality of the urinary tract that could cause the infection.

Common Questions

The surgery called to say they need another fresh urine sample because the first sample was contaminated. What happened?

If the skin and genital area were not cleaned well prior to collecting the sample, the urine may have lots of epithelial cells present in the microscopy and the culture may grow a number of different types of bacteria and is assumed to be contaminated. The culture will not be useful because it cannot be determined if the bacteria originated inside or outside the urinary tract. A contaminated specimen can be avoided by following the directions to carefully clean yourself and by collecting a mid-stream sample.

My doctor said I had symptoms of a urinary tract infection and prescribed antibiotics without waiting for the results of the culture. Why?

The reason is because bacteria known as E. coli cause the majority of lower urinary tract infections. This organism is usually susceptible to a variety of antibiotics. Your doctor may start you on one of these antibiotics to relieve your symptoms while waiting for results from the culture.

What happens if my infection goes untreated?

If your infection is not treated, sometimes it can move from the lower urinary tract to the upper urinary tract and infect the kidney itself, and possibly, enter the bloodstream, causing septicaemia. Symptoms of septicaemia include fever, chills, elevated white blood cell count, and fatigue. Your doctor will often use blood cultures to determine if you have septicaemia and will prescribe antibiotics accordingly.

What puts me at risk for recurrent urinary tract infections (UTI)?

There are a wide variety of factors that predispose a person to acquire a UTI. After the neonatal period, the incidence in females is higher than in males due to the anatomical differences in the female genitourinary tract. In infants and young children, congenital abnormalities are associated with UTI. In adults, sexual intercourse, diaphragm use, diabetes, pregnancy, reflux, neurologic dysfunction, renal stones, and tumours all predispose to UTI. In a hospital, nursing home, or home care setting, indwelling catheters and instrumentation of the urinary tract are major contributing factors to acquiring a UTI.

Last Review Date: August 14, 2017