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Urine Culture

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Last Update: May 1, 2023.


Urinary tract infections (UTI) are one of the leading causes of infections in the United States. By the age of 18 years or older, at least 10% of females would have been diagnosed with a UTI. By the age of 24 years, 1 in 3 females would be treated for a UTI.[1] UTIs are one of the most common nosocomial infections, accounting for 35% to 40% of all hospital-acquired infections.[2] One of the most common nosocomial infections is catheter-associated UTI (CAUTI), each year, accounting for over 1 million cases in hospital and nursing home patients.[3] A urine culture is the gold standard test for revealing the causative microorganism for a UTI.[4][5] Sterile technique is often the standard in which all collection methods are compared. Owing to patient discomfort and clinical setting standards, sterile collection procedures are often forgone for self-collection techniques where the patient is in control of their sample. Special consideration is worthy of discussion, as the risk of contamination is maximized, and operator error may result in inconsistent urine collections, especially during the preanalytic phase of urine culture.[6] Given this apparent and immediate issue with the integrity of the urine culture and the risk of overdiagnosis, antibiotic stewardship must be maintained in order to safeguard the patient. Furthermore, the risk of antibiotic resistance is always central in order to recognize how healthcare providers practice antibiotic stewardship, where overdiagnosis is eliminated, and proper antibiotic selection is achieved. The proper utilization of the urine culture ameliorates these concerns and helps combat this very common nosocomial 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.[7] 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.[8]

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.[7] 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.[7] 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.[7] 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.[9][10][11] 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.[12] This measure decreases the risk of false-positive cultures, directly leading to a decrease in overtreatment while maintaining appropriate antibiotic stewardship.


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.[6] However, based on a meta-analysis of preservation techniques, the statistical analysis of this data was rated as low.[7] 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.[13] 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.[14]


Routine bacterial urine cultures are not always necessary in the evaluation of outpatients with uncomplicated UTIs and simple lower UTIs, such as uncomplicated cystitis.[15][16] 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.[16][17] 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.).[17] 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.[18] 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.[19] 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.[12][20] 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.[21]

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.[22][23] 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.[5] Positive urine cultures are observed when there is significant microbial growth determined by standard microbiological criteria.[24] 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.[5] 
  • 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.[25]
  • CA-ASB: Positive urine culture in the absence of UTI symptoms.[26] 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.[27][28] These cases do not require treatment and generally resolve upon the removal of catheters.[26]
  • Bacteriuria: The most commonly used cut-off for significant bacteriuria is greater than or equal to 100,000 CFU/ml of urine.[29] 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.[5] 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.[30] 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. 

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.[31]  

Culture results are invariably affected by faulty collection techniques, leading to the contamination of urine and invariably, by urogenital flora.[4] 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.[12] 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.  


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.[32] 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.[1] 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.[33] 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.[16][34]

Clinical Significance

Accurate diagnosis of patients experiencing symptoms of a UTI is paramount in efforts to practice proper antibiotic stewardship, by limiting antibiotic misutilization and overutilization.[35] Some of the pitfalls of inappropriate antibiotic use include an increased incidence of Clostridium difficile infections, adverse drug reactions, and colonization or infection of resistant bacteria.[34] Some of the advantages of urine culture stewardship include absolute decreases in the total number of unnecessary urine cultures, the inappropriate treatment of ASB, as well as the costs related to the overtreatment of various infections. Since hospitalized patients have the highest risk of UTI as a nosocomially acquired infection, efforts to increase clinical acumen while decreasing unnecessary testing and antibiotic use benefit the patient by decreasing chances of antibiotic resistance as well as allocating resources properly for those who truly need urine cultures and subsequent treatment. 

Review Questions


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Disclosure: Hadeer Sinawe declares no relevant financial relationships with ineligible companies.

Disclosure: Damian Casadesus declares no relevant financial relationships with ineligible companies.

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