Urine culture

Urine culture is a test that detects and identifies bacteria and yeast in your urine, which may be causing a urinary tract infection (UTI). Urine is the fluid that contains water and wastes and that is produced by the kidneys. It travels from the kidneys, through tubes called ureters to the bladder, and then is eliminated from the body through the urethra. Women and girls get urinary tract infections (UTIs) more often than men and boys. Even preteen girls may have frequent urinary tract infections. For men and boys with a culture-proven urinary tract infection, further tests may be done to rule out the presence of a kidney stone or structural abnormality that could cause the infection.

If someone has frequent and/or recurrent urinary tract infections (UTIs), culture and susceptibility testing may be performed with each infection. For those who have frequent urinary tract infections (UTIs), their bacteria may become resistant to antibiotics over time, making careful selection of antibiotic and the full course of treatment essential.

For a urine culture, a small sample of urine is placed on one or more agar plates (a thin layer of a nutrient media) and incubated at body temperature. Any bacteria or yeast that are present in the urine sample grow over the next 24 to 48 hours as small circular colonies. The size, shape, and color of these colonies help to identify which bacteria are present, and the number of colonies indicates the quantity of bacteria originally present in the urine sample. A laboratorian observes the colonies on the agar plate, counting the total number and determining how many types have grown. Ideally, if a good clean catch sample was collected for the test (see below), then the only bacteria present should be due to an infection. Typically, this will be a single type of bacteria that will be present in relatively large numbers. Sometimes, more than one type of bacteria will be present. This may be due to an infection that involves more than one pathogen; however, it is more likely to be due to contamination from the skin picked up during the urine collection.

The laboratorian will take a colony from each type and perform a gram stain. The laboratorian examines the microorganisms under the microscope. Different types of bacteria will exhibit characteristic colors and shapes. For instance, the bacterium Escherichia coli, which causes the majority of urinary tract infections, will appear as pink (gram-negative) rods under the microscope. Lactobacillus, which is a common vaginal contaminant in women’s urine samples, will appear as thin purple (gram-positive) rods. Some of the bacteria, such as Lactobacillus, are easy for an experienced laboratorian to identify, are nonpathogenic, and do not require any further investigation. Others, such as gram-negative rods, represent groups of similar bacteria and will require additional testing to determine exactly which type of bacteria is present.

If there is no or little growth on the agar after 24 to 48 hours of incubation, the urine culture is considered negative for pathogens and the culture is complete. If there are one or more pathogens present, further testing is performed. Testing is done to identify which bacteria are present and sensitivity testing is done to identify antibiotics that are likely to cure the infection.

Sensitivity is a term used when microbe such as bacteria and fungi are unable to grow in the presence of one or more antimicrobial drugs. Sensitivity testing is performed on bacteria or fungi causing an individual’s infection after they have been recovered in a culture of the specimen. Sensitivity  testing is used to determine the potential effectiveness of specific antibiotics on the bacteria and/or to determine if the bacteria have developed resistance to certain antibiotics. The results of sensitivity test can be used to help select the drug(s) that will likely be most effective in treating an infection.

Bacteria and fungi have the potential to develop resistance to antibiotics and antifungal drugs at any time. This means that antibiotics once used to kill or inhibit their growth may no longer be effective.

My doctor said I had symptoms of a urinary tract infection and prescribed antibiotics without performing a urine culture. Why?

In certain situations, a healthcare practitioner may choose a therapy while a urine culture is incubating; and in other cases, the practitioner may prescribe therapy without ever ordering a urine culture based on knowledge and experience. Bacteria known as Escherichia coli (E. coli) cause the majority of lower urinary tract infections. This microorganism is usually susceptible to a variety of antibiotics, such as trimethoprim-sulfamethoxazole, ciprofloxacin, and nitrofurantoin. Knowing this, your doctor may rely on current susceptibility patterns for E. coli to choose an antibiotic that is likely to be effective in most cases. In most people with uncomplicated disease, the urinary tract infection (UTI) will be resolved after therapy with one of these antibiotics. Based on this information, your healthcare practitioner may prescribe one of them without performing a culture.

Urine culture test

Urine culture test requires a urine sample. Because of the potential to contaminate urine with bacteria and cells from the surrounding skin during collection (particularly in women), it is important to first clean the genital area. Women should spread the labia of the vagina and clean from front to back; men should wipe the tip of the penis. Start to urinate, let some urine fall into the toilet, then collect one to two ounces of urine in the sterile container provided, then void the rest into the toilet. This type of collection is called a mid-stream clean catch urine.

You may be instructed not to urinate for at least an hour before the urine culture test and/or to drink a glass of water 15-20 minutes before sample collection. This will help to ensure that you can produce enough urine for the sample. Follow the instructions provided for collecting a clean catch urine sample.

For catheterized specimens, a urine sample is taken by inserting a thin flexible tube called a catheter through the urethra into the bladder. This is performed by a trained healthcare practitioner. The urine is collected in a sterile container at the other end of the tube. First, the area around the opening of the urethra is thoroughly washed with a germ-killing (antiseptic) solution. The tube is inserted into the urethra. The urine drains into a sterile container, and the catheter is removed.

Rarely, the health care provider may choose to collect a urine sample by inserting a needle directly into the bladder from the abdominal wall and draining the urine. However, this is most often done only in infants or to immediately screen for bacterial infection.

The urine is sent to a laboratory. Tests are done to determine if there are germs in the urine sample. Other tests may be done to determine the best medicine to fight the germs.

During the culture process, pathogens are isolated (separated out from any other microbes present). Each pathogen, if present, is identified using biochemical, enzymatic, or molecular tests. Once the pathogens have been identified, it is possible to determine whether susceptibility testing is required. Susceptibility testing is not performed on every pathogen; there are some that respond to established standard treatments. For example, strep throat, an infection caused by Streptococcus pyogenes (also known as group A streptococcus), can be treated with ampicillin and does not require a test to predict susceptibility to this class of antibiotics.

Susceptibility testing is performed on each type of bacteria or fungi that may be relevant to the individual’s treatment and whose susceptibility to treatment may not be known. Each pathogen is tested individually to determine the ability of antimicrobials to inhibit its growth. This is can be measured directly by bringing the pathogen and the antibiotic together in a growing environment, such as nutrient media in a test tube or agar plate, to observe the effect of the antibiotic on the growth of the bacteria. Resistance can also be determined by detection of a gene that is known to cause resistance to specific antibiotics.

How long does a urine culture take?

The urine is taken to a lab to determine which, if any, bacteria or yeast are present in the urine. Bacterial cultures usually require 24-48 hours to grow the pathogen and obtain a pure culture for further testing. Cultures for fungus and tuberculosis may take much longer — up to 6 to 8 weeks since these microbes grow more slowly.

Traditional sensitivity testing assays require 18-24 hours of incubation; more rapid assays are becoming available that may provide results in less than 24 hours. Molecular tests to detect resistance genes vary from same day results to several days.

Since the wait time for results is a limitation of susceptibility testing, developing new, faster, susceptibility testing techniques is an active area of research. As the FDA approves more of these rapid tests, they are being added to the testing menu in clinical microbiology laboratories.

When is urine culture ordered?

A urine culture may be ordered when a person has symptoms that indicate the possibility of a urinary tract infection (UTI), such as:

• A strong, persistent desire to urinate
• A burning sensation during urination
• A cloudy, strong-smelling urine
• Lower back pain

There are 4 major types of urinary tract infections (UTIs): urethritis, cystitis, acute urethral syndrome, and pyelonephritis. Urinary tract infections may also be classified as uncomplicated or complicated. Escherichia coli is the leading cause of uncomplicated community-acquired urinary tract infection. Risk factors that predispose one to complicated urinary tract infections include: underlying diseases that are associated with kidney infection (eg, diabetes), kidney stones, structural or functional urinary tract abnormalities, and indwelling urinary catheters. Another classification of urinary tract infections is as upper urinary tract infection (related to the kidney, renal pelvis, or ureter) or lower urinary tract infection (urinary bladder and urethra). The classic symptoms of upper urinary tract infection are fever (often with chills) and flank pain; frequent painful urination, urgency, and dysuria are more often associated with lower urinary tract infection.

People with urinary tract infections (UTIs) may also have pressure in the lower abdomen and small amounts of blood in the urine. If the urinary tract infection is more severe and/or has spread into the kidneys, it may cause flank pain, high fever, shaking, chills, nausea or vomiting.

Sometimes, antibiotics may be prescribed without requiring a urine culture for young women with signs and symptoms of a urinary tract infection and who have an uncomplicated lower urinary tract infection. If there is suspicion of a complicated infection or symptoms do not respond to initial therapy, then a culture of the urine is recommended.

Pregnant women without any symptoms are recommended to be screened during the first trimester or first prenatal visit for bacteria in their urine, which could affect the health of the developing baby.

A urine culture may be ordered with a urinalysis or as follow up to abnormal results on a urinalysis.

How is urine culture test used?

The urine culture is used to diagnose a urinary tract infection (UTI) and to identify the bacteria or yeast causing the infection. It may be done in conjunction with susceptibility testing to determine which antibiotics will inhibit the growth of the microbe causing the infection. The results will help a healthcare practitioner determine which drugs are likely to be most effective in treating a person’s infection.

Urine is produced by the kidneys, a pair of bean-shaped organs that are located at the bottom of the ribcage in the right and left sides of the back. The kidneys filter waste out of the blood and produce urine, a yellow fluid, to carry wastes out of the body. Urine travels through tubes called ureters from the kidneys to the bladder, where it is stored temporarily, and then through the urethra as it is voided. Urine is generally sterile, but sometimes bacteria or, more rarely, yeast can move from the skin outside the urethra and migrate back up the urinary tract to cause a urinary tract infection.

Most urinary tract infections are considered uncomplicated and are easily treated. However, if they are not addressed, the infection may spread up through the ureters and into the kidneys. A kidney infection is more dangerous and can lead to permanent kidney damage. In some cases, a urinary tract infection may lead to an infection in the bloodstream (sepsis, septicemia) that can be life-threatening.

People with kidney disease or with other conditions that affect the kidneys, such as diabetes or kidney stones, and people with weakened immune systems may be more prone to frequent, repeated and/or complicated urinary tract infections.

Urine culture results interpretation

Results of a urine culture are often interpreted in conjunction with the results of a urinalysis and with regard to how the sample was collected and whether symptoms are present. Since some urine samples have the potential to be contaminated with bacteria normally found on the skin (normal flora), care must be taken with interpreting some culture results.

Typically, the presence of a single type of bacteria growing at high colony counts is considered a positive urine culture. For clean catch samples that have been properly collected, cultures with greater than 100,000 colony forming units (CFU)/mL of one type of bacteria usually indicate infection. In some cases, however, there may not be a significantly high number of bacteria even though an infection is present. Sometimes lower numbers (1,000 up to 100,000 CFU/mL) may indicate infection, especially if symptoms are present. Likewise, for samples collected using a technique that minimizes contamination, such as a sample collected with a catheter, results of 1,000 to 100,000 CFU/mL may be considered significant.

Although a variety of bacteria can cause urinary tract infections (UTIs), most are due to Escherichia coli, bacteria that are common in the digestive tract and routinely found in stool. Other bacteria that may cause UTIs include species of Proteus, Klebsiella, Enterococcus, and Staphylococcus. Occasionally, a UTI may be due to a yeast, such as Candida albicans; urethritis is often due to a sexually transmitted disease such as herpes, chlamydia, or gonorrhea.

A culture that is reported as “no growth in 24 or 48 hours” usually indicates that there is no infection. If the symptoms persist, however, a urine culture may be repeated on another sample to look for the presence of bacteria at lower colony counts or other microorganisms that may cause these symptoms. The presence of white blood cells and low numbers of microorganisms in the urine of a symptomatic person is a condition known as acute urethral syndrome.

If a culture shows growth of several different types of bacteria, then it is likely that the growth is due to contamination. This is especially true in voided urine samples if the organisms present include Lactobacillus and/or other common nonpathogenic vaginal bacteria in women. If the symptoms persist, the healthcare practitioner may request a repeat culture on a sample that is more carefully collected. However, if one type of bacteria is present in significantly higher colony counts than the others, for example, 100,000 CFUs/mL versus 1,000 CFUs/mL, then additional testing may be done to identify the predominant bacteria.

If a culture is positive, susceptibility testing may be performed to guide treatment. Any bacterial infection may be serious and can spread to other areas of the body if not treated. Pain is often the first indicator of an infection. Prompt treatment, usually with antibiotics, will help to alleviate the pain.

Normal Results

Normal values depend on the test being performed. Normal results are reported as “no growth” and are a sign that there is no infection.

• No growth (Organism present <10,000 colony forming units (CFU)/mL or mixed flora.)

Normal value ranges may vary slightly among different laboratories. Some labs use different measurements or test different samples. Talk to your doctor about the meaning of your specific test results.

Abnormal Results

A “positive” or abnormal test means germs, such as bacteria or yeast, are found in the urine sample. This likely means that you have a urinary tract infection or a bladder infection. If there is only a small amount of germs, your health care provider may not recommend treatment.

Sometimes, bacteria that do not cause urinary tract infections may be found in the culture. This is called a contaminant. You may not need to be treated.

If the skin and genital area were not cleaned well prior to collecting the sample, the urine culture may grow three or more different types of bacteria and is assumed to be contaminated. The culture will be discarded 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 clean catch urine sample.

People who have a urinary catheter in all of the time may have bacteria in their urine sample, but it does not cause a true infection. This is called being colonized.

In general, the isolation of more than 100,000 colony forming units (CFU)/mL of a urinary pathogen is indicative of urinary tract infection (UTI). Isolation of 2 or more organisms above 10,000 colony forming units (CFU)/mL may suggest specimen contamination. For specimens contaminated with the usual bacterial flora, bacteria that are potentially pathogenic are identified.

Although urine is normally sterile, contamination by organisms normally present in the urethra or on periurethral surfaces can allow a proliferation of these organisms yielding misleading urine culture results.

Urine held at ambient temperature for more than 30 minutes supports the growth of both pathogens and contaminants, leading to potentially inaccurate colony counts.

Urine obtained from catheter bags at the bedside and Foley catheter tips are unacceptable for culture.

What happens if my infection goes untreated?

If your infection is not treated, it can move from the lower urinary tract to the upper urinary tract and infect the kidney itself, and possibly, enter the bloodstream, causing septicemia. Signs and symptoms of septicemia include fever, chills, elevated white blood cell count, and fatigue. If a healthcare practitioner suspects that you have septicemia, he or she will typically order a blood culture and will prescribe antibiotics accordingly.

What puts me at risk for recurrent urinary tract infections?

There are a wide variety of factors that predispose a person to get a urinary tract infection (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, kidney stones, and tumors 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 urinary tract infection (UTI).

Urine culture and sensitivity

Urine culture and sensitivity testing is used to determine which antimicrobials will inhibit the growth of the bacteria or fungi causing a specific urinary tract infection (UTI). The results from urine culture and sensitivity test will help a healthcare practitioner determine which drugs are likely to be most effective in treating a person’s urinary tract infection (UTI). A urine sample for culture and sensitivity testing should be collected before the start of any treatment with an antimicrobial drug, unless the test is used to monitor the effectiveness of treatment.

Some types of urinary tract infections (UTIs) may require testing because the bacteria or fungi isolated from an infection site are known to have unpredictable susceptibility to the drugs usually used to treat them. Some examples include staphylococci (“staph”) and Pseudomonas aeruginosa.

Sometimes there may be more than one type of pathogen isolated from an infected urine. Sensitivity testing may be used to determine which antibiotic or antibiotic combinations will be most effective in treating all the different types of bacteria causing the urinary tract infection.

What does urine culture and sensitivity test result mean?

Results of the urine culture and sensitivity testing are usually reported as:

• Susceptible — likely, but not guaranteed to inhibit the pathogenic microbe; may be an appropriate choice for treatment
• Intermediate — may be effective at a higher dosage, or more frequent dosage, or effective only in specific body sites where the antibiotic penetrates to provide adequate concentrations
• Resistant — not effective at inhibiting the growth of the organism in a laboratory test; may not be an appropriate choice for treatment

These categories are based on the minimum inhibitory concentration (MIC). This is the lowest concentration of an antibiotic that will be effective in inhibiting growth of the bacteria. Though results may be expressed as the minimum inhibitory concentration (MIC), in units such as micrograms/milliliter, the laboratory will often include in the report an interpretation of what the results mean (e.g., susceptible, intermediate or resistant).

If there is more than one pathogen identified in a urine culture, the laboratory will contain the results for each one.

A healthcare practitioner will choose an appropriate antibiotic from those on the report that were categorized as “Susceptible.” If there are no “Susceptible” choices, or the patient is allergic to drugs in the susceptible category, then the practitioner may select one categorized as “Intermediate.” This may require a higher dosage and may involve a longer duration of therapy as well as a higher risk for medication side effects.

A pathogen may be “Resistant” to all of the drugs that are usually used to treat that type of infection. If this is the case, then the practitioner may prescribe a combination of antibiotics that work together to inhibit the bacteria when neither one alone will be effective. These drug therapies may be more expensive and may have to be given intravenously, sometimes for extended periods of time. Some infections caused by resistant bacteria have proven very difficult to treat.

How do microbes become resistant to antimicrobial drugs?

Resistance may be innate (natural) or acquired. Natural resistance is part of the microbe’s normal physical and genetic characteristics. Since microbes multiply very rapidly; they go through many generations in a short period of time. There is always the potential for antimicrobial resistance to arise through a genetic change (mutation). If this change gives the microbe a survival advantage, it may be passed on to subsequent generations.

An acquired resistance may develop through a selection process. When someone is treated with an antimicrobial drug, the most susceptible microbes are the ones that are killed first. If treatment is stopped before all of the pathogens are killed, the survivors may develop a resistance to that particular antimicrobial drug. The next time they are exposed to the same drug, it may be ineffective as the bacteria and their progeny are likely to retain resistance to that antimicrobial drug.

Resistance can spread when resistant microbes share their genetic material with susceptible ones. This may occur more frequently in a healthcare setting, where many patients are treated with antimicrobial drugs. For instance, resistant strains of bacteria, such as methicillin resistant Staphylococcus aureus (MRSA), have been a problem in hospitals for decades and are increasingly common in the community.

A resistant microbe may spread to other people throughout a community. Once a strain of bacteria has become resistant to one or more antimicrobial drug, the only recourse is to try to inhibit its spread and to try to find another one that will kill it. The second or third choice antimicrobial drugs that are available are often more expensive and associated with more side effects. This presents a challenge that is compounded by the fact that microbes are becoming resistant faster than new antimicrobial drugs are being developed.

Are there other ways of testing for resistance?

Sometimes molecular methods are used to look for changes (mutations) in a microbe’s genetic material that enables it to grow in the presence of certain antimicrobial drugs. For instance, methicillin-resistant Staphylcoccus aureus (MRSA) contain the mecA gene that confers resistance to the antibiotics methicillin, oxacillin, nafcillin, and dicloxacillin. Detection of the mecA gene using a molecular based test allows the rapid detection of MRSA prior to culturing the bacteria. Someone carrying this microbe in their nasal passages can be isolated from other patients in the hospital so that the resistant staph are not transmitted to others.