Bedside Laboratory and Microbiologic Procedures

Obtaining a Urine Specimen

Several methods are available for obtaining a urine specimen. They can be found in Table 67.1 and are listed in order of increasingly precise collection techniques. They come at the cost of increasing difficulty, patient discomfort, or both.

General Considerations Regarding Urine Collection

The advantages and disadvantages of each of the techniques listed in Table 67.1 can be determined only by the purpose of the urine test and the clinical context. The clinical context influences interpretation of the results. For the great majority of clinical scenarios, the basic dichotomy is between specimens obtained for infectious versus noninfectious reasons. With the exception of testing for red blood cells (RBCs) and white blood cells (WBCs), most of the noninfectious tests (e.g., ketones, glucose, bilirubin, protein) are not affected by the collection method. Urine specimens collected to diagnose infection can be contaminated in a number of ways, and the clinical scenario intricately influences the choice and interpretation of tests.

Urinary tract infections (UTIs) are either symptomatic or asymptomatic, and the symptoms determine which collection method is required ( Fig. 67.1 ). Symptomatic female patients without potential complications who present for the first time require no further urine testing, and should be treated empirically based on local patterns of susceptibility for urinary pathogens. However, in symptomatic patients who have failed a course of therapy or have potential complicating factors, testing is recommended and extremely low levels of bacteriuria (10 ² colony-forming units [CFUs]/mL) and pyuria are of clinical significance. This may be obscured in some clinicians' minds by an alternative, more widely promulgated fact: In asymptomatic patients the threshold for “significant bacteriuria” is 1000-fold higher at greater than 10 ⁵ CFUs/mL. Symptomatic patients constitute a clinically distinct group who require a urine test that is much more sensitive and thus will render a false-positive result with much lower levels of contaminants. Although many studies do not show a statistically significant increase in contamination rates with less stringent urine collection techniques, most show increased accuracy with more meticulous or invasive collection methods. Because it takes only marginally longer, it makes sense to always strive for the highest-quality urine specimen available, especially in view of the delays, repeated testing, and additional cost entailed by false-positive results. A frequent misconception is that contaminated specimens are characterized by the isolation of multiple pathogens, but in fact, up to 50% of symptomatic women may have polymicrobial infections.

The issue of whether a patient is symptomatic might appear trivial, but the clinical practice of checking for UTI in most patients with any type of abdominal pain has important implications. Studies of urine collection and testing in symptomatic patients focus on the classic signs and symptoms of UTI (e.g., urgency, frequency, dysuria, flank pain, costovertebral angle tenderness) and do not include patients with nonspecific abdominal pain. Whether undifferentiated abdominal pain or fever constitutes a symptom of UTI has never been studied, and how to apply the results of studies done on patients with classic symptoms to those with nonspecific symptoms is unclear. Patients with classic symptoms need the most careful urine collection method because they have the most riding on the outcome of the test. This group of patients should include those with systemic signs of infection (e.g., fever and chills) who are unable to accurately report their symptoms and patients in whom failure to diagnose asymptomatic bacteriuria would be potentially dangerous (e.g., the immunocompromised, neonates and infants, pregnant patients, diabetics) or for whom urine cultures are going to be necessary because of a history of relapsing, recurrent, complicated, or childhood UTI.

In cooperative, motivated males and females with symptoms of uncomplicated lower UTI or pyelonephritis who are capable of diligently performing the necessary maneuvers, a midstream clean catch (MSCC) specimen is as accurate as a catheterized specimen, especially when the possibility of urethral or prostatic trauma and patient discomfort are considered. Lower resource utilization and avoidance of urethral or prostatic trauma and patient discomfort are additional advantages to an MSCC specimen. In patients who are unable to provide an MSCC specimen, or in children in whom thorough cleansing is more difficult, the increased accuracy afforded by a catheterized specimen is usually warranted.

If no symptoms of UTI are present, the urine examination can be considered a screening test. In asymptomatic patients, routine screening for bacteriuria is unwarranted in all but two clinical situations: pregnant women and all patients scheduled for urologic surgery. If only a urine culture is to be performed, some would argue that any spontaneously voided specimen would suffice because the diagnosis of asymptomatic bacteriuria depends on 10 ⁵ or more CFUs of a single pathogen per milliliter of urine. With such criteria, contaminants are usually easily identified. Because performing cultures on all such patients is prohibitively costly, dipstick testing, urinalysis (UA), or both are commonly used for screening. With these tests, contamination by bacteria, leukocytes, or erythrocytes results in diagnostic confusion. The advantages of a less-contaminated specimen are worth the minimal, extra effort of asking the patient to provide an MSCC sample. The approach in Fig. 67.1 covers the vast majority of situations. A few circumstances and techniques deserve special mention.

Urine Dipstick

Urine dipstick tests are available to test 10 separate parameters. The unassuming appearance and commonplace use of the urine dipstick might lead one to mistakenly underestimate its technical sophistication. Each colored square on a urine dipstick involves a biochemically complex assay, and therefore it is essential to meticulously follow the manufacturer's instructions for storage and use. Even with optimal storage and testing conditions, the false-negative and false-positive rates of these tests are problematic. In addition, most of the tests are susceptible to interference from a variety of substances ( Table 67.2 ).

Method

Test urine specimens as soon as possible after they are collected. If the urine has been standing, stir or shake the specimen well because cells sink rapidly in a container. Immerse the test strip completely for 1 second or less. Draw the edge of the strip along the rim of the specimen container and lightly tap it to remove excess urine, thus avoiding mixing the reagents between different test patches. Next, hold the strip horizontally or place it on a clean gauze pad until the recommended time has elapsed. Most strips are designed so that all the test results can be read together after 1 to 2 minutes ( Fig. 67.2 ).

Microscopic UA

Microscopic UA is performed to identify cells, bacteria, and other microbes, as well as formed elements such as casts and crystals ( Fig. 67.3 ). The following discussion focuses on the findings of significance in diagnosing UTI: WBCs, bacteria, and WBC casts. The presence of WBCs with bacteria distinguishes infection from colonization (bacteriuria without pyuria). Some authorities state that significant infection without pyuria occurs in less than 5% of cases, thus making pyuria alone a sensitive marker of infection. Other studies do not support reliance on pyuria by itself as an indicator of infection. The presence of WBC casts distinguishes pyelonephritis (“upper UTI”) from cystitis (“lower UTI”).

Microscopic UA is performed by one of five methods. Traditionally, the most common technique has been examination of unstained centrifuged urine. It has the advantage of concentrating formed elements that might otherwise be missed. Its disadvantage is that the presence and quantity of elements in a specimen will depend on many uncontrolled factors: the volume of the specimen, the duration and speed of centrifugation, the fragility of the formed elements, the volume of the “drop” in which the pellet is resuspended, and the size of the microscope's HPF.

• 1.

  Examination of unspun urine in a hemocytometer counting chamber. A hemocytometer is a precisely milled slide etched with measured squares, which allows exact enumeration of the cells in each square. Because the distance between the etched surface and the coverslip is known exactly, it is possible to determine the number of cells per unit volume of specimen. Enough fresh unspun urine is placed on the slide to fully cover the counting area, and the cells are counted. There should usually be less than 1 WBC/µL, although more than 10 WBCs/µL and more than 5 RBCs/µL are unequivocally abnormal. The threshold for diagnosing UTI is usually set at 8 or more WBCs/µL. Bacteria do not sink to the surface of the hemocytometer, so counting them through the many focal planes of the chamber is not possible, although methods to estimate the bacterial count per unit volume have been described. The hemocytometer is accurate, fast (time need not be spent on staining or centrifugation), and relatively easy to master. Its major drawbacks are cost (approximately $150 for the slide and cover slip) and fragility (easily destroyed if dropped). These characteristics are problematic given the conditions and resources in many EDs, although their use has been advocated by some. Formed elements other than WBCs and RBCs (e.g., casts) occur in such low concentrations that they are encountered in the hemocytometer only by chance, and therefore microscopy of spun urine is needed for their identification.

• 2.

  Examination of unspun, unstained urine placed on a regular microscope slide. This qualitative method is sometimes used for the diagnosis of UTI. Using 1 organism/HPF as a positive result, the sensitivity and specificity of detecting 10 ⁵ CFUs/mL are between 60% and 90%. This method identifies only 1 WBC/HPF with the highly pyuric state of 250 WBCs/µL, which has led some to advocate the use of more than 1 WBC per low-power field as a criterion for infection.

• 3.

  Examination of unstained, centrifuged urine. With this method, 10 mL of urine is centrifuged at approximately 450 g (1000 to 4000 rpm) for 3 to 5 minutes. Roughly 9 mL of supernatant is poured off and the pellet is resuspended in the remaining fluid. This suspension is placed on a slide with a coverslip and examined. The larger formed elements, especially casts, tend to migrate to the edge of the coverslip, and they can be seen with low magnification. One or two casts, depending on the clinical context, may be normal; more are not. The morphology of the more commonly encountered formed elements of urine sediment is shown in Fig. 67.3 . The significance of each is beyond the scope of this text, but this information can be found in a standard textbook of clinical laboratory procedures and diagnostic testing. When examining centrifuged urine, more than 5 WBCs/HPF in the middle of the coverslip has traditionally been taken as being indicative of abnormal pyuria. Most authors have estimated that 10 WBCs/µL is equivalent to approximately 1 WBC/HPF; thus, this oft-cited threshold for diagnosing UTI is actually equivalent to 50 WBCs/µL in unspun urine. As the gold standard for the diagnosis of UTI is more than 8 WBCs/µL of unspun urine, many infections will escape detection with this method. Various numbers of bacteria per HPF have been used as criteria for the diagnosis of UTI. A threshold of 10 to 20 organisms/HPF has been recommended to rule out bacteriuria at the 10 ⁵ -CFU/mL level. As noted previously, this threshold would not exclude infection in symptomatic patients.

• 4.

  Examination of Gram-stained, uncentrifuged urine. Also a semiquantitative measurement, it is estimated that 1 bacterium/HPF is equivalent to 10 ⁵ CFUs/mL in bacterial culture. A drop of urine is placed on the slide, allowed to air-dry, and then heat-fixed and Gram-stained.

• 5.

  Examination of Gram-stained, centrifuged urine. This method is probably the optimal technique, short of culture, for the assessment of bacteriuria. It is more than 95% sensitive and more than 60% specific at 10 ⁴ CFUs/mL, a concentration of bacteriuria that is an order of magnitude lower than the previously described methods. Detection of 1 organism per oil-immersion field constitutes a positive result. Specificity is increased to 95% if 5 organisms/HPF are seen.

Summary of Tests Used in the Diagnosis of UTI

The three tests commonly used to evaluate a patient for the presence or absence of UTI are urine dipstick, microscopic UA, and urine culture. Each represents an increasing degree of expense, delay, and resources. A brief discussion of their relative strengths and weaknesses ensues.

The Bottom Line

It is well established that female patients with symptoms of uncomplicated lower UTI can be treated without culture because the prevalence of disease is 50% or greater in women with classic urinary symptoms. Treatment is generally benign, and 95% of urine cultures that are positive will yield a limited number of organisms with predictable antibiotic susceptibilities. Some authors recommend dipstick or microscopic UA (or both) because a negative test might prompt more careful consideration of alternative diagnoses in this group, with a high incidence of sexually transmitted disease. If none is found, such patients can be treated empirically.

Fluoroquinolone antibiotics are no longer recommended as empiric treatment for uncomplicated UTI. Traditional choices have included trimethoprim-sulfamethoxazole or macrodantin, but both of these agents have high resistance rates in many locations, so choices should be based on local microbial susceptibility patterns, if available.

Urine testing is more likely to influence clinical management in patients with an intermediate pretest probability of infection. Urine microscopy may also help in distinguishing pyelonephritis (WBC casts), vaginitis (absence of pyuria or hematuria in a meticulous MSCC or catheterized specimen), and urethritis (pyuria, rarely hematuria) from cystitis (pyuria and often hematuria). In the ED, the ease of performing a dipstick test argues for its use without UA because it is equally sensitive unless formed elements such as casts, crystals, Trichomonas, or other parasites are suspected. In patients with pyelonephritis, urine cultures are warranted because they alter therapy in approximately 5% of cases. In most asymptomatic patients, a negative dipstick or UA result has sufficient negative predictive value to rule out disease unless the patient is pregnant or undergoing urologic surgery. Special clinical considerations in some patients (e.g., the immunocompromised, diabetic females at high risk for UTI) may mandate adjustments to this approach. Recommendations vary regarding infants. Cultures are recommended for all febrile infants younger than 2 months and for children who appear sick or have a high pretest probability of infection. In a 2009 study, combined microscopic and dipstick UA was only 64% sensitive (and 91% specific) for culture-proven UTI in febrile infants younger than 24 months, thus suggesting the use of culture unless an alternative source of infection is clear.

Indications

Blood cultures are indicated when the clinical findings suggest an otherwise unidentifiable bacteremic state ( Box 67.2 ). Twenty-five percent of patients with documented bacteremia have periods without fever. In the elderly the proportion is even higher, with 50% of bacteremic patients older than 65 having a temperature between 97.1°F (36.2°C) and 100.9° F (38.3°C) and at least 13% with no documented temperature higher than 99.1°F (37.3°C) at any time. In the elderly, increasing age, vomiting, altered mental status, urinary incontinence, presence of a Foley catheter, or greater than 6% band forms is predictive of a positive blood culture. The subjective impression of “having fever” in adults is not a reliable indicator of the presence of fever, although the subjective impression of “no fever” is much more likely to be accurate. Prediction models to optimize the use of this costly test have been explored but are cumbersome, add little to educated clinical judgment, and lack widespread validation or acceptance. Many studies have shown that blood cultures in patients with uncomplicated pneumonia or pyelonephritis are of very limited clinical value, although a 2010 prospective investigation of patients with upper UTI found that malignancy, an indwelling urinary catheter, and ongoing antimicrobial treatment were clinical conditions that made it significantly more likely that blood cultures would be discordant with urine cultures and that they would reveal clinically important additional information. Blood cultures are obtained during 2.8% of all ED visits in the United States, and in a single 3-year period this rate increased by 33%. As disease prevalence is unlikely to have changed so rapidly, this increase is probably due to changes in practice. These changes have been coincident with regulatory agency–mandated blood cultures in patients being evaluated for pneumonia and have led to calls for more stringent criteria for obtaining blood cultures.