A urine culture is a test to find germs (such as bacteria) in the urine that can cause an infection. Bacteria can enter through the urethra and cause a urinary tract infection (UTI). A sample of urine is added to a substance that promotes the growth of germs. If no germs grow, the culture is negative.
A urine culture is a test that can detect bacteria in your urine. This test can find and identify the germs that cause a urinary tract infection (UTI). Bacteria, which typically cause UTIs, can enter the urinary tract through the urethra. In the environment of your urinary tract, these bacteria can grow rapidly and develop into an infection.
Specimen Collection
There are a variety of methods aimed at specimen collection to diagnose a UTI. Some of the factors that dictate the method used include patient comfort, the ability to void, and reducing the small risk of iatrogenic infection. Sterile collection methods can be employed, such as a suprapubic puncture or urethral catheterization, in an effort to reduce overdiagnosis and subsequent overtreatment.[rx] Even so, patients are instructed to collect their own samples from a variety of acceptable techniques.
Specimen Collection
There are a variety of collection techniques for urine culture, including suprapubic aspiration, straight catheter technique, and mid-stream catch with or without cleansing. In pediatric patients who are not toilet trained, diaper collection, and sterile bag, urine collection methods are used. Suprapubic collection is the best method to avoid specimen contamination with bacteria, particularly in the distal urethra. Owing to patient discomfort, invasiveness, lack of indication (except in rare instances), and inappropriate resource use, this method is rarely deployed. Urine collection with a single catheter (straight catheter technique) is the next best option. Still, due to labor intensiveness as well as the possibility of introducing bacteria into the bladder, potentially causing a UTI, this technique is seldom used and only when indicated. The previously aforementioned methods of specimen collection are therefore reserved for those patients who are unable to self-collect. Hence, the most common method a urine sample is obtained for urine culture is via a clean-catch midstream technique, which is neither invasive nor uncomfortable. Colony counts from these samples correlate reasonably well compared to suprapubic aspiration and single catheter technique.[rx]
The current standards for self-collection include mid-stream clean-catch technique, mid-stream catch without prior cleansing, and random sampling delivered without instruction. There are no clinically significant differences seen between the various self-collection techniques.[rx] However, studies have shown that depending on the patient’s demographic, such as adult male, adult female, or infant/child, there may be preferred methods of sample collection over other methods. For females, contamination and diagnostic accuracy did not significantly change between midstream urine collection with or without prior cleansing; there is no recommendation without regard to cleansing prior to collection.[rx] In adult males, contamination was significantly decreased when mid-stream catch is utilized as the method of collection, becoming favorable over first-void specimen collection. Mid-stream collection was not significantly altered with prior cleansing. However, in children and infants, mid-stream collection with prior cleansing was favorable in reducing contamination over other methods, including mid-stream collection without cleansing, sterile bag urine collection, and diaper collection.[rx] Therefore, pre-collection cleansing procedures have been considered unnecessary in most adult populations as they do not decrease the risk of contamination from commensal bacteria.[rx][rx][rx] Even so, patients continue to follow the traditional directive of cleansing as the first step in urine specimen collection despite no change in diagnosis, course, or treatment.
Specimen Transportation
Owing to the probable increase risk of growth of colony-forming units (CFU) non-indicative of the patient’s true sample, urine specimens must be plated within two hours of collection, unless refrigerated or placed in a preservative.[rx] This measure decreases the risk of false-positive cultures, directly leading to a decrease in overtreatment while maintaining appropriate antibiotic stewardship.
Procedures
Specimen Preservation and Processing
Preservation of the urine sample can be achieved with a boric acid solution or refrigeration for up to 24 hours. Both techniques yield adequate preservation of the sample. Samples that are left at room temperature for greater than 4 hours run the risk of bacterial overgrowth of causative and contamination organisms.[rx] However, based on a meta-analysis of preservation techniques, the statistical analysis of this data was rated as low.[rx] Nonetheless, common gram-negative organisms causing UTIs such as Escherichia coli and Klebsiella pneumoniae, have been noted to be inhibited when boric acid is used as a storage medium. Therefore, careful consideration of the storage medium should be practiced, and timely refrigeration must be prioritized.
Specimens are processed routinely using calibrated loops for plating. This method allows for CFU/mL findings as well as the isolation of colonies for identification and susceptibility testing. Some of the most utilized media are blood agar and MacConkey agar. The temperature of the plates should be kept between 35 to 37 degrees Celcius with a recommended incubation time of 24 to 48 hours. However, Oligella urolytica, a slow-growing, gram-negative, and rare UTI-causing organism, has been reported to have an incubation of over 48 hours.[rx] Specimens from outpatients do not need to be plated on selective media. However, in hospitalized patients, where enterococci are the second leading cause of UTI, laboratory technicians should consider inoculating urine specimens to a medium that is selective for these gram-positive cocci.[rx]
Indications
Routine bacterial urine cultures are not always necessary in the evaluation of outpatients with uncomplicated UTIs and simple lower UTIs, such as uncomplicated cystitis.[rx][rx] An important classification of uncomplicated UTI versus complicated UTI distinguishes the need for urine culture. Since UTIs are composed of lower UTIs (e.g., cystitis) and upper UTIs (e.g., pyelonephritis), clinically differentiating the two by symptomology is necessary as the first step in determining the need for urine culture. A patient experiencing cystitis could report dysuria (with or without frequency), urgency, hematuria, or suprapubic pain, while a patient suffering from pyelonephritis may or may not have the symptoms of cystitis, but will typically report fever, chills, flank pain with or without costovertebral tenderness.[rx][rx] Should these patients have a complicating factor, a urine culture is likely warranted. Some of the complicating factors include male sex, chronic obstruction, chronic renal insufficiency, nephrolithiasis, poorly controlled diabetes, pregnancy, indwelling urinary catheters, indwelling urinary stent or nephrostomy tube, and immunosuppression (chronic high-dose corticosteroid use, use of other immunosuppressive agents, neutropenia, etc.).[rx] Furthermore, outpatients with recurrent UTIs, treatment failure, complicated UTIs, and inpatient UTIs require urine culture to not only document infection, but to confirm the causative organism in order to prevent complications and for antimicrobial susceptibility resistance. These examples warrant further investigation beyond clinical diagnosis and urinalysis.
Additionally, new-onset or worsening sepsis without evidence of an alternate source is also another appropriate indication for urine culture. New-onset or worsening sepsis is a major cause of morbidity and mortality in hospitalized patients globally and should be swiftly recognized clinically for the purposes of swift urine culture collection.[rx] Fever or alteration of consciousness without evidence of a source may also warrant a urine culture. For patients in early pregnancy or prior to certain urology procedures, screening for asymptomatic bacteriuria is warranted. Additionally, preoperative evaluations may trigger the utilization of urine culture, especially when mucosal bleeding is expected. Finally, urine cultures are sometimes appropriate in cases of spinal cord injury, where the patient may experience an increase in spasticity, autonomic dysreflexia, and a sense of unease.[rx] These patients are at an increased risk of UTI due to autonomic dysregulation leading to stagnating urine, which becomes a nidus for infection.
Urine culture is not indicated and is therefore deemed inappropriate when the urine characteristics are odorous, cloudy, or discolored in the absence of other localizing signs or symptoms, reflex urine cultures based on results of urinalysis such as pyuria in the absence of other indications, and to document successful response to therapy.[rx][rx] Screening for asymptomatic bacteria in most groups is also unnecessary, as it does not alter the course of therapy. Patients with asymptomatic bacteriuria are typically not treated unless pregnant. Yet, some studies have shown that in pregnant women with pyelonephritis, the patient course dictates antibiotic treatment, not necessarily the culture and sensitivities themselves.[rx]
What is being tested?
Potential Diagnosis
The positive findings of a urine culture can lead to the diagnosis of UTI (uncomplicated vs. complicated), asymptomatic bacteriuria (ASB), catheter-associated UTI (CA-UTI), and catheter-associated asymptomatic bacteriuria (CA-ASB). These diagnoses lead to the possible identification of the source of sepsis. Proper diagnosis lends itself to proper antibiotic stewardship and decreases in morbidity and mortality. As up to 25% of hospitalized patients in North America receive indwelling catheter placement, utilization of the urine culture is of utmost importance to determine potential diagnoses.[rx][rx] Consequently, differentiation between catheterized patients and non-catheterized patients is common, as is the differentiation between UTI and asymptomatic bacteriuria.
Normal and Critical Findings
Normal Findings
Urine is normally sterile. However, there is a possibility of contamination. Hence, samples from patients without UTI symptoms with low colony counts certainly below the threshold for bacteriuria, and no detection of organisms, are considered to be normal samples.
Critical Findings
-
UTI – UTI symptoms. Gold standard confirmation is the urine culture.[rx] Positive urine cultures are observed when there is significant microbial growth determined by standard microbiological criteria.[rx] Although not completely standardized, many laboratories set the cut-off at greater than or equal to 100,000 CFUs/ml for a UTI. However, this particular threshold may miss relevant infections. Consequently, other recommendations have noted a cut-off of greater than or equal to 1,000 CFUs/ml in order to capture other bacterial infections.[rx]
-
CA-UTI – According to the Infectious Diseases Society of America’s (IDSA) 2010 guideline for diagnosis of CA-UTI, it is defined as patients with an indwelling catheter with the presence of symptoms or signs compatible with UTI with no other identified source of infection. They must also have greater than or equal to 1000 CFU/ml with more than one bacterial species in a single catheter urine specimen or in a midstream voided urine specimen in patients whose urinary catheter (urethral, suprapubic or condom) has been removed within the past 48 hours. According to the United States Centers for Disease Control and Prevention (CDC), the patient must meet the following three criteria: 1) The patient must have an indwelling urinary catheter in place for more than 2 days on the date of the event, 2) The patient has a fever (of greater than or equal to 38 degrees Celsius, costovertebral angle (CVA) pain or tenderness, suprapubic tenderness, urgency, frequency or dysuria, and 3) The patient has a urine culture with no more than two species of organisms identified, at least one being a bacterium of greater than or equal to 1000 CFU/ml.[rx]
-
CA-ASB – Positive urine culture in the absence of UTI symptoms.[rx] Asymptomatic catheter-associated bacteriuria and candiduria exhibit a urine culture of at least 100,000,000 CFU/mL of an identified organism(s) in the absence of signs and symptoms of a UTI.[rx][rx] These cases do not require treatment and generally resolve upon the removal of catheters.[rx]
-
Bacteriuria – The most commonly used cut-off for significant bacteriuria is greater than or equal to 100,000 CFU/ml of urine.[rx] Asymptomatic bacteriuria is present when the patient does not have any signs of a UTI clinically coupled with 100,000 CFU/ml exceeded in two consecutive samples of midstream urine (from women). For men, a single detection of more than 100,000 CFU/ml is adequate for diagnosis.[rx] Although pyuria is non-diagnostic in itself, the detection of leukocytes could support the diagnosis of CA-ASB.
The most common cause of UTIs in both inpatient and outpatient settings is Escherichia coli, accounting for the overwhelming majority of cases. E. coli is followed by coagulase-negative staphylococci, Klebsiella species, Proteus species, and Enterobacter species.[rx] Each unique organism can be part of urine culture results. Owing to the differences in the microbiology of each organism, proper identification leads to increased antibiotic stewardship by selecting the proper antibiotic coverage, subsequently leading to decreases in antibiotic resistance.
- Protein – in the urine (proteinuria) can usually be detected by dipstick when present in large amounts. Protein may appear constantly or only intermittently in the urine, depending on the cause. Proteinuria may occur normally after strenuous exercises, such as marathon running, but is usually a sign of a kidney disorder. Small amounts of protein in the urine may be an early sign of kidney damage due to diabetes. Such small amounts may not be detected by dipstick. In these cases, urine will need to be collected over a period of 12 or 24 hours and tested by a laboratory.
- Glucose – in the urine (glucosuria) can be accurately detected by dipstick. The most common cause of glucose in the urine is diabetes mellitus, but the absence of glucose does not mean a person does not have diabetes or that the diabetes is well controlled. Also, the presence of glucose does not necessarily indicate diabetes or another problem.
- Ketones – in the urine (ketonuria) can often be detected by dipstick. Ketones are formed when the body breaks down fat. Ketones can appear in the urine as a result of starvation or uncontrolled diabetes mellitus and occasionally after drinking significant amounts of alcohol.
- Blood – in the urine (hematuria) is detectable by dipstick and confirmed by viewing the urine with a microscope and other tests. Sometimes the urine contains enough blood to be visible, making the urine appear red or brown.
- Nitrites – in the urine (nitrituria) are also detectable by dipstick. High nitrate levels indicate a urinary tract infection.
- Leukocyte esterase – (an enzyme found in certain white blood cells) in the urine can be detected by dipstick. Leukocyte esterase is a sign of inflammation, which is most commonly caused by a urinary tract infection.
- The acidity (pH) of urine – is measured by a dipstick. Certain foods, chemical imbalances, and metabolic disorders may change the acidity of urine. Sometimes a change in acidity can predispose the person to kidney stones.
- The concentration – of urine (also called the osmolality, roughly indicated by specific gravity) can vary widely depending on whether a person is dehydrated, how much fluid a person has drunk, and other factors. Urine concentration is also sometimes important in diagnosing abnormal kidney function. The kidneys lose their capacity to concentrate urine at an early stage of a disorder that leads to kidney failure. In one special test, a person drinks no water or other fluids for 12 to 14 hours. In another test, a person receives an injection of vasopressin (also called antidiuretic hormone). Afterward, urine concentration is measured. Normally, either test should make the urine highly concentrated. However, in certain kidney disorders (such as nephrogenic diabetes insipidus), the urine cannot be concentrated even though other kidney functions are normal.
- Sediment – in urine can be examined under a microscope to provide information about a possible kidney or urinary tract disorder. Normally, urine contains a small number of cells and other debris shed from the inside of the urinary tract. A person who has a kidney or urinary tract disorder usually sheds more cells, which form sediment if urine is spun in a centrifuge (a laboratory instrument that uses centrifugal force to separate components of a liquid) or allowed to settle.
Interfering Factors
Urine culture results may be deemed faulty and inconclusive due to patient factors. Recent antibiotic use is a major culprit, as this therapy may mask the presence of UTI-causing organisms. Furthermore, the use of diuretics or the consumption of large amounts of fluids may also dilute the urine and invariably lead to a decrease in the number of bacteria present in the sample. Moreover, the large consumption of ascorbic acid has been long known to interfere with the results of urine dipstick results.[rx]
Culture results are invariably affected by faulty collection techniques, leading to the contamination of urine and invariably, by urogenital flora.[rx] Operator error in the handling of urine specimens may also lend to increasing CFUs, leading to false-positive results. Unless refrigerated or kept in a preservative, urine samples should be plated within two hours of collection.[rx] Urine samples where plating is delayed, especially over 24 hours, are deemed useless due to the possibility of a bacterial overgrowth that is not representative of the patient’s original sample. Consequently, laboratory delay is a significant issue interfering with the validity of the urine culture.
Complications
The various stages of urine collection, whether collection itself, storage, and preservation, have a tremendous impact on the results of a urine culture. Without adequate care, specimens can become contaminated with perineal, vaginal, or periurethral flora. The presence of the true pathogenic agent can be obscured due to the contamination, whether due to an overgrowth or an inhibition of the true pathogens. Even more than that, the medium in which the specimen is stored also plays a significant role in the true urinary pathogen. Inhibition of Escherichia coli and Klebsiella pneumoniae have been observed with the use of boric acid as the storage and preservation medium.[rx] Owing to these issues with contamination and obscuration of true UTI-causative organisms, misdiagnosis, and subsequent poor patient management and faulty antibiotic stewardship will result, with the most feared complication becoming a complicated UTI and possibly leading to urosepsis.[rx] Consequently, proper detection of UTI or asymptomatic bacteriuria is of paramount importance. For instance, swift detection of asymptomatic bacteriuria in pregnancy is necessary in order to prevent the feared complication of pyelonephritis with subsequent harm to the child.[rx] Ordering urine cultures when indicated and proper handling of the urine specimen provides for proper diagnosis and therefore preventing complications associated with poorly diagnosed and treated UTI.
Patient Safety and Education
Specimen collection by means of clean-catch midstream technique poses no risk to the patient. Despite the longstanding belief that pre-cleansing yields an uncontaminated specimen, several studies have shown that pre-cleansing has no significant effect on test results. Prevention of UTI is worthy of discussion and has been traditionally under-researched in the past. Patients should be educated on correct wiping methods, adequate hydration, frequent urination, avoiding feminine products, precoital bathing, and postcoital voiding, and avoid the use of a number of certain birth control products. With these increased measures aimed at improving hygiene, health behaviors, and sexual practices, UTI-related morbidity, and the use of antibiotics for these infections would invariably decrease.[rx][rx]
Common Questions
How is the test used?
- The urine culture is used, along with results from a urinalysis, to diagnose a urinary tract infection (UTI) and to identify the bacteria or yeast causing the infection. If a urine culture is positive, susceptibility testing may be done 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 your infection.
- A urine culture is used, as recommended by several health organizations, to screen pregnant women for asymptomatic bacteriuria, a condition in which significant amounts of bacteria are in the urine but do not cause symptoms. About 2%-10% of pregnant women in the U.S. have this condition that can lead to more serious kidney infections as well as increased risk of preterm delivery and low birth weight.
When is it ordered?
- A urine culture may be ordered when you have signs and symptoms of a urinary tract infection (UTI) and/or results of a urinalysis show that you may have a UTI.
Some signs and symptoms of a UTI include:
- A strong, frequent urge to urinate, even when you have just gone and there is little urine voided
- Pain and/or a burning sensation during urination
- Cloudy, strong-smelling urine
- Lower back pain
- You may also have pressure in the lower abdomen and small amounts of blood in the urine. If the UTI 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 UTI 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 with a urine culture early in their pregnancy (e.g., during the second trimester) or during the first prenatal visit for bacteria in their urine.
What does the test result mean?
- 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.
Positive urine culture: 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)/milliliter 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.
- Results from a urinalysis can be used to help interpret the results of a urine culture. For example, a positive leukocyte esterase (a marker of white blood cells) and nitrite (a marker for bacteria) help confirm a UTI.
- If a culture is positive, susceptibility testing may be performed to guide treatment. (See the article on Antibiotic Susceptibility Testing for more details on results.)
- Although a variety of bacteria can cause UTIs, most are due to Escherichia coli (E. coli), bacteria that are common in the digestive tract and routinely found in stool.
Other bacteria that commonly cause UTIs to include
- Proteus
- Klebsiella
- Enterobacter
- Staphylococcus
- Acinetobacter
Occasionally, a UTI may be due to yeast, such as Candida albicans.
- Negative urine culture: 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 an asymptomatic person is a condition known as acute urethral syndrome.
- Contamination: If a culture shows the 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.
Can a urine culture be used to test for infections other than UTIs, such as sexually transmitted diseases (STDs)?
- Yes. Urine cultures can detect some sexually transmitted diseases. However, a urine culture is not the test of choice for sexually transmitted diseases in adults. Some STDs such as chlamydia may be tested using a urine sample, but the testing method used detects chlamydia genetic material in the urine and is not a culture. Tell your healthcare practitioner if you think you have a sexually transmitted disease, so the practitioner can order the appropriate test. (For example, read the articles on Chlamydia Testing and Gonorrhea Testing.) Urine cultures may be used to test for STDs in children.
- For another example, a urine culture may be used to help diagnose infections of the urinary tract and genital tract caused by mycobacteria. Typically, this test requires that the first urine voided in the morning be collected.
My healthcare practitioner’s office called to say they need a new urine sample, the first was contaminated. What happened?
- 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 midstream clean catch urine sample.
My healthcare practitioner said I had symptoms of a urinary tract infection and prescribed antibiotics without performing a urine culture. Why?
- Bacteria are known as Escherichia coli (E. coli) cause the majority of lower urinary tract infections. This microbe is usually susceptible to a variety of antibiotics, such as trimethoprim-sulfamethoxazole, ciprofloxacin, and nitrofurantoin. In most people with an uncomplicated UTI, the infection will be cured after treatment with one of these antibiotics. Based on this information, your healthcare practitioner may prescribe one of them without performing a 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 kidneys and possibly spread to the bloodstream, causing septicemia and sepsis, a serious and potentially life-threatening condition. Signs and symptoms of septicemia include fever, chills, elevated white blood cell count, and fatigue. If a healthcare practitioner suspects septicemia, the practitioner will typically order a blood culture as well as other tests 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 UTI. UTIs are more common in girls and women than in boys and men because of the differences in their genitals and urinary tracts. Some infants and young children have abnormalities of the urinary tract that they are born with (congenital) that increase their risk of UTIs. In adults, sexual intercourse, diabetes, pregnancy, poor bladder control, kidney stones, and tumors are examples of factors that increase the risk of UTIs. In a hospital, nursing home, or home care setting, urinary catheters are major risk factors for UTIs.
Is there anything else I should know?
- If you have frequent and/or recurrent UTIs, culture and susceptibility testing may be performed with each infection. If you have frequent UTIs, careful selection of antibiotics and completing the full course of treatment can be important.
References
People Also Reading
Cystourethroscopy – Indications, Procedure, Result
Cholesterol Screening Test – Indications, Procedure, Result
Urine Analysis / Urinalysis; Types, Normal value,Exam Result, Reports
Urodynamic Testing – Indications, Procedure, Result
Creatinine Clearance – Types, Test, Procedure, Result
Lower Limb Examination – Technique, Procedure, Result
Cystoscopy – Indications, Procedure, Results
Upper Limb Examination – Technique, Procedure, Result
Urine Storage – Anatomy, Mechanism, Functions
Urine Elimination – Anatomy, Mechanism, Functions
Composition of Urine – Anatomy, Mechanism, Functions
Urine Transport – Anatomy, Types, Mechanism, Functions
About the author