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Urine Chemistry (Microscopy and Culture) Tests

What is Urine?

Urine is a yellowish fluid made by the kidneys. Urine is waste product resulting from the body's metabolic activity, the chemical processes required for life. It is composed primarily of water, salts and minerals such as sodium, potassium, calcium and chloride, and other substances such as urea and uric acid. The kidneys make urine by filtering excess water and waste products from the blood as it travels through the kidney blood vessels. Urine leaves each kidney via two tubes called ureters that connect to the bladder. Urine is then stored in the bladder until you need to urinate (pass water). Urine in the bladder is passed via a tube called the urethra.

Normal urine varies in colour from a very pale yellow to a deep amber, depending on how much fluid you drink. Drinking more fluid will dilute the urine and make it paler, while drinking less results in a darker, more concentrated urine. Discolouration can be caused by some foods, medications, and health conditions, e.g., kidney stones, bile duct problems, and liver disease. Cloudy urine can indicate infection of the urinary tract or chronic kidney disease.

What are Microscopy and Culture Tests?

Urine microscopy and culture detects whether there are bacteria in your urine that can cause an infection. The urine culture results are reviewed together with the urine microscopy, and any signs and symptoms that you have.

Urine microscopy involves examining the urine under a microscope to look for bacteria and fungi, and blood cells. Microscopy focuses on the numbers of white blood cell in the urine sample, which indicate an infection.

Urine is cultured in a round petri dish that contains a growth medium that enables any bacteria or fungi in the urine to grow. Once the urine is put on the medium, the dish is closed and placed in an incubator for about a day. If present in the urine, bacteria and fungi grow and become visible colonies. These cultures can be used to determine the type of bacteria or fungus and how many of these organisms are present in the urine culture.

Why are Microscopy and Culture Tests important?

When in the bladder, urine is usually sterile (i.e., without bacteria or other organisms). However, bacteria sometimes enter the urethra and travel to other parts of the urinary system, causing a urinary tract infection (often called a UTI). Most common are lower UTIs that involve the bladder (cystitis) and urethra (urethritis); an upper UTI affects the kidneys (pyelonephritis) and ureters.

UTIs can cause a frequent and urgent need to pass urine and pain and burning when passing urine. Lower UTIs are generally not a major problem but should be treated immediately. Ongoing infection worsens symptoms, causing pain, fever, tiredness, and nausea/vomiting. Left untreated, the infection can travel from the urethra and bladder to the kidneys. Infection can damage the kidneys, causing a permanent loss of kidney function. For people with kidney problems, infection can increase the risk of kidney failure. Additionally, upper UTIs can spread to the blood causing sepsis, a life-threatening over reaction by the body's immune system to an infection.

Who should have Microscopy and Culture Tests?

Your doctor may wish to carry out microscopy and culture testing to see if you have a UTI. Testing may be indicated when your urine shows signs of infection, such as when:

  • results of a urine test stick dipped in your urine are abnormal (e.g., urine contains higher than normal levels of protein, sugar, and blood cells);
  • your urine is discoloured, cloudy or foul-smelling; or
  • you have pain or difficulty when urinating, lower back pain, or fever.

Urine microscopy and culture may be repeated after your UTI has been treated with an antibiotic (for a bacterial infection) or an antifungal medicine (for a fungal infection). This ensures that the medicine has cleared up the infection.

How to take a urine sample for Microscopy and Culture Tests?

Microscopy and culture testing requires a fresh sample of urine taken mid-stream. You do this yourself using a self-collection test kit, which contains full instructions and the various items that you will need to collect and send your urine sample for testing. Before starting, wash your hands, complete the request form, complete and stick the label to the sample tube, and prepare the plastic-lined urine collection box. To collect your mid-stream urine sample, pass the first part of your urine and then collect the next part of the flow in the collection tube. DO NOT USE THE FIRST OR LAST PART OF YOUR URINE FLOW for this test. Then carefully fill the sample tube with urine from the collection box. Screw the tube lid on and place it in the protective packing wallet and return the sample to our laboratory.

What do Microscopy and Culture Test results indicate?

If one or two organisms grow, these can be identified and tested for their antibiotic sensitivities, so that the most appropriate treatment plan can be recommended.

If your result is negative and shows no single important colonies of bacteria it means that there is no evidence of an infection in your urinary tract. However, sometimes the result is negative at the start of an infection or when an infection has been partially treated, because there are too few organisms to form a colony. In this case, if your symptoms persist, then you may need to repeat the urine testing. We will be able to inform you if there was growth, but below the threshold for a urinary tract infection to be confirmed.

Your culture result may be neither positive nor negative for a UTI, meaning that you neither definitely have a UTI nor definitely do not have a UTI. This was because the culture showed considerable growth of three or more types of organisms, probably due to contamination of the urine sample during collection. Contamination can be due to skin cells, vaginal cells, or stools. In this case, you may need to repeat the urine testing. Contamination is unlikely if care is taken when collecting the sample.

What are the risk factors for a UTI?

There are many factors that increase the risk of a UTI. UTIs are more common in women than in men, because the shorter urethra in women means bacteria have a shorter distance to travel to reach the bladder, and because of toilet hygiene, some types of contraception, pregnancy, menopause, and surgery. Other risk factors for UTIs include sexual intercourse, urinary tract abnormalities or blockages (e.g., kidney stones) of the urinary tract, diseases with an impaired immune system (e.g., diabetes), and urinary catheters (a tube used to drain urine from the bladder, e.g., when urination is difficult or after surgery).

How to avoid a UTI

Almost all cases of UTIs, even if they occur frequently, can be prevented by simple measures, such as the following:

  • Drinking plenty of water and other fluids helps to dilute your urine, causing you to pass water more frequently and thus flush the bacteria out of your urinary tract before an infection can start. Some people drink cranberry juice to reduce UTIs symptoms but the evidence is not conclusive.
  • After a bowel movement, wipe from front to back to prevent bacteria in stools from coming into contact with the urethral entrance.
  • When possible, empty your bladder when you need to rather than waiting.
  • Wash your genital area after sexual intercourse, because bacteria can enter the urethra during the time of intercourse.
  • Some methods of contraception (e.g., diaphragms and unlubricated/spermicide-treated condoms) can increase bacterial growth and the number of UTIs.
  • Using feminine toiletries, such as deodorants and douches, on the genital area may not only cause irritation but upset the vagina's natural balance of bacteria, making the conditions more favourable for bacterial growth and infection.
  • A catheter must be inserted when the urethral area is clean, and should remain inserted only for as long as necessary to reduce the likelihood of bacteria in urine.

Elements covered in our Urine Chemistry

Set out below is an example report, so that you are aware of the elements covered in this test panel. If bacteria are cultured, antibiotic sensitivies will also be displayed. Please note that a doctor provides an interpretation of your results.

WBCs1 / µL
RBCs< 1 / µL
CastsNot seen
Epithelial cellsNot seen
CrystalsNot seen
OrganismsNot seen
URINE CULTURENo bacterial growth.
Reviewed by: Dr Loraine Haslam MBBS, DRCOG, DFSRH, LoC SDI, LoC IUT, MRCGP
GMC registration number: 4524038
Date: 29 November 2022
Next review: 28 November 2024
All UK registered doctors can have their registration checked on
The Medical Register at the GMC website.

Urine Chemistry (Microscopy and Culture) Tests Reviews By Our Patients

  • Overall Rating
    Based on 1 review
  • ★★★★★
    Hello, today, two days after the test, my urine is again cloudy with an unpleasant smell and I have pain when urinating. Can we repeat the test and tell me if I have resistance to antibiotics and which antibiotics to I treat the infection? Thank you in advance.
    G. V. - 18/11/23
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