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Sampling and evaluation of voided urine in the diagnosis of urinary tract infection in adults

Sampling and evaluation of voided urine in the diagnosis of urinary tract infection in adults
Author:
Alain Meyrier, MD
Section Editor:
Stephen B Calderwood, MD
Deputy Editor:
Allyson Bloom, MD
Literature review current through: Dec 2022. | This topic last updated: Sep 14, 2022.

INTRODUCTION — Urine collected in a normal individual by suprapubic aspiration of the bladder is sterile and does not contain leukocytes. This method represents the gold standard in the diagnosis of urinary tract infection (UTI) [1,2]. It is, however, not performed in clinical practice. Instead, urine samples are generally obtained after natural micturition; in this setting, some degree of artifactual contamination with normal urethral organisms must be accepted.

This topic discusses the collection and analysis of voided urine for the diagnosis of UTIs in adults. More detailed discussions on acute simple cystitis and complicated UTI in women and men and children are found elsewhere:

(See "Acute simple cystitis in females".)

(See "Acute simple cystitis in adult males".)

(See "Acute complicated urinary tract infection (including pyelonephritis) in adults".)

(See "Urinary tract infections and asymptomatic bacteriuria in pregnancy".)

(See "Acute infectious cystitis: Clinical features and diagnosis in children older than two years and adolescents".)

URINE SAMPLING — The ideal voided urine sample for evaluation of UTI is one that accurately represents the bladder bacterial count with minimized contamination by bacteria colonizing the distal urethra and genital mucosa. In theory, this would be a clean-catch, midstream sample of the first micturition of the day. In fact, there is no clinical evidence that this ideal specimen yields more accurate results. Collection of a midstream urine, with or without cleaning of the urethral meatus, at the time of clinical evaluation likely produces a reasonable specimen for analysis [3].

The likelihood of detecting a bladder bacteriuria by voided urine culture is highest if urine is collected on arising. This sample is likely to be most concentrated and bacteria in the bladder will have had time to multiply overnight. However, this ideal sample is not practical since most cultures are obtained at the time the patient is seeing the clinician. With samples collected later in the day, the combination of a more dilute urine and partial bacterial washout due to multiple voids may lower the colony count below the accepted definition for bacteriuria diagnostic of a UTI. (See 'Definition of a positive culture' below.)

An optimal clean-catch, midstream urine is collected through the following steps in attempts to minimize the degree of contamination with bacteria from the urethra:

Local disinfection of the meatus and adjacent mucosa should be performed with a non-foaming antiseptic solution, such as Dakin’s solution (diluted sodium hypochlorite solution 0.5%); this region should then be dried with a sterile swab to avoid mixture of the antiseptic with urine.

Contact of the urinary stream with the mucosa should be minimized by spreading the labia in females and by pulling back the foreskin in uncircumcised males.

The initial stream of the voided specimen should be discarded since the initial urine flushes urethral contaminants. It is the subsequent midstream sample that should be sent to the laboratory.

However, clinical studies do not demonstrate that cleaning the meatus is associated with lower rates of contamination [3-6]. Thus, for patients in whom the cleaning step may be impractical or difficult, a midstream urine collected (with the labia spread, for females) is likely an appropriate sample.

For males with suspected chronic bacterial prostatitis, evaluation of the last few drops of urine after prostatic massage is indicated. Firm prostatic massage per rectum, from lateral to midline on each side, causes the contents of the prostatic ducts to be expressed; vertical strokes in the midline will then project the secretions into the urethra and permit counting of leukocytes. Of note, this maneuver should be avoided when acute bacterial prostatitis is suspected because of the risk of bacteremia. (See "Chronic bacterial prostatitis", section on 'Obtaining and testing prostatic specimens'.)

Urine sampling techniques in young children are discussed elsewhere. (See "Urine collection techniques in infants and children with suspected urinary tract infection".)

URINE HANDLING — When a urine sample is collected for culture, it should be sent immediately to the bacteriology laboratory since bacteria will continue to proliferate in the warm medium of freshly voided urine, leading to increased bacterial counts (see "Microbiology specimen collection and transport"). If such immediate referral is not possible, the container should be transported in iced water and then stored in a refrigerator at 4°C. When, a midstream urinary sample is obtained at home and brought into the laboratory, the patient is instructed to keep the tightly closed container in a plastic bag or package containing cold water and ice cubes until the sample is delivered to the lab. Cooling stops bacterial growth, but the following day the bacteria can still grow on culture medium.

However, refrigeration of urine may alter urinary leukocytes and thus affect interpretation of the urinalysis.

DIPSTICKS

Indications and use — Dipsticks to evaluate for urine leukocyte esterase and nitrite can be used as a screening tool for the diagnosis of UTI. Dipsticks are generally performed whenever UTI is suspected. However, we do not routinely collect urine for dipstick in young nonpregnant females with a history clearly suggestive of a UTI (ie, typical symptoms without vaginal discharge or irritation), as the dipstick generally does not provide additional useful information [7-9]. The use of dipsticks for the diagnosis of UTI is discussed in detail elsewhere. (See "Acute simple cystitis in females", section on 'Diagnostic approach' and "Acute simple cystitis in adult males", section on 'Diagnostic approach' and "Acute complicated urinary tract infection (including pyelonephritis) in adults", section on 'Diagnostic approach'.)

In general, dipsticks to evaluate for leukocyte esterase and nitrite should not be performed in patients without any symptoms consistent with a UTI, as a positive dipstick, which would denote the presence of pyuria and/or bacteriuria, does not indicate a UTI in an asymptomatic patient. The rationale for this is similar to the reasons not to screen for asymptomatic bacteriuria, which are discussed in detail elsewhere [10]. (See "Asymptomatic bacteriuria in adults".)

Accuracy — Dipsticks detect the presence of leukocyte esterase and nitrite in the urine.

Leukocyte esterase corresponds to pyuria. Leukocyte esterase may be used to detect >10 leukocytes per high power field (sensitivity of 75 to 96 percent; specificity of 94 to 98 percent) [11].

A positive nitrite test is a reliable index of significant bacteriuria, although a negative test does not exclude bacteriuria. Normally no detectable nitrite is present.

The majority of bacteria that cause UTIs (E. coli, Proteus mirabilis, and Klebsiella) produce nitrate reductase, an enzyme that transforms urine nitrate, a metabolite of alimentary origin, into nitrite that is detected by dipsticks. When bacteriuria with one of these organisms is significant, the test is positive in about 80 percent of cases in which the urine has incubated for at least four hours in the bladder [12]. Other potential urinary pathogens (Staphylococcus, Pseudomonas, Group B Streptococcus, Acinetobacter, Enterococcus faecalis, and fungi) do not produce a nitrate reductase, and thus the nitrite test is not positive in infections caused by these organisms.

Other possible causes for a negative nitrite test despite the bacteriuria include early phase of infection, insufficient bladder incubation time for conversion of nitrate to nitrite, low urinary excretion of nitrate, decreased urine pH (due to cranberry juice, vitamin C, or other dietary supplements), high (>5 g/L) glycosuria, high urine specific gravity (>1.02) and proteinuria >1 g/L [13,14]. False-positive nitrite tests can occur with substances that turn the urine red, such as the bladder analgesic phenazopyridine or the ingestion of beets. (See "Urinalysis in the diagnosis of kidney disease", section on 'Red to brown urine'.)

Most studies have supported the diagnostic value of the nitrite and leukocyte esterase results, particularly when they are concordant [15,16]. A meta-analysis including 70 publications concluded that the urine dipstick test alone is useful when both nitrite and leukocyte esterase tests are positive (sensitivity 68 to 88 percent) [15].

The diagnostic value of dipstick testing has been evaluated in both primary care and emergency settings. In a review of six studies that included females aged 17 to 70 with suspected UTI in primary care settings, positive dipstick findings (nitrite or leukocyte esterase and blood) had sensitivity and specificity of 75 and 66 percent, respectively [17]. In a systematic review of four studies that evaluated the utility of dipstick results in addition to history and physical examination findings in diagnosing acute UTI in symptomatic females presenting to the emergency room, a negative dipstick urinalysis accurately ruled out the diagnosis of UTI (as confirmed by urine culture) when the pretest probability was low [18]. Across the studies, which included 948 females, the prevalence of UTI ranged from 40 to 60 percent and only a positive nitrite reaction was useful to rule in a UTI and only a negative leukocyte esterase or blood reaction were accurate in ruling out a UTI.

However, other studies have suggested that dipstick results are of lower clinical utility. In one study, 434 adult females with suspected lower UTI in a primary care setting were assessed; sixty-six patients had confirmed UTI. The presence of nitrite, leukocyte esterase, and blood on the dipstick as well as clinical criteria (urine cloudiness, dysuria, and nocturia) were evaluated for diagnostic value. The negative predictive value was 67 percent for the absence of all features, and the positive value was 82 percent for the presence of three features. The authors concluded that dipstick results can modestly improve diagnosis, but cannot adequately rule out infection [19]. Similarly, in a study of 2252 females with overactive bladder, dipstick test was not sufficient to identify patients with UTI (sensitivity and specificity 44 and 86 percent, respectively) [20].

MICROSCOPY FOR PYURIA

Interpretation of pyuria — In truly infected patients, a significant number of leukocytes (>10/microL or 10,000/mL) should generally be present [21]. Given the very high association between infection and pyuria, an absence of pyuria on microscopic assessment can suggest colonization instead of infection when there is bacteriuria (although bacteriuria and pyuria does not necessarily signify infection, particularly if there are no symptoms). Hemocytometry is the preferred method of microscopic assessment for pyuria, but the less accurate method of counting leukocytes in the sediment of centrifuged urine is more commonly employed [22].

In a study of females with symptoms of UTI, a urine leukocyte count ≥8 cells/microL, as measured by hemocytometry, was found in 61 of 62 females who had evidence of bladder bacteriuria through culture of suprapubic aspiration or urethral catheterization samples [1]. In contrast, only 7 of 34 asymptomatic females had ≥8 urine leukocytes/microL, of whom three were found to have asymptomatic Chlamydia trachomatis infection of the cervix. In a separate study of females with urinary symptoms and low count bacteriuria (>102 to 104 colony forming units/mL), pyuria defined as ≥20 leukocytes/microL was associated with isolation of urinary pathogens (E. coli and Staphylococcus saprophyticus) in contrast to other organisms [23].

The threshold of 8 cells/microL on hemocytometry corresponds to 2 to 5 leukocytes per high power field in the sediment of centrifuged urine. However, assessment of pyuria by the latter method is subject to some technical pitfalls [24]. Two important variables are contamination with vaginal secretions in females and the volume of supernatant in which the centrifuged pellet is resuspended, which will affect the leukocyte count.

White blood cell casts in the urine are indicative of kidney inflammation, which may reflect pyelonephritis or other renal conditions.

The presence of bacteria in the absence of pyuria, especially when various strains are found, is usually due to contamination during sampling. When the patient is asymptomatic, finding various bacterial strains should not be considered a UTI.

However, in a symptomatic patient who has complaints consistent with cystitis and bacteriuria, but does not have pyuria, a repeat urine sampling should be done. If the pattern is the same, with bacteriuria but no pyuria and with persistent symptoms of urethral inflammation, this is consistent with the "acute urethral syndrome" [1] and antibiotic treatment should generally not be undertaken at that point. However, this is a vague clinical entity that could potentially be an equivalent of bacteriuria at low counts. (See 'Definition of a positive culture' below.)

Sterile pyuria — Whereas true infection without pyuria is unusual, pyuria can occur in the absence of apparent bacterial infection, particularly in patients who have already taken antimicrobials [25]. Other causes of sterile pyuria include:

Contamination of the urine sample by the sterilizing solution used to clean the meatus

Contamination of the urine sample with vaginal leukocytes from vaginal secretions

Chronic interstitial nephritis

Nephrolithiasis (see "Kidney stones in adults: Diagnosis and acute management of suspected nephrolithiasis")

Uroepithelial tumor (see "Malignancies of the renal pelvis and ureter")

Painful bladder syndrome/interstitial cystitis (see "Interstitial cystitis/bladder pain syndrome: Clinical features and diagnosis")

Intra-abdominal inflammatory process adjacent to the bladder

Infection with atypical organisms, such as Chlamydia, Ureaplasma urealyticum, or tuberculosis [1,26] (see "Clinical manifestations and diagnosis of Chlamydia trachomatis infections" and "Mycoplasma hominis and Ureaplasma infections" and "Urogenital tuberculosis")

In the case of uroepithelial tumors, both malignant cells and leukocytes are shed [27]. The tumor can cause inflammation that results in the appearance or exacerbation of sterile pyuria. Malignant cells are difficult to distinguish from leukocytes on routine urinalysis.

Also, some females with UTI may have low bacterial counts in their midstream urine. If the clinical laboratory does not quantify bacterial counts below a certain threshold, they may not be identified as having bacteriuria despite consistent symptoms and pyuria. (See 'Definition of a positive culture' below.)

URINE CULTURE

Indications for urine culture — The role of pretreatment urine culture in the evaluation of suspected UTI is to confirm the presence of bacteriuria and to identify and provide antibiotic susceptibility information on the causative organism (often retrospectively, if treatment is empirically given). Culture of a clean-catch voided urine specimen is warranted for these purposes among most patients with suspected UTI, except for healthy nonpregnant young females with typical symptoms of acute simple cystitis (ie, without fever or concern for ascending infection) who have no risk factors for resistant infection [7,8,22]. The use of urine culture in the diagnosis of UTI is discussed in detail elsewhere. (See "Acute simple cystitis in females", section on 'Diagnostic approach' and "Acute simple cystitis in adult males", section on 'Diagnostic approach' and "Acute complicated urinary tract infection (including pyelonephritis) in adults", section on 'Diagnostic approach'.)

In general, urine culture should not be performed in nonpregnant patients without any symptoms consistent with a UTI, as bacteriuria does not indicate a UTI in an asymptomatic patient [10]. This is discussed in detail elsewhere. (See "Asymptomatic bacteriuria in adults".)

The use of urine culture in the evaluation of asymptomatic bacteriuria and suspected UTI in pregnant persons is also discussed in detail elsewhere. (See "Urinary tract infections and asymptomatic bacteriuria in pregnancy".)

Definition of a positive culture — In asymptomatic patients, the standard threshold for bacterial growth on a midstream voided urine that is reflective of bladder bacteriuria as opposed to contamination is ≥105 colony forming units (CFU)/mL. However, in symptomatic females with pyuria, lower midstream urine counts (ie, ≥102/mL) have been associated with the presence of bladder bacteriuria. Thus, in such instances, the findings of a colony count <105 but ≥102/mL may still be indicative of a UTI. Lower bacterial counts still representative of infection are also seen in males, in patients already on antimicrobials, and with organisms other than E. coli and Proteus species.

Typically, normal values in a noninfected midstream, clean-catch sample are <105 CFU/mL, with bacterial growth primarily due to E. coli from fecal contamination [28-32]. In early studies, >95 percent of patients with bacterial counts ≥105 CFU/mL in voided urine, but only a minority of those with lower counts had concomitant bacteriuria on a catheterized specimen [28].

Subsequent studies have identified a substantial number of females with symptoms and pyuria consistent with a UTI but colony counts <105 CFU/mL in voided urine [1,23,24,33-36]. This was demonstrated in a study of 202 premenopausal, nonpregnant females who presented with at least two symptoms of acute cystitis, collected a midstream, clean-catch urine, and subsequently underwent urethral catheterization to collect a bladder urine specimen. Of the 121 females who had E. coli grow in a catheterized specimen, 49 (40 percent) had counts of <105 CFU/mL in their voided urine [37]. A threshold of ≥102 CFU/mL in voided specimens had a 93 percent positive predictive value for bladder bacteriuria with E. coli. Another study estimated that 88 percent of females with symptoms and a CFU count ≥102/mL on voided urine have a UTI [33].

It is not well understood why some infected females have low colony counts. One possibility is that low counts reflect insufficient sensitivity of conventional urine cultures. In a study that included 220 females with symptoms of acute cystitis and 86 asymptomatic females, urine was tested with both standard culture and quantitative polymerase chain reaction (qPCR) for E. coli, S. saprophyticus, and sexually transmitted pathogens [38]. Among symptomatic females, 81 percent of urine cultures were positive for any uropathogen while 95 percent of samples were qPCR positive for E. coli (19 were positive for S. saprophyticus qPCR, 1 for Mycoplasma genitalium, and 1 for Trichomonas vaginalis). In contrast, urine culture and qPCR were positive for E. coli in only 11 and 12 percent, respectively. These findings suggest that almost all females with typical urinary complaints and a negative culture still have an infection with E. coli.

Management of these patients is similar to those with higher colony counts. (See "Acute simple cystitis in females".)

There are also several other settings in which a colony count of ≤105/mL often represents true infection rather than contamination:

Among patients already being treated with antimicrobials.

Among males, in whom contamination is a much lesser problem. (See "Acute simple cystitis in adult males".)

When organisms other than E. coli and Proteus are present. Included in this group are Pseudomonas, Klebsiella, Enterobacter, Serratia, and Moraxella species, particularly in symptomatic patients with an indwelling bladder catheter. (See "Catheter-associated urinary tract infection in adults".)

SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Urinary tract infections in adults".)

INFORMATION FOR PATIENTS — UpToDate offers two types of patient education materials, "The Basics" and "Beyond the Basics." The Basics patient education pieces are written in plain language, at the 5th to 6th grade reading level, and they answer the four or five key questions a patient might have about a given condition. These articles are best for patients who want a general overview and who prefer short, easy-to-read materials. Beyond the Basics patient education pieces are longer, more sophisticated, and more detailed. These articles are written at the 10th to 12th grade reading level and are best for patients who want in-depth information and are comfortable with some medical jargon.

Here are the patient education articles that are relevant to this topic. We encourage you to print or e-mail these topics to your patients. (You can also locate patient education articles on a variety of subjects by searching on "patient info" and the keyword(s) of interest.)

Beyond the Basics topics (see "Patient education: Urinary tract infections in adolescents and adults (Beyond the Basics)")

SUMMARY

Ideal voided urine specimen In theory, the ideal voided urine specimen for evaluation of a UTI is a clean-catch, midstream sample of the first micturition of the day, but there is no clear clinical evidence that such a specimen yields more accurate results. Collection of a midstream urine, with or without cleaning of the urethral meatus, at the time of clinical evaluation likely produces a reasonable specimen for analysis. (See 'Urine sampling' above.)

Dipstick/urinalysis interpretation – Dipsticks, which detect the presence of leukocyte esterase and nitrite in the urine, can be used as a screening tool and are generally performed whenever UTI is suspected. Leukocyte esterase corresponds to pyuria. A positive nitrite test is a reliable index of significant bacteriuria, although a negative test does not exclude bacteriuria. (See 'Dipsticks' above.)

Lack of pyuria suggests against UTI – In truly infected patients, a significant number of leukocytes (>10/microL) should generally be present. Given the very high association between infection and pyuria, microscopic assessment for pyuria can be helpful in distinguishing between colonization and infection when there is bacteriuria and compatible symptoms. (See 'Microscopy for pyuria' above.)

Pyuria does not always indicate UTI or bacteriuria – Whereas true infection without pyuria is unusual, pyuria can occur in the absence of apparent bacterial infection, particularly in patients who have already taken antimicrobials. Other causes of sterile pyuria include contamination from vaginal secretions and other causes of uroepithelial inflammation. When the more common causes of sterile pyuria have been eliminated, patients with dysuria and frequency should be evaluated for atypical organisms, such as Chlamydia, Ureaplasma urealyticum, or tuberculosis. (See 'Sterile pyuria' above.)

Role of urine culture – The role of pretreatment urine culture in the evaluation of suspected UTI is to confirm the presence of bacteriuria and to identify and provide antibiotic susceptibility information on the causative organism (often retrospectively, if treatment is empirically given). Culture of a clean-catch voided urine specimen is warranted for these purposes among most patients with suspected UTI, except for healthy nonpregnant young females with typical symptoms of acute simple cystitis who have no risk factors for resistance. (See 'Indications for urine culture' above.)

Definition of a positive culture – In asymptomatic patients, the standard threshold for bacterial growth on a midstream voided urine that is reflective of bladder bacteriuria as opposed to contamination is ≥105 colony forming units (CFU)/mL. However, in symptomatic females with pyuria, lower midstream urine counts (ie, ≥102/mL) have been associated with the presence of bladder bacteriuria and thus may still be indicative of a UTI. Lower bacterial counts still representative of infection are also seen in males, in patients already on antimicrobials, and with organisms other than E. coli and Proteus species. (See 'Definition of a positive culture' above.)

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