MEDICAL MICROBIOLOGY INVITED ARTICLE

L. Barth Reller and Melvin P. Weinstein, Section Editors

Laboratory Diagnosis of Urinary Tract Infections

in Adult Patients
Michael L. Wilson1,2 and Loretta Gaido1,2
1
Department of Pathology and Laboratory Services, Denver Health Medical Center, and 2Department of Pathology, University of Colorado School of Medicine,
Denver, Colorado

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Urinary tract infections (UTIs) are among the most common bacterial infections and account for a significant part of the
workload in clinical microbiology laboratories. Enteric bacteria (in particular, Escherichia coli) remain the most frequent
cause of UTIs, although the distribution of pathogens that cause UTIs is changing. More important is the increase in resistance
to some antimicrobial agents, particularly the resistance to trimethoprim-sulfamethoxazole seen in E. coli. Physicians dis-
tinguish UTIs from other diseases that have similar clinical presentations with use of a small number of tests, none of which,
if used individually, have adequate sensitivity and specificity. Among the diagnostic tests, urinalysis is useful mainly for
excluding bacteriuria. Urine culture may not be necessary as part of the evaluation of outpatients with uncomplicated UTIs,
but it is necessary for outpatients who have recurrent UTIs, experience treatment failures, or have complicated UTIs, as well
as for inpatients who develop UTIs.

Urinary tract infections (UTIs) are among the most common
bacterial infections. It has been estimated that symptomatic
UTIs result in as many as 7 million visits to outpatient clinics,
1 million visits to emergency departments, and 100,000 hos-
pitalizations annually [1]. UTIs have become the most common
hospital-acquired infection, accounting for as many as 35% of
nosocomial infections, and they are the second most common
cause of bacteremia in hospitalized patients [2, 3]. The annual
cost to the health care system of the United States attributable
to community-acquired UTI alone is estimated to be approx-
imately $1.6 billion [4].
UTIs are challenging, not only because of the large number
of infections that occur each year, but also because the diagnosis
of UTI is not always straightforward. Physicians must distin-
guish UTI from other diseases that have a similar clinical pre-
sentation, some UTIs are asymptomatic or present with atypical
signs and symptoms, and the diagnosis of UTIs in neutropenic
patients (who do not typically have pyuria) may require dif-
ferent diagnostic criteria than those used for the general patient
population. Because of these factors, physicians frequently rely
on a small number of imperfect laboratory tests to augment
clinical impressions; even when clinical diagnoses are un-
equivocal, physicians may order laboratory tests to identify the
cause of the infection and/or to provide isolates for anti-
microbial susceptibility testing. It therefore comes as no sur-
prise that the laboratory examination of urine specimens ac-
counts for a large part of the workload in many hospital-based
laboratories. In fact, in many clinical laboratories, urine cultures
are the most common type of culture, accounting for 24%–
40% of submitted cultures; as many as 80% of these urine
cultures are submitted from the outpatient setting.
The purpose of this review is to summarize the laboratory
diagnosis of routine UTI using current diagnostic methods. The
review will not cover the diagnosis of UTI in special patient
populations, a topic that merits a separate review.

Received 15 January 2003; accepted 3 December 2003; electronically published 6 April

CAUSES OF UTIs
2004.
The etiological agents of community-acquired and hospital-
Reprints or correspondence: Dr. Michael L. Wilson, Dept. of Pathology and Laboratory
Services, Denver Health Medical Center, Mail Code 0224, 777 Bannock St., Denver, CO 80204- acquired UTIs differ (table 1) [5–14]. Only a limited amount
4507 (michael.wilson@dhha.org). of data has been published regarding changes in the frequency
Clinical Infectious Diseases 2004; 38:1150–8
 2004 by the Infectious Diseases Society of America. All rights reserved.
of causative agents among outpatients. Enteric bacteria (in par-
1058-4838/2004/3808-0019$15.00 ticular, Escherichia coli) have been and remain the most frequent

1150 • CID 2004:38 (15 April) • MEDICAL MICROBIOLOGY

cause of UTI, although there is some evidence that the per-
centage of UTIs caused by E. coli is decreasing [6, 15]. In
contrast, significant changes in the causes of nosocomial UTI
have been reported since 1980. Bronsema et al. [13] reported
that, from 1980 through 1991, the percentage of UTIs caused
by E. coli, Proteus species, and Pseudomonas species decreased,
whereas the percentage of UTIs caused by yeasts, group B strep-
tococci, and Klebsiella pneumoniae increased. Weber et al. [6]
reported different changes in the causative agents of UTI, with
a decrease in the percentage of UTIs caused by Enterobacter
species, but with an increase in the percentage of UTIs caused
by Acinetobacter species and Pseudomonas aeruginosa. Candida
albicans is the most common cause of funguria, followed by
Candida glabrata, Candida tropicalis, Candida parapsilosis, Can-
dida krusei, and other yeasts [16].
SPECIMEN COLLECTION, TRANSPORTATION,
AND PROCESSING
Specimen collection. Suprapubic aspiration is the best
method to avoid contamination of specimens with bacteria in
the distal urethra. This collection method is used infrequently
because it is not indicated clinically (except in rare circum-
stances), it is invasive and uncomfortable, and it requires too
much time and too many resources to be practical. Collection
of urine by use of a single catheter (straight catheter technique)
is the next-best technique for obtaining urine specimens with
minimal contamination, but, again, it is not indicated clinically
for most patients because it is too labor intensive and costly
for routine use and it is invasive. It has added disadvantages,
because the process of inserting a catheter through the urethra
can introduce bacteria into the bladder (and thereby cause
UTI), and rare complications have been reported.
Most urine specimens are obtained from adult patients via
the clean-catch midstream technique. This technique has the
following advantages: it is neither invasive nor uncomfortable,
it is simple and inexpensive, it can be performed in almost any
clinical setting, there is no risk of introducing bacteria into the
bladder by catheterization, and there is no risk of complications.
Colony counts from urine specimens collected by this method
correlate reasonably well with those of specimens collected via
suprapubic aspiration or straight catheterization [15]. The ob-
vious disadvantage of this technique is that the urine sample
passes through the distal urethra and can become contaminated
with commensal bacteria. Simple procedures that have been
developed to decrease the contamination rate include cleans-
ing of skin and mucous membranes adjacent to the urethral
orifice before micturition, allowing the first part of the urine
stream to pass into the toilet, and collecting urine for culture
from the midstream [17]. Although the clean-catch midstream
method is accepted and used widely, the available evidence
suggests that the cleansing procedures may not decrease urine
contamination rates significantly and, therefore, may be un-
necessary as a routine [18–23]. There may be difficulties with
proper collection of samples from elderly patients, as well as
from those patients who have physical or other types of im-
pairments, which adds to the importance of collecting speci-
mens properly to avoid contamination.
As discussed below, correct processing and handling of urine
specimens, as well as correct interpretation of test results, is
dependent on the method used to collect the specimen. It is,
therefore, of obvious importance for clinicians to specify the
method of collection on the test requisition slip. Other infor-
mation that should be included on the test requisition slip
includes the date and time of specimen collection, patient dem-
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ographic information, and any clinically relevant information
(e.g., whether the patient was treated with antimicrobial agents
or whether anatomic abnormalities, stones, or an indwelling
urinary catheter were present).
Specimen transportation. Several studies have demon-
strated the adverse effect of delays in transportation or pro-
cessing of urine specimens on their quality [24–26]. In each
study, urine specimens were plated within 2 h after collection
and then were plated again after delays of up to 24 h; results
were compared to determine whether delays in plating resulted
in an increase in colony counts. In each of the studies, some
of the cultures that were delayed showed increases in the num-
ber of colony forming units (cfu) per mL to 1105 cfu/mL,
thereby leading to false-positive results. It should be noted that
these 3 studies were performed before the publication of current
criteria for interpreting quantitative urine cultures and that the
effect on interpretation would have been even greater if colony
counts of 102 or 103 cfu/mL were used to define probable in-
fection in specific patients [15]. On the basis of the results of
these and other similar studies, it is currently recommended
that urine specimens be plated within 2 h after collection unless
specimens have been refrigerated or kept in a preservative [17].
Specimen processing. Routine urine cultures should be
plated using calibrated loops for the semiquantitative method.
This method has the advantage of providing information re-
garding the number of cfu/mL, as well as providing isolated
colonies for identification and susceptibility testing. The types
of media used for routine cultures should be limited to blood
agar and MacConkey’s agar. For urine specimens obtained from
outpatients, it is not necessary to routinely inoculate a medium
that is selective for gram-positive bacteria, because nearly all
UTIs in outpatients are caused by aerobic and facultative gram-
negative bacteria (table 1) [27, 28]. Even in patient populations
in which Staphylococcus saprophyticus is a common cause of
UTIs, it is not necessary to use selective media. In contrast,
urine specimens obtained from hospitalized patients are likely
to contain enterococci, which have emerged as the second most
MEDICAL MICROBIOLOGY • CID 2004:38 (15 April) • 1151
 Table 1. Percentage distribution of etiologic agents of urinary tract infections among outpatients
and inpatients, by pathogen.

Outpatients Inpatients
Percentage Percentage
Pathogen with pathogen Reference(s) with pathogen Reference(s)
Escherichia coli 53–72 [5–9] 17.5–56.7 [5, 6, 8–14]
Coagulase-negative staphylococci 2–7.5 [5, 7] 2.1–12.5 [5, 8–14]
Klebsiella species 6–12 [5–7] 6.2–15.0 [5, 6, 8–14]
Proteus species 4–6 [5–7] 3.8–8.2 [5, 6, 8–13]
Enterobacter species 0.6–5.8 [5–7] 0.9–6.5 [5, 6, 8–14]
Morganella morganii 3.1–4.4 [6] 4.7–6.0 [6]
Citrobacter species 0.1 [5] 0.2–3 [5, 8, 9, 11–13]
Enterococcus species 1.7–12 [5–7] 6.5–15.8 [5, 6, 8–14]

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Staphylococcus aureus 2 [5, 7] 1.6–3.5 [5, 8–12,14]
Staphylococcus saprophyticus 0.2–2 [5, 7] 0.4 [5]
Pseudomonas species 0.1–4 [5–7] 1.3–11 [5, 6, 8–14]
Candida species … … 9.4–15.8 [8, 9, 14]
Other 3–8 [5–7] 1.8–26.3 [5, 6, 8, 10–14]

common cause of nosocomial infections. Laboratories may
want to consider inoculating urine specimens obtained from
hospitalized patients, or from patients in whom gram-positive
bacterial infection is suspected but not documented, to a me-
dium that is selective for gram-positive cocci. A medium such
as phenylethyl alcohol suppresses the growth of swarming Pro-
teus species and other gram-negative bacilli that can overgrow
gram-positive cocci in the specimen. Urine cultures should be
incubated overnight at 35C–37C in ambient air before being
read. There is no added benefit to incubating routine urine
cultures for 48 h, provided that specimens are incubated for a
full 24 h and that urine specimens containing !104 uropath-
ogens or specimens from patients with suspected funguria are
incubated for 48 h [29–31].
Most pathogenic yeasts grow well on blood agar plates, so
it is unnecessary to use selective fungal media for urine cul-
tures, even for samples obtained from patients with suspected
funguria. Selective fungal media can be used in those rare
instances in which there is a high clinical probability that a
UTI is caused by a more fastidious yeast or mold. Urine
specimens obtained from patients with suspected mycobac-
terial UTIs should be processed and plated to the appropriate
mycobacterial media [32].
NONCULTURE METHODS FOR THE
LABORATORY DIAGNOSIS OF UTI
Detection of bacteriuria by urine microscopy. Bacteriuria
can be detected microscopically using Gram staining of un-
centrifuged urine specimens, Gram staining of centrifuged
specimens, or direct observation of bacteria in urine specimens.
Gram stain of uncentrifuged urine specimens is a simple
method. A volume of urine is applied to a glass microscope
slide, allowed to air dry, stained with Gram stain, and examined
microscopically. The performance characteristics of the test are
not well-defined, because different criteria have been used to
define a positive test result. In one study, the test was found
to be sensitive for the detection of ⭓105 cfu/mL but insensitive
for the detection of lower numbers of bacteria (table 2) [28].
Other investigators have found the test to be of low sensitivity
for the detection of UTI [33–42].
The urine Gram stain test has the important advantage of
providing immediate information as to the nature of the in-
fecting bacterium or yeast (rarely infectious agents such as mi-
crosporidia) and thereby guiding the physician in selecting em-
piric antimicrobial therapy. This is of importance in some
settings, but the Gram stain test has 3 disadvantages that limit
its usefulness in most clinical settings. First, it is an insensitive
test, being reliably positive only if the concentration of bacteria
in the urine is ⭓105 cfu/mL; infections with bacterial concen-
trations of 102–103 cfu/mL may not be detected by this test.
Second, the test is too labor intensive for it to be practical for
most clinical microbiology laboratories to offer it on more than
a select basis. Last, because it may not detect bacteria at con-
centrations of 102–103 cfu/mL, it should not be used in the
outpatient setting for patients with uncomplicated UTIs. Be-
cause of these limitations, its use should be limited to patients
with cases of acute pyelonephritis, patients with invasive UTIs,
or other patients for whom it is important to have immediate
information as to the nature of the infecting pathogen.
Detection of bacteriuria by nitrite test. Bacteriuria can be
detected chemically when bacteria produce nitrite from nitrate.

1152 • CID 2004:38 (15 April) • MEDICAL MICROBIOLOGY

 Table 2. Performance characteristics of Gram staining for detection of bacteriuria.

Performance characteristics, %
Predictive value
Specimen, colony count Sensitivity Specificity Positive Negative Reference(s)
Uncentrifuged urine
NDa 96 95 54 100 [33]
b
ND 91 99 93 99 [33]
⭓10 cfu/mL
5
81–97 71–96 31–90 92–100 [34–36, 38]
⭓104 cfu/mL 86–96 75–99 59–98 80–99 [28, 40]
Centrifuged urine
⭓105 cfu/mL 92–100 8–94 7–77 98–100 [37, 39, 41]
⭓10 cfu/mL
4
74 86 78 84 [39]
⭓103 cfu/mL 63 91 89 69 [39]

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NOTE. The criteria used to assess the clinical importance of isolates and the laboratory methods
used varied between studies; the data are presented only as an overview of reported performance
characteristics of the test. All numbers are rounded to the nearest whole number. ND, not done.
a
⭓1 bacterium per oil immersion field.
b
⭓5 bacteria per oil immersion field.

The biochemical reaction that is detected by the nitrite test is
associated with members of the family Enterobacteriaceae (the
pathogens most commonly responsible for UTIs), but the use-
fulness of the test is limited because nitrite production is not
associated with urinary-tract pathogens such as S. saprophyticus,
Pseudomonas species, or enterococci [43]. Another limitation
to the test is that it requires testing a specimen of the first urine
produced in the morning, as ⭓4 h are required for bacteria to
convert nitrate to nitrite at levels that are reliably detectable.
Detection of pyuria by urine microscopy. Pyuria can be
detected and quantified microscopically by measuring the uri-
nary leukocyte excretion rate, counting leukocytes with a hem-
ocytometer, counting leukocytes in urine specimens using
Gram staining, or counting leukocytes in a centrifuged speci-
men. The advantages to urine microscopy are that leukocytes,
leukocyte casts, and other cellular elements are observed di-
rectly. One disadvantage to urine microscopy is that leukocytes
deteriorate quickly in urine that is not fresh or that has not
been adequately preserved. In addition, each of these methods
has disadvantages that limit its usefulness as a routine test [28].
Because of these disadvantages, urine microscopy should be
limited to patients in whom pyelonephritis or other more se-
rious infections are suspected.
The most accurate microscopic method for quantitating py-
uria is to measure the urinary leukocyte excretion rate [43].
Patients with symptomatic UTIs have urinary leukocyte excre-
tion rates of ⭓400,000 leukocytes/h [43]. The test is impractical
for clinical use, however, making it necessary for laboratories
to use other methods. A simple and inexpensive alternative is
to count urine leukocytes with a hemocytometer. Comparison
of hemocytometer counts with urinary leukocyte excretion rates
has shown that a hemocytomer count of ⭓10 leukocytes/mm3
correlates with a urinary leukocyte excretion rate of ⭓400,000
leukocytes/h [43]. Moreover, the correlation of hemocytometer
counts with urine colony counts has shown that patients with
symptomatic UTIs and bacterial concentrations of 1105 cfu/
mL have urine leukocyte counts of ⭓10 leukocytes/mm3 [43].
The correlation of hemocytometer cell counts for patients with
bacterial concentrations of !105 cfu/mL was studied by Stamm
et al. [15], who found that urine leukocyte counts of ⭓8 cells/
mm3 correlated with bacterial concentrations of !105 cfu/mL
in specimens obtained by suprapubic aspiration or straight
catheterization from acutely dysuric female subjects. Although
using a hemocytometer to count leukocytes is easier than mea-
suring urinary leukocyte excretion rates, it is impractical for
clinical laboratories to use a hemocytometer to count leukocytes
on a routine basis. The most practical microscopic method
involves counting the number of leukocytes in the sediment of
centrifuged urine specimens. As reviewed by Pappas [43], this
method is inaccurate because of inadequate standardization of
the method. For these reasons, and to facilitate the processing
of large numbers of specimens, most laboratories use rapid
tests for leukocyte esterase as a surrogate for microscopic leu-
kocyte counts.
Detection of pyuria by leukocyte esterase tests. Leukocyte
esterase tests are based on the hydrolysis of ester substrates by
proteins with esterolytic activity [44]. Human neutrophils pro-
duce as many as 10 proteins with esterolytic activity. These
proteins react with ester substrates to produce alcohols and
acids that then react with other chemicals to produce a color
change that is proportional to the amount of esterase in the
specimen [44]. These tests have the advantage of detecting both
esterases in intact leukocytes and esterases released after cell
lysis; therefore, even specimens that have not been preserved

MEDICAL MICROBIOLOGY • CID 2004:38 (15 April) • 1153

properly may yield a positive test result. Leukocyte esterase tests
can yield false-positive test results when the urine is contam-
inated with bacteria present in vaginal fluid; when the specimen
contains eosinophils or Trichomonas species, both of which can
act as sources of esterases; and when oxidizing agents or for-
malin react with the test strips to generate false-positive test
results [44, 45]. Leukocyte esterase tests may show a decrease
in positive test results when the specimen has an elevated spe-
cific gravity and/or elevated levels of protein and glucose; when
boric acid preservatives are present; when large amounts of
ascorbic or oxalic acid are present; and when the patient has
received antimicrobial agents, such as cephalothin, cephalexin,
or tetracycline [44, 45]. High concentrations of tetracycline may
result in false-negative test results [45]. As shown in table 3,
the studies. Nonetheless, the results are sufficiently consistent
to allow some conclusions to be made. First, the 2 tests, when
used together, perform better than either test performs when
used alone. Second, the tests have better performance char-
acteristics for detecting bacteriuria at high colony counts than
at low colony counts [51]. Third, these tests have low sensitivity,
high specificity, low positive-predictive values, and high neg-
ative-predictive values. Taken together, the performance char-
acteristics of these tests make them useful as a way to rule out
bacteriuria on the basis of a negative test result.
A number of drugs can change the color of urine; abnormal
urine color may affect urine tests that are based on the inter-
pretation of color changes. In some cases, this can mask color
changes, and in others, it may result in false-positive interpre-

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when it is used alone, the leukocyte esterase test has a relatively
low sensitivity and specificity and low positive predictive values
as a test for UTIs, with higher negative predictive values [28,
35, 38, 46–54].
Simultaneous detection of bacteriuria and pyuria. Com-
mercial urinalysis products include tests for both nitrite and
leukocyte esterase, thus providing tests for both bacteriuria and
pyuria. As shown in table 3, a number of clinical evaluations
have defined the performance characteristics of these tests. The
evaluations are not directly comparable because the studies
occurred over a 20-year period in a number of different lab-
oratories and health care settings, there were a multiplicity of
study designs, and various commercial products were used in
tations [45].
CULTURES AND THE LABORATORY
DIAGNOSIS OF UTIs
Routine bacterial urine cultures. Urine culture may not be
necessary as part of the evaluation of outpatients with uncom-
plicated UTIs [55, 56]. However, urine cultures are necessary
for outpatients who have recurrent UTIs, experience treatment
failures, or have complicated UTIs. Urine cultures are also nec-
essary for inpatients who develop UTIs. The bacterial culture
remains an important test in the diagnosis of UTI, not only
because it helps to document infection, but also because it is

Table 3. Performance characteristics of leukocyte esterase and nitrite tests, alone or in combination,
for detection of bacteriuria and/or pyuria.

Performance characteristics
Predictive values
Test, colony count Sensitivity Specificity Positive Negative Reference(s)
Leukocyte esterase
⭓105 cfu/mL 68–98 59–96 19–86 91–97 [35, 48, 49, 53, 54]
⭓104 cfu/mL 64–77 59–83 16–52 89–96 [47, 49, 53]
⭓103 cfu/mL 62–79 55–84 3–81 51–99 [49, 52, 53]
Nitrite
⭓105 cfu/mL 19–45 95–98 50–78 82–89 [48, 49, 53, 54]
⭓104 cfu/mL 8–39 97–98 27–81 85–87 [49, 53]
⭓103 cfu/mL 0–50 48–98 0–82 37–99 [49, 52, 53]
Leukocyte esterase and nitrite
⭓105 cfu/mL 35–84 98–100 84 98 [48, 53]
⭓103 cfu/mL 0–45 62–98 0–66 42–99 [52, 53]
Leukocyte esterase and/or nitrite
⭓105 cfu/mL 67–100 67–98 40–95 84–96 [28, 38, 48–50]
⭓10 cfu/mL
4
74–79 66–82 42–54 91–92 [49, 50]
⭓103 cfu/mL 71–84 41–83 49–81 46–90 [49, 50, 52]

NOTE. The criteria used to assess the clinical importance of isolates and the laboratory methods used varied between
studies; the data are presented only as an overview of reported performance characteristics of the tests. All numbers are
rounded to the nearest whole number. cfu, colony-forming units,

1154 • CID 2004:38 (15 April) • MEDICAL MICROBIOLOGY

 Table 4. Interpreting culture results for urine specimens yielding common
urinary tract pathogens.
Probability of
contamination, no. of Quantitation,
microorganisms isolated cfu/mL
a
Low probability
1 !102
1 ⭓10 2
2 !102 for each
2 ⭓102 for each
2 ⭓102 for 1
⭓3 ⭓10 for 1
5
⭓3 ⭓105 for each
b
High probability
1 !102
1 ⭓10 2
2 ⭓105 for each
2 ⭓105 for 1
2 !105 for each
⭓3 ⭓105 for 1
⭓3 ⭓10 for each
5
NOTE. cfu, colony-forming units.
a
Urine specimens obtained via aspiration (suprapubic, bladder, ureter, renal pelvis, kidney)
or single (straight) catheterization, specimens obtained in the operating room, and urine spec-
imens obtained from patients receiving antimicrobial therapy.
b
Urine specimens obtained via clean catch technique, from indwelling catheters (urinary
or suprapubic), or from nephrostomy tubes, ureterostomy tubes, or ileal loops.
necessary for determination of the identity of the infecting
microorganism(s) and for antimicrobial susceptibility testing.
This is particularly true because of the increased incidence of
antimicrobial resistance.
The most commonly used criterion for defining significant
bacteriuria is the presence of ⭓105 cfu per milliliter of urine
[15, 57, 58]. This criterion was established only for women
with acute pyelonephritis or women who were asymptomatic
but had multiple urine cultures that yielded this number of
bacteria; however, the criterion is often applied to other patient
populations [15]. Most patients with UTIs, however, do not
fall into either category, and 30%–50% of patients with acute
urethral syndrome will have colony counts of !105 cfu/mL [15].
For this reason, many laboratories have opted to use lower
colony counts as a criterion for interpreting and reporting re-
sults. One common criterion is a colony count of 104 cfu/mL,
which would be expected to increase the sensitivity of the test
without making the test impractical for clinicians and labo-
ratories to use.
Catheterized patients (who may have low concentrations of
bacteria that can progress to higher concentrations) and many
patients with infections of the lower urinary tract have colony
counts much lower than 105 cfu/mL if the specimens are ob-
tained via suprapubic aspirate or catheterization [59]. Accord-
Interpretation
Probable contaminant
Significant isolate
Probable contaminants
Significant isolates
Significant isolate and contaminant
Significant isolate and contaminants
Probable contaminants
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Probable contaminant
Significant isolate
Significant isolates
Significant isolate and contaminant
Probable contaminants
Significant isolate and contaminants
Probable contaminants
ingly, the most appropriate diagnostic criterion for urine culture
specimens obtained via suprapubic aspirate or catheterization
is a bacterial concentration of ⭓102 cfu/mL [15, 59].
Routine follow-up cultures for test-of-cure are not recom-
mended for patients who have been treated for asymptomatic
bacteriuria, acute uncomplicated cystitis, or acute uncompli-
cated pyelonephritis [60] and for whom there is evidence of
an appropriate clinical response to therapy [2]. Follow-up cul-
tures are, however, recommended for patients with infections
that do not respond to therapy, patients who have recurrent
UTIs, patients who have anatomic or functional abnormalities
of the urinary tract, or patients who continue to have unex-
plained abnormal urinalysis findings.
Anaerobic bacterial urine cultures. The normal flora of
the large intestine, vagina, and skin contain large numbers of
anaerobic bacteria. Because anaerobic bacteria cause UTIs only
in rare circumstances, however, recovery of anaerobic bacteria
from urine by culture is of no clinical relevance for most pa-
tients with UTIs. Urine cultures for anaerobic bacteria should
be limited to patients with anatomic abnormalities (e.g., en-
terovesicular fistulae) that increase the likelihood of infection
with anaerobic bacteria.
Fungal urine cultures. As stated previously, microbiologic
detection of almost all cases of funguria can be achieved using
MEDICAL MICROBIOLOGY • CID 2004:38 (15 April) • 1155
routine bacterial media. There are limited data regarding the
use of tests other than culture to detect funguria. Huang et al.
[61] reported that pyuria did not correlate with funguria, re-
gardless of whether patients had concomitant bacteriuria or an
indwelling urinary catheter. Kauffman et al. [16] reported that,
of 648 patients with funguria whose urine specimens underwent
urinalysis, 354 (54.6%) had pyuria and 230 (35.5%) had he-
maturia. Of the 648 patients, only 410 had urine specimen
reports that included a comment as to the presence or absence
of yeasts; 247 (60.2%) of these 410 patients had urine specimens
that were positive for yeasts [16]. On the basis of these obser-
vations, and because the nitrite test would be of no use in the
detection of funguria, there appears to be limited value in using
urinalysis in the detection of funguria at this time. This con-
clusion may change as further information is published re-
garding the clinical outcomes of patients with funguria, the
results of laboratory testing of urine specimens, and the effects
of chemotherapy.
Mycobacterial urine cultures. Although it is an uncom-
mon finding in the United States, extrapulmonary tuberculosis
may involve the genitourinary tract. The traditional laboratory
diagnosis of mycobacterial UTI is by use of acid-fast smears
and mycobacterial cultures [62], but more recent data suggests
that the diagnosis can also be made by use of nucleic acid
amplification tests [63, 64]. There are, however, only limited
data about the use of such assays for the diagnosis of genito-
urinary tuberculosis, and none of these assays have been cleared
or approved by the US Food and Drug Administration for this
indication. Until better data are available, the authors recom-
mend against the routine use of nucleic acid amplification tests,
particularly with patients for whom there is low clinical sus-
picion of genitourinary tuberculosis.
Because nontuberculous mycobacteria, such as Mycobac-
terium smegmatis, may be present as colonizing flora (and to
reduce the number of contaminating bacteria), the external
genitalia should be washed before specimens are obtained [64].
The best specimen for mycobacterial urine cultures is the first
voided urine. Multiple specimens may be needed, because my-
cobacterial culture results are positive for 25%–95% of patients
and smears are positive for 50%–70% of patients with tuber-
culous genitourinary tract infections [62].
Interpretation of urine culture results. Microbiologists
need to interpret the microbiologic relevance of growth on
culture plates to determine whether further identification and
antimicrobial susceptibility testing are necessary. Most culture
results can be interpreted readily; no growth and gross con-
tamination are both unambiguous results, as are pure cultures
of common pathogens growing in a quantity of 1105 cfu per
milliliter of urine. The interpretation of cultures that yield
pure growth in lower quantities is also clear for specimens
obtained via suprapubic aspiration or straight catheterization.
1156 • CID 2004:38 (15 April) • MEDICAL MICROBIOLOGY
On the other hand, interpretation of urine cultures that yield
mixed flora in varying quantities can be difficult. Although a
number of algorithms have been developed to guide the in-
terpretation of urine cultures, the large number of potential
combinations of microorganisms—in varying quantities—
and the need to correlate these results with different types of
UTIs limits the usefulness of any algorithm. One algorithm
is presented in table 4.
Irrespective of the algorithm used to guide interpretation,
laboratories should report culture results with interpretive
guidelines to help the ordering physician assess the clinical
relevance of the results. Cultures that yield unambiguous cul-
ture results should be interpreted and reported as such. Test
reports for cultures that yield mixed flora in varying quantities
Downloaded from http://cid.oxfordjournals.org/ at University of Texas at Austin on October 19, 2014
should specify the microorganisms that were recovered, the
quantity of each microorganism, and the probable clinical im-
portance of each isolate.
Antimicrobial susceptibility testing. Each laboratory
should have guidelines by which pathogens are tested for an-
timicrobial susceptibility. These guidelines should be developed
and antimicrobial susceptibility tests should be performed and
reported according to the most recent version of the NCCLS
guidelines. Bacterial or fungal isolates of uncertain clinical im-
portance should not be tested for antimicrobial susceptibility
for purposes of routine patient care.
CONCLUSION
Most patients with uncomplicated acute cystitis have cases that
are clinically straightforward, and they may not require any
laboratory testing beyond urinalysis. For a significant number
of patients, however, the clinical history and physical findings
alone may be insufficient to make a definitive diagnosis of UTI.
For those patients and for patients with complicated UTIs,
laboratory tests are necessary to make the diagnosis and to
provide specific information regarding the identity and the an-
timicrobial susceptibility pattern of pathogens. Both the lab-
oratory diagnosis and the clinical diagnosis of laboratory test
results must be made in light of the method of collection used;
clinicians should specify the method of collection on test req-
uisition forms. Of the available laboratory tests, urinalysis is
helpful primarily as a means of excluding bacteriuria, but it is
not a surrogate for culture. Although cultures identify patho-
gens, the accurate interpretation of culture results requires clin-
ical information that is usually available only to the clinician.
We hope that infectious diseases physicians, in particular, will
understand both the strengths and the limitations of the lab-
oratory-based diagnostic studies for UTIs that have been re-
viewed in this article, and we hope that they will incorporate
this understanding with current treatment guidelines [65] to
optimize patient care.
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