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. Urine in the bladder is normally sterile (containing no organisms), however, if bacteria or yeasts are introduced into the urinary tract, they can multiply and casue a urinary tract infection (called a UTI). Bacteria are usally present around the opening of the urethra (the tube that leads from the bladder to the outside of the body). Urine collection for culture (MCS) must be performed carefully in order to avoid contaminating the sample with these bacteria.

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. For this reason, urine samples should be refrigerated (at about 4°C) after collection and transported to the laboratory as soon as possible.

Uncomplicated urinary tract infections (UTIs or cystitis) mainly occur in non-pregnant women who do not have any abnormality of the urinary tract. Acute uncomplicated cystitis (bladder infection) and pyelonephritis (kidney infection) are most commonly caused by Escherichia coli (70 to 95% of cases) and Staphylococcus saprophyticus (5 to 10% of cases).

Complicated UTIs occur inpatients with underlying abnormalities of the urinary tract. E.coli is the most common pathologen (20 to 50% of cases), but a wider range of bacteria (eg Klebsiella, Proteus, Pseudomonas species) also cause infection. Symptomatic UTIs caused by yeasts such as Candida are uncommon.

UTIs in men are uncommon; although more likely to occur with increasing age and abnormalities of the urinary tract. Prostate infection (prostatitis) should be considered in men. Measuring the PSA level on a blood test may be useful.

How is the sample collected for testing?

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

Guidelines for collection of mid-stream urine sample:

Female patients:

  • Open the sterile urine jar and hold it in one hand. Sit on the toilet with your legs wide apart. Use the fingers of your other hand to hold your labia apart- the urine must not touch either your labia or your fingers. Starting passing the urine directly into the toilet. After a few seconds, catch your urine in the container. Once the container is half filled (20-30mls), screw the cap on tightly. DO NOT contaminate the urine with your fingers.
Male patients:
  • Open the urine jar and hold it in one hand. If you are not circumcised, retract your foreskin. Start passing the urine directly into the toilet. After a few seconds, catch your urine in the container. Once the container is half filled, screw the cap on tightly. DO NOT contaminate the urine with your fingers.
REMEMBER: Do not collect the first portion of urine you pass.
  • Hands should be washed before and after collection.
  • Ensure the container is labelled with your name, date of birth and date of collection.

Uncontaminated specimens can also be obtained from people who are catheterised 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 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. The growth of mixed bacterial types on urine culture or the presence of large numbers of squamous epithelial cells (cells originating from the skin and not the bladder) on microscopy usually indicates a poorly collected specimen and contamination with normal genital tract flora.

A small amount of urine (usually 10 microlitres) is then cultured and on agar plates which are placed in an incubator for 24 hours. The culture is usually considered ‘negative’ if no significant growth is found on the plates after 24 hours. Occasionally cultures may be prolonged to look for unusual organisms.

If bacteria or yeasts are growing, the total number of organisms is counted (colony count), with the concentration of viable bacteria in a urine sample expressed as colony forming units per litre (CFU/L). UTI is usually defined as a bacteria count >108 CFU/L from a midstream urine sample. Lower bacterial counts (105 CFU/L or  more) may also indicate UTI in women with symptoms, patients with a UTI caused by organisms other than Escherichia coli and Proteus species, men and patients already taking antibiotics.

Organisms are identified by growth characteristics, proteomic testing with MALDI-ToF and/or additional biochemical testing. 

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

The Test

How is it used?

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

When is it requested?

A urine sample for culture should be obtained before starting antibiotics when symptoms of UTI are present in:

  • pregnant women
  • men
  • aged-care facility residents
  • if antibiotics have been recently taken
  • if recurrent infection
  • if there are risk factors of multidrug-resistant bacteria (e.g. recent travel or hospitalisation)
A urine sample is not always required for culture in non-pregnant women with a first episode of uncomplicated UTI (cystitis). Symptoms of UTI (cystitis) include pain or burning on passing urine, increased frequency or urgency of passing urine and occassionally tenderness above the pubic area.

Treatment can usually be started based on symptoms or with a dipstick test done in the doctor's surgery. However, if not responding to treatment and symptoms persist a urine specimen should be sent to the lab for culture.
A urine sample should always be submitted if symptoms are present such as fever >38ºC, vomiting or flank pain which might indicate upper urinary tract infection (kidney infection/pyelonephritis).

It is recommended that pregnant women in the first trimester (first three months of pregnancy), even without symptoms should be screened for bacteria in their urine as there is an increased risk of developing kidney infection (pyelonephritis) in later pregnancy.

There is no need for a post-treatment urine culture to confirm resolution of infection for people without symptoms, except for pregnant women.

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 symptoms persist. Prior antibiotic use might result in a specimen which shows no bacterial growth but a large numbers of pus cells present (‘sterile pyuria’). Sterile pyuria may also result if particular organisms are present which are not able to be readily cultured. A sexually transmitted infection (STI) screen on the urine is recommended in this situation to check for organisms such as Chlamydia and Gonorrhoea.

With the symptoms of a UTI, the presence of pus cells and bacteria, as indicated by a positive culture, suggests an infection and prompt antibiotic treatment is recommended to prevent complications of infection.
If pus cells are absent on urine testing, the diagnosis of UTI is unlikely and antibiotic treatment is usually not indicated.

When there are no symptoms of a UTI but there is evidence of bacteria in the urine sample, this is termed ‘asymptomatic bacteriuria’ and antibiotic treatment should be avoided. Asymptomatic bacteriuria becomes common with age. Treating with antibiotics where there are no symptoms is not beneficial, may cause side-effects and promote antibiotic resistant organisms. Treatment of asymptomatic bacteriuria is only required in pregnant women.
 

Is there anything else I should know?

Females get UTIs more often than males and laboratory testing of urine is not always required. UTIs are uncommon in males and a specimen should be tested in the laboratory. The doctor may order further tests in males to exclude prostate infection or underlying structural abnormalities or kidney stones. Sexually transmitted infections should always be considered as they can cause symptoms that mimic UTI.

Common Questions

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

The urine sample may not have been a good 'mid-stream' specimen and have lots of epithelial (skin)cells present which suggests contamination. The culture result may not be useful as it might just represent bacteria present from outside the urinary tract.
A contaminated specimen can be avoided by carefully following the directions to obtain a mid-stream sample and not the first portion of the urine passed.

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: November 13, 2019