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426 BASIC SKILLS IN INTERPRETING LABORATORY DATA
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TABLE 18-10.
CLINICAL
ORGANISM
TYPE OF
ORGANISM
FINDINGS AND
INFECTIONS
DIAGNOSTIC
METHOD POSITIVE RESULT REFERENCE
Mycoplasma
pneumoniae
Plasmodium
falciparum,
P. vivax,
ovale,
P.
P. malariae
Pneumocystis
jirovecii
(carinii
Atypical
bacteria
Protozoa
Fungus with
protozoal
characteristics
Pneumonia,
tracheobronchitis,
pharyngitis
include high
fever (cyclic with
P. vivax, P. ovale,
P. malariae), chills,
nausea, vomiting,
severe headache,
anemia, abdominal
pain; lifethreatening with
P.
falciparum
Pneumonia,
infection
serology
Detection of M pneumoniae
Thick and thin
stained with
Giemsa or
Wright’s stain
(gold standard)
Fluorescentassisted
microscopy with
acridine orange
after Giemsa or
methenamine
silver stain of
induced sputum,
tissue biopsy
4-fold or greater rise in
antibody titer between
paired sera (acute and
convalescent samples)
DNA
Presence of malarial
parasites
when dyes are taken up by
the nucleus of the parasite
antigens
DNA sequences
Detection of trophic or
cystic forms
4,13,56
55
57
Rickettsia
rickettsii
(Rocky
spotted fever)
Rickettsia Fever, chills,
headache and rash
in patient with
recent tick bite;
myalgias, malaise,
nausea, vomiting,
abdominal pain,
focal neurologic
vasculitis may result
in life-threatening
complications
DFA or IFA Detection of cysts or
trophozoites
Detection of P jirovecii-
1,3-β--glucan
serum test
IFA (gold
standard)
EIA or LA
Detection of R rickettsii DNA
Positive values >
4-fold or greater rise in
between paired sera (acute
and convalescent samples)
antibodies
sequences
48,52
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 427
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TABLE 18-10.
CLINICAL
ORGANISM
TYPE OF
ORGANISM
FINDINGS AND
INFECTIONS
DIAGNOSTIC
METHOD POSITIVE RESULT REFERENCE
Strongyloides
stercoralis
Parasite Abdominal
infection;
disseminated
infection
(hyperinfection
syndrome with
pneumonitis,
sepsis)
Taenia solium Tapeworm Neurocysticercosis
(infection within
brain tissue)
causing seizures,
headache, focal
muscular and
subcutaneous
abscesses
Toxoplasma
gondii
Protozoa Encephalitis,
myocarditis,
lymphadenitis,
polymyositis,
chorioretinitis,
during pregnancy,
congenital
ova and parasites
Detection of antibodies
Detection of adult worms,
to T
solium glycoprotein
58
59
antigens
Detection of anticysticercal
antibodies or cysticercal
antigens
Positive IgG antibody 60,61
Giemsa or Diff-
Demonstration of
tachyzoites
tissue
Detection of T gondii-
Ureaplasma
urealyticum
Atypical
bacteria
infections, including
prostatitis, PID,
bacterial vaginosis,
urethritis; systemic
Growth within 5 days 13,56
selective media
Detection of NA or gene
targets
infection in
neonates and
immunocompromised
Source: References 4,13,44–61.
each bacterium based on several factors. Some drugs, such as
piperacillin–tazobactam, are assigned higher MIC breakpoint
values for susceptibility because they achieve higher serum
and site concentrations than other antibiotics. Because of this,
a simple number comparison of the MIC between antibiotics
should not be performed. e choice of antibiotic should be
based on the knowledge of the MICs that are acceptable for a
particular antibiotic–bacteria combination, the site of infection, the penetration of the antibiotic to the site of infection,
as well as the clinical and economic parameters listed previously. In the sample report in Figure18-5, oxacillin (nafcillin)
or cefazolin would be an acceptable choice for the treatment of
S aureus bacteremia in a patient without drug allergies because
these agents are active against the infecting organism, have
428 BASIC SKILLS IN INTERPRETING LABORATORY DATA
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Patient Name: Jane Doe
Medical Record Number: 1111111
Specimen Collection Date and Time: Dec 12, 2014, 0730
Specimen Type: Blood
Organism Identification: Staphylococcus aureus
ANTIMICROBIAL SUSCEPTIBILITY
Antibiotic
Penicillin
Ampicillin/Sulbactam
Cefazolin
Oxacillin
Trimethoprim/Sulfa
Vancomycin
Clindamycin
Erythromycin
MIC
(mcg/mL)
16
4
8
0.5
10
0.5
0.5
0.5
Interpretive
Category
Resistant
Susceptible
Susceptible
Susceptible
Susceptible
Susceptible
Susceptible
Susceptible
FIGURE 18-5.
susceptibility.
been demonstrated to be eective in the treatment of systemic
staphylococcal infections, have a relatively narrow spectrum,
and are inexpensive. Minicase 2 is an example illustrating the
use of a bacterial culture and susceptibility report in the antibiotic decision-making process.
e decision regarding the specic antibiotics that will be
routinely reported in an individual susceptibility report for a
bacterial isolate is typically based on input from a hospital or
institutional multidisciplinary committee (eg, Antimicrobial
Subcommittee, Infectious Diseases Subcommittee, Antimicrobial Stewardship Team) comprised of infectious diseases
physicians, infectious diseases pharmacists, and representatives from the Infection Control Committee and the microbiology laboratory. e choice of specic drugs to report is
oen based on the hospital formulary, the level of control of
antibiotic use that is desired, and the tests that are used by
the microbiology laboratory for susceptibility testing. Tables
that outline the antibiotics that should be routinely tested and
reported for each bacterium can be found in the CLSI Performance Standards and Guidelines for Antimicrobial Susceptibility Testing.
Several methods can be used for reporting antibiotic susceptibility of individual bacterial isolates, including general reporting, selective reporting, and cascade reporting. General reporting
involves reporting all antibiotics that were tested for susceptibility against the organism without any restrictions. Selective
reporting involves reporting certain antibiotic susceptibility test
results on an individual bacterial isolate based on dened criteria, such as the bacteria identied, the site of infection, antibiotics available on the hospital formulary, etc. An example of
selective reporting would be the exclusion of cefazolin from the
susceptibility report of a CSF sample growing E coli because
cefazolin is not a suitable treatment option for meningitis. Cas-
cade reporting involves the preferential release of susceptibility
information for rst-line choices for the treatment of a particular
21,26-28
organism or infection (usually narrow spectrum and inexpensive), with the reporting of second-line antibiotic susceptibility
results (usually broad spectrum and costly) only if the rst-line
agents are inactive against the infecting organism or are inappropriate for the treatment of the particular infection. An example
of cascade reporting is the reporting of amikacin susceptibility results against P aeruginosa only if the organism displays
resistance to both gentamicin and tobramycin, which are less
expensive aminoglycoside agents. Both selective reporting and
cascade reporting are oen used as antimicrobial stewardship
activities to control the inappropriate use of broad-spectrum or
expensive antibiotics.
62
Hospital Susceptibility Reports (Hospital
CumulativeAntibiograms)
Most hospitals prepare and publish an annual cumulative report
of antimicrobial susceptibility proles of the bacteria that have
been isolated from patients within their hospital, healthcare
system, or institution, called a cumulative antibiogram. For the
cumulative antibiogram to be clinically useful, the susceptibility data from patient isolates should be appropriately collected,
analyzed, and reported according to the CLSI guidelines, which
are outlined in Table18-11.
e cumulative antibiogram contains information on the
percent of isolated bacteria that were susceptible to antibiotics
tested over the time frame of the antibiogram, as illustrated in
Figure18-6.62 is percent susceptibility information is derived
by dividing the number of organisms susceptible to a particular
antibiotic by the total number of single-patient isolates collected
and reported (with duplicate patient isolates removed). e calculations can be performed either manually or through the use
of automated systems that have been programmed using appropriate denitions to remove duplicate patient isolates. Cumulative antibiograms usually contains separate data tables for the
susceptibility reporting of gram-positive, gram-negative, and
anaerobic bacteria (if performed).
e specic data published in the cumulative antibiogram
should be based on input from the hospital/healthcare system’s
multidisciplinary committee (eg, Infectious Diseases Subcommittee, Antimicrobial Stewardship Committee) that is oen
comprised of infectious diseases physicians, infectious disease
pharmacists, infection preventionists, and the microbiology
laboratory. e cumulative antibiogram report typically contains information on the antibiotic susceptibility patterns of
isolates obtained from patients in the hospital (either admitted with infection or who developed infection in the hospital)
but may also include the susceptibility of organisms causing
infection in outpatients if the hospital/medical center also
serves a substantial outpatient population. In addition, each
hospital or healthcare system may further stratify their susceptibility data by various parameters, such as patient care
unit (eg, Burn Unit, MICU, Pediatric Unit, Med-Surg Unit,
outpatient clinic, nursing home), patient age, site of infection
(eg, bloodstream isolates, UTI isolates), patient characteristics
(eg, cystic brosis, transplant patients, hematology/oncology
patients), or by organism (eg, susceptibility of S aureus). For
62
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MINICASE 2
Using Laboratory Test Results to Guide the Choice of a Directed Antibiotic
Regimen for the Treatment of Pyelonephritis
Diana J., a 27-year-old woman, presents to the urgent care clinic
with reports of urinary frequency and urgency, pain on urination,
and hematuria for the past 2 days. She also reports fever of 101.6°F
and intractable nausea and vomiting during the past 24 hours. At
presentation, she is febrile (102.3°F), hypotensive (90/60mm Hg),
and lethargic; physical exam reveals right costovertebral angle
and suprapubic tenderness. A urine dipstick performed in the
clinic is leukocyte esterase positive, and a urine pregnancy test is
negative. Because she appears ill, the clinic physician sends the
patient to the local emergency department (ED) for admission. Her
past medical history is significant for recurrent UTIs, with three
episodes over the past 6 months that have required antibiotic
therapy, including oral trimethoprim–sulfamethoxazole and
oral ciprofloxacin. She reports no known drug allergies. Upon
admission to the ED, urinalysis, urine culture, and blood cultures
are performed.
QUESTION: What is an appropriate recommendation for emipric
antibiotic therapy for this patient?
DISCUSSION: Based on her presenting symptoms and the
findings on her physical examination, this patient most likely
has acute pyelonephritis, an upper tract UTI, making the
acquisition of urinalysis, urine culture, and blood cultures
important for guiding directed antimicrobial treatment. This is
especially important in this patient because she has received
multiple recent courses of antibiotics for her past UTIs, which
put her at risk for infection with resistant bacteria. Because
she is hypotensive and is experiencing significant nausea
and vomiting, she should initially receive empiric parenteral
antibiotic therapy that displays activity against the likely
causative organisms of pyelonephritis and has proven efficacy
in the treatment of complicated UTIs (eg, ceftriaxone because
she does not have any antibiotic allergies). The patient
should receive ceftriaxone as empiric therapy, which can be
de-escalated to cefazolin based on the results of the blood and
urine culture and susceptibility test results that follow.
URINALYSIS: Yellow, cloudy; pH 7; specific gravity 1.015; protein
negative; RBC trace; WBC 50 to 100/hpf; leukocyte esterase
positive; nitrite positive.
Midstream Urine Culture/Susceptibility: > 100,000 CFU/mL
of Ecoli
ANTIBIOTIC
TESTED MIC RESULT
Ampicillin >32 mcg/mL R
Ampicillin–
sulbactam
Cefazolin 1 mcg/mL S
Ceftriaxone 1 mcg/mL S
Imipenem 1 mcg/mL S
Gentamicin 0.5 mcg/mL S
Ciprofloxacin 4 mcg/mL R
Trimethoprim–
sulfamethoxazole
R = resistant; S = susceptible.
8 mcg/mL S
>4/76 mcg/mL R
CLSI
INTERPRETATION
Blood Culture/Susceptibility: E coli
ANTIBIOTIC
TESTED MIC RESULT
Ampicillin >32 mcg/mL R
Ampicillin–
sulbactam
Cefazolin 1 mcg/mL S
Ceftriaxone 1 mcg/mL S
Imipenem 1 mcg/mL S
Gentamicin 0.5 mcg/mL S
Ciprofloxacin 4 mcg/mL R
Trimethoprim–
sulfamethoxazole
R = resistant; S = susceptible.
8 mcg/mL S
>4/76 mcg/mL R
CLSI
INTERPRETATION
some organisms, the cumulative antibiogram only will contain information regarding the presence of bacterial resistance
mechanisms, particularly when routine susceptibility testing
is dicult to perform, such as in the case of H inuenzae
in which the percentage of isolates that produce β-lactamase
enzyme during the time period of the cumulative antibiogram
will be reported. Other information that may be incorporated
into a cumulative antibiogram includes graphs demonstrating
resistance trends, antibiotic dosing guidelines, recommended
empiric antibiotic choices based on infection type, and antibiotic cost data.
62
e cumulative antibiogram is a useful tool for selecting
empiric antibiotic therapy, where an antibiotic is selected based
on the local susceptibility patterns of the most likely infecting
organism causing the patient’s infection (Table18-7) while waiting for the results of culture and susceptibility tests, as described
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TABLE 18-11.
1. To serve as a continuously useful tool to guide appropriate empiric antibiotic therapy, the cumulative antibiogram should
be compiled, analyzed, and reported at least annually.
of the antibiogram) should be included in the cumulative susceptibility report regardless of site of isolation, susceptibility
pattern of the bacteria, or other phenotypic characteristics. The inclusion of duplicate clinical isolates from the same
patient will lead to overreporting of bacterial resistance.
To provide a reasonable statistical estimate of susceptibility, only species of bacteria in which at least 30 isolates have
3.
been collected, tested, and reported during the time period of the antibiogram should be included.
nonpatient sources should not be included in the antibiogram.
5.
The cumulative susceptibility report should include all antibiotics that were tested for susceptibility, regardless of whether
6.
Only bacterial isolates for which all routine antibiotics have been tested for susceptibility should be included. Results of
if only isolates resistant to primary agents were then analyzed for susceptibility to secondary agents, this will bias the
resistance results toward higher levels of resistance to the secondary agents.
isolates are removed and there are a sufficient number of isolates collected (> 30) during the time frame of the
antibiogram.
Source: Reference 62.
FIGURE 18-6.
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 431
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in Minicase 3.62 Antibiotic therapy must oen be initiated at
the suspicion of infection because many infectious diseases are
oen acute where a delay in treatment may result in signicant
morbidity or mortality (eg, meningitis and pneumonia). Once
the culture and susceptibility results of the infecting bacteria are
MINICASE 3
Using the Cumulative Antibiogram
to Choose Empiric Antibiotic
Therapy
David M. is a 45-year-old man who sustained multiple
traumatic injuries after a motorcycle accident. He has
required multiple surgeries over the past 10 days for
fracture stabilization. In the last 12 hours, he has spiked
a temperature to 39°C and has developed shaking chills.
His other vital signs are stable, and his physical exam does
not demonstrate any significant focal findings. Urinalysis,
urine culture, and blood cultures are performed to determine
the potential etiology for his new fever. In addition, a chest
radiograph is obtained, which does not demonstrate any
pulmonary infiltrates. The microbiology laboratory calls the
surgical floor later that day to report that the blood culture
results are positive for gram-negative rods. The patient is
allergic to penicillin (nonurticarial rash); the local hospital
antibiogram is pictured in Figure18-6.
QUESTION: What empiric antibiotic therapy should be used
to treat this patient’s gram-negative rod bacteremia while
waiting for the culture and susceptibility results?
DISCUSSION: Nosocomial gram-negative bacteremia is
a potentially life-threatening infection that requires early,
aggressive antibiotic therapy. The choice of whether to use
monotherapy or combination therapy while waiting for culture
and susceptibility results in this setting often depends on the
clinical condition of the patient and local susceptibility patterns.
Combination antibiotic therapy might be considered initially if
the patient is critically ill (septic shock) from the bacteremia
because it might provide some synergistic antibacterial activity
as well as enhanced coverage against a wide range of potential
infecting bacteria. Based on the hospital antibiogram in
Figure18-6, it is desirable to choose an antibiotic that displays
good activity (>85% susceptible) against gram-negative
bacteria isolated at the institution (eg, P aeruginosa, E coli,
K pneumoniae, S marcescens, and Enterobacter cloacae) and
choose an antibiotic with proven efficacy in the treatment of
bacteremia. Because the patient is clinically stable and displays
only a rash to penicillin, some useful therapeutic options based
on review of the hospital antibiogram include meropenem,
ceftazidime, or cefepime. If the patient were to clinically
deteriorate on monotherapy, an aminoglycoside (tobramycin)
or a fluoroquinolone (ciprofloxacin) could be added to the
carbapenem or cephalosporin while waiting for the culture
and susceptibility results. The antibiotic regimen could then
be modified to more directed therapy, if possible, once the final
culture and susceptibility results were available.
known, antibiotic therapy should be deescalated or directed, if
necessary, to an agent with more targeted activity against the
organism
Surveillance Susceptibility Testing of Large
NumbersofIsolates
Surveillance susceptibility testing is a useful method to monitor the susceptibility of bacteria to antimicrobial agents over
time and can be performed in an individual hospital or within
a geographic location (eg, regionally, nationally, and internationally).20 Surveillance studies typically report the overall
susceptibility of the bacteria to particular antibiotics using
CLSI breakpoints, along with other susceptibility parameters,
such as the MIC50 and the MIC90. To determine the MIC50 or
MIC90, the MIC values from the bacterial population studied
are arranged in ascending order, where the MIC50 is the MIC
value representing 50% of the bacterial population (the MIC
value of the isolate that represents 50% of the bacterial population studied) and the MIC90 is the MIC that represents 90%
of the bacterial population (the MIC value of the isolate that
represents 90% of the bacterial population studied). e MIC90
value is usually higher than the MIC50 value. is information
is useful for detecting the emergence of subclinical antibiotic
resistance in which the MIC50 and MIC90 of a particular agent
may be increasing over time but are still below the MIC susceptibility breakpoint.
Additional Considerations When Interpreting
Susceptibility Results
e successful treatment of a patient’s infection involves an
understanding of the interactions among the patient, the
infecting organism, and the antibiotic. It is important to note
that antimicrobial susceptibility testing only measures one of
these factors, namely, the activity of the antibiotic against the
infecting organism in a laboratory setting. e current methodologies for antibiotic susceptibility testing are unable to
reproduce theinteraction between the antibiotic and the bacteria at thesite of infection in which a multitude of host factors (eg, immune system function, concomitant disease states)
and drug factors (eg, pharmacokinetic parameters, including
concentration of free drug at the site of infection and protein
binding) play an integral role.
LABORATORY TESTS USED FOR
DIAGNOSIS OF SPECIFIC INFECTIONS
Bacterial Meningitis
Meningitis is an infectious diseases medical emergency requiring prompt, accurate diagnosis and treatment. Meningitis may
be caused by bacteria, viruses, fungi, or mycobacteria, and it produces a resulting clinical presentation of acute or chronic meningitis depending on the causative organism. In a patient with
suspected meningitis, a lumbar puncture is performed to obtain
CSF for laboratory analysis to aid in the diagnosis of the infection,
including the potential causative organism.
2,63-67
In patients who
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present with papilledema, altered consciousness, new-onset seizures, or focal neurologic ndings, a head computed tomography
may be performed prior to the lumbar puncture to exclude the
presence of a space-occupying lesion, which may put the patient
at risk for brain herniation aer lumbar puncture.
63,66
Alumbar
puncture involves the aseptic insertion of a spinal needle into
the subarachnoid space at the lumbar spine level (between L3,
L4, orL5) for the aspiration of 5 to 20 mL of CSF for analysis.
63,64
When inserting the spinal needle, the opening pressure may be
measured (normal opening pressure is 50 to 195mm H20 in
adults) and is oen elevated in patients with meningitis (especially C neoformans meningitis) and concomitant cerebral edema
or intracranial focus of infection.
63,66
e CSF should be placed
in three to four separate sterile screw-cap tubes and immediately
transported to the laboratory for rapid processing. e rst two
tubes of CSF are used for microbiologic (eg, Gram stain, fungal
stains, acid-fast bacilli stain, culture, and antigen detection) and
chemical studies (eg, general appearance, glucose, and protein),
whereas the last tubes are used for determination of the WBC
count and dierential. e typical CSF chemistry, hematology,
and microbiologic ndings in patients with meningitis caused by
dierent pathogens are listed in Table18-12.
63-67
Chemistry and Hematology
In patients with meningitis, the CSF oen appears cloudy
because of the presence of WBCs, protein, and bacteria.66
e chemistry and hematology results from the CSF analysis
directly correlate with the probability of infection so that negative ndings exclude the likelihood of meningitis in almost all
63,65,66
cases.
onstrate marked abnormalities in the chemistry analysis of the
CSF, with protein concentrations of >100 mg/dL and glucose
Patients with acute bacterial meningitis oen dem-
concentrations <45 mg/dL (or a CSF/blood glucose ratio of <0.5)
due, in part, to disruption of the blood–brain barrier.
Hematologic analysis of the CSF involves measurement of the
WBC count with corresponding dierential. Patients with acute
bacterial meningitis oen demonstrate an elevated CSF WBC
count (>1,000 cells/mm3) with a neutrophilic predominance
(>80% neutrophils). In contrast, patients with viral, fungal, or
mycobacterial meningitis oen display lower CSF WBC counts
(5 to 1,000 cells/mm3) with a predominance of lymphocytes. In
cases of a traumatic lumbar puncture (surrounding blood vessels are damaged during needle insertion), peripheral blood can
enter the subarachnoid space and contaminate the CSF, making
interpretation of the CSF WBC dicult. When interpreting the
CSF WBC count aer a traumatic tap, there should be one WBC
for every 500 to 1,000 RBCs (based on blood composition); this
ratio should be used to calculate a corrected CSF WBC during
CSF analysis/interpretation.
Cerebrospinal Fluid Stain and Culture
For patients with suspected bacterial meningitis, a Gram stain
and culture should be performed on CSF. Gram stain will demonstrate an organism in 60% to 90% of patients with bacterial meningitis and is helpful in selecting appropriate empiric
antibiotic therapy.
Gram stain diminishes to 40% to 60% in patients who have
received antibiotics prior to the lumber puncture (also known
as partially treated meningitis).
caused by viruses, fungi, or mycobacteria, the Gram stain is
usually negative, and specialized tests should be used, such as
the India ink stain or cryptococcal antigen test for the detection of Cryptococcus neoformans or the acid-fast stain for the
detection of Mycobacterium tuberculosis.
2,63,65-67
However, the sensitivity of the CSF
2,65
In patients with meningitis
63,66
TABLE 18-12.
BACTERIAL
NORMAL
Opening pressure
(mm H
0)
2
<180 >195
3
) 0–5
<30 (newborns)
No predominance
MENINGITIS VIRAL INFECTION
1,000–20,000
(mean 800)
50–2,000
(mean 80)
≥ >50% lymphs,
ratio)
Gram stain
<50 >100
45–100
(two-thirds of
serum)
<45
(< one-half of
serum)
60–90 Negative Negative 37–87
30–150 40–150
45–70 30–70
(% positive)
Source: References 63–67.
FUNGAL
MENINGITIS
20–2,000
(mean 100)
TUBERCULOUS
MENINGITIS
5–2,000
(mean 200)
>50% lymphs >80% lymphs
>50
<40
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 433
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All CSF specimens should be processed for culture based
on the type of meningitis (acute versus chronic) and the organism suspected of causing the infection. In patients with bacterial meningitis, the cultures are oen positive within 24 to
48hours. In patients with nonbacterial meningitis, culture specimens should be incubated for longer periods of time (up to 2 to
6 weeks), because some organisms take longer to grow.
Other Specialized Tests
Several specialized tests may be performed on CSF specimens to
aid in the detection of the causative organism, including bacterial antigen detection using LA, latex xation, or enzyme immunoassay (EIA); fungal antigen detection; antibody detection; and
bacterial, viral, or mycobacterial PCR assays.
63-67
Bacterial antigen testing on CSF specimens is a rapid diagnostic test with results available within 10 to 15 minutes. Commercially available tests use antibody-coated particles that bind
to specic capsular antigens of the most common pathogens
that cause acute bacterial meningitis, including S pneumoniae,
N meningitidis, H inuenzae type B, and group B streptococci.
e tests are performed by combining CSF (although they can
also be performed using urine or serum) with antibody-coated
particles and observing for agglutination, which signies the
presence of the bacterial antigen in the specimen. If visible
agglutination does not occur, either the antigen is not present or it is present in insucient amounts to cause detectable
agglutination. Routine bacterial antigen detection of CSF specimens isnot currently recommended because the results lack
high specicity/sensitivity (not better than the traditional Gram
stain), have an inadequate negative predictive value, and their
use has rarely impacted patient treatment or been demonstrated
to be cost-eective.
3,63,67
However, bacterial antigen testing may
be useful in patients with negative Gram stains or in patients
who have received previous antimicrobial therapy.
2,63-65,67
Nucleic-acid amplication tests, including PCR, are rapid
and accurate tests for the diagnosis of meningitis due to bacteria, viruses, and fungi.
66,67
CSF PCR results are oen positive
early in the course of infection and even remain positive during the rst week of therapy.66 Several commercial PCR assays
are available that amplify small amounts of specic DNA of the
target organism followed by subsequent identication and verication. e FilmArray meningitis/encephalitis panel (BioFire
Diagnostics, Salt Lake City, UT) is a multiplex PCR with high
sensitivity of 94.2% and specicity of 99.8% that rapidly (<1 hr)
detects 14 common causes (six bacteria [Escherichia coli K1,
Haemophilus inuenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, Streptococcus pneumoniae];
seven viruses [Cytomegalovirus, Enterovirus, Herpes simplex
virus 1, Herpes simplex virus 2, Human herpesvirus 6, Human
parechovirus, Varicella zoster virus], and Cryptococcus neofor-
mans) of meningitis/encephalitis directly from CSF.
66,67
Streptococcal Pharyngitis
Acute pharyngitis is one of the most common infections encountered in medicine and can occur in both children and adults.
Acute pharyngitis can be caused by several organisms (eg, bacteria and viruses), which produce similar signs and symptoms of
infection. Antibiotic therapy is recommended only for patients
with pharyngitis caused by bacteria, especially group A streptococci (Streptococcus pyogenes).68 Because group A strep pharyn
gitis comprises only a small percentage (20% to 30%) of patients
with acute pharyngitis, it is important that a rapid, reliable diagnostic test be available to avoid unnecessary antibiotic use in
patients with acute viral pharyngitis.
68
e gold standard diagnostic test for acute pharyngitis caused
by group A streptococcus is the throat culture, which oen takes
1 to 2 days for results. erefore, rapid antigen detection tests
(RADTs) have been developed to expedite and conrm the
diagnosis of group A streptococcal pharyngitis, with most tests
yielding results within 15 minutes.
68,69
Positive RADT test results
expedite the initiation of antibiotic treatment in the appropriate
patient. Several RADT tests are commercially available, with the
newer tests employing EIA or chemiluminescent DNA probes
(>95% specicity and ≥90% sensitivity).
68,69
ere are limited
studies comparing the performance of dierent RADT tests to
throat culture (the gold standard), so current recommendations
suggest that traditional throat culture be performed in children
and adolescents with a negative RADT test result to denitively
exclude group A streptococcal pharyngitis.
68,69
Pneumonia
Several obstacles make the diagnosis of bacterial pneumonia
quite dicult. First, the respiratory tract is colonized with bacteria that may or may not be contributing to the infectious process. When obtaining a sample for culture, lower respiratory tract
secretions can become contaminated with secretions or bacteria
colonizing the upper respiratory tract; therefore, expectorated
sputum samples should be evaluated to determine if contamination with saliva or upper respiratory tract ora has occurred
(assessing of the adequacy of the sample).
other than normal respiratory ora are isolated, the clinician
must determine the relative importance and signicance of the
organism(s) as a potential cause of pneumonia, in addition to
assessing the patient for signs and symptoms of pneumonia. It is
estimated that 40% to 60% of hospitalized patients with CAP are
unable to produce a sputum sample; and 40% to 60% of produced
samples that are submitted are judged as being inadequate.70 For
this reason, in some patients, adequate sputum specimens are difcult to obtain without invasive procedures. Invasive procedures,
such as BAL or protected specimen brush (PSB), are occasionally used to aid in the diagnosis of pneumonia in patients who
are unable to expectorate an adequate sputum sample (especially
in patients not responding to appropriate empiric therapy), in
immunocompromised patients, and in patients with hospitalacquired pneumonia (HAP) or ventilator-associated pneumonia
2,19,70,71
(VAP).
Despite the best eorts at obtaining a lower respiratory tract sputum specimen for culture, as many as 30% to 50% of
patients with pneumonia have negative culture results.
To obtain an adequate expectorated sputum sample, the
patient should be instructed to provide sputum generated
from a deep cough. All expectorated sputum samples should
be screened to ensure that the specimen is adequate and has
not been contaminated by saliva or upper respiratory tract ora
prior to processing for culture.
2,70,71
Information used to assess
1,2,4,6,7,70,71
If bacteria
70,71
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434 BASIC SKILLS IN INTERPRETING LABORATORY DATA
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the adequacy of an expectorated sputum sample is derived
from visualization of the Gram stain of the specimen. Expectorated sputum specimens that contain >25 WBCs/hpf (unless
the patient is neutropenic) and <10 squamous epithelial cells/
hpf are considered adequate for further processing and cul-
4,70,71
ture.
Samples with >10 epithelial cells/hpf are representa-
tive of upper respiratory tract contamination (saliva) and should
not be processed for culture. e sputum Gram stain from an
adequate sputum specimen may be used to guide empiric antibiotic therapy when the specimen is purulent and contains a
predominant organism. Antibiotic therapy should be modied
based on the culture results, especially if they reveal an infecting organism.
Because of the diculty with collection and low yield with
sputum culture, several rapid direct detection tests have been
developed, including urinary antigen detection (Streptococ-
cus pneumoniae and Legionella pneumophila serogroup 1) or
NA-based methods on respiratory specimens.
70,71
e S pneu-
moniae urinary antigen test may be useful in hospitalized
patients who are unable to produce a sputum sample, in patients
with severe pneumonia requiring intensive care unit admission,
in patients at risk for pneumococcal pneumonia (eg, asplenic,
alcohol abuse, liver disease), in patients with pneumonia and
concomitant pleural eusion, and in patients who have received
antibiotics before a specimen for culture has been obtained.
70,71
Several NA-based rapid (in 1 hour) detection methods are commercially available for the detection of respiratory viruses and
bacteria capable of causing upper and lower respiratory tract
infections, and include tests such as the Verigene Respiratory
Pathogens Flex Test (Luminex; detects three Bordetella spp.
and 13 viral targets, including adenovirus, inuenza, parainuenza, rhinovirus, and RSV), the FilmArray Respiratory EZ
Panel (BioFire Diagnostics; detects coronavirus, adenovirus, ve
inuenza, human rhinovirus/enterovirus, parainuenza, RSV,
human metapneumovirus, B pertussis, M pneumoniae, and C
pneumoniae), the FilmArray Respiratory Panel (BioFire Diagnostics; detects four coronaviruses, adenovirus, ve inuenza,
human rhinovirus/enterovirus, four parainuenza viruses, RSV,
human metapneumovirus, B pertussis, B parapertussis M pneu-
moniae, and C pneumoniae), and the FilmArray Pneumonia
Panel (BioFire Diagnostics; detects eight viruses, 18 bacteria
associated with HAP and seven genetic markers of resistance).70
Additionally, serologic tests may also be used in the diagnosis of
pneumonia caused by atypical bacteria such as L pneumophila,
Mycoplasma pneumoniae, or Chlamydia pneumoniae because
they are dicult to culture in the laboratory.
2,3,70,71
In patients with HAP or VAP, semiquantitative analysis of
tracheal aspirates or sputum cultures or quantitative analysis
from BAL specimens may occasionally be performed to dierentiate between infection and colonization based on the history
of prior antibiotic use and the number of organisms recovered
in the sputum specimen.19 Diagnostic thresholds for pneumonia
based on colony counts recovered from a quantitative BAL specimen may dier among institutions. Studies evaluating quantitative BAL or PSB specimens for the diagnosis of HAP or VAP
use a diagnostic threshold between 103 and 105 CFU/mL of an
organism for the diagnosis of pneumonia.
2,19,70
Genitourinary Tract Infections
Urinary Tract Infections
Urinary tract infections (UTIs) are common infections, prompting >8 million oce visits and more than 100,000 hospitalizations per year.
patients because of the close proximity of the urethra (which
is shorter than in male patients) to the perirectal and vaginal
regions, which are both colonized with bacteria. Because of this
anatomic dierence, bacteria are able to easily ascend the urethra in female patients and potentially cause infection in the
bladder (cystitis) and upper urinary tract (pyelonephritis). In
addition, hospitalized patients (male and female) with indwelling urinary catheters are at increased risk for developing UTIs,
with approximately 20% of catheterized patients developing a
UTI, even with only short-term catheterization.
Under normal circumstances, urine within the bladder is
sterile because all anatomic sites within the urinary tract above
the urethra are not colonized with bacteria. However, the urethra is colonized with bacteria. If noninvasive urine collection
methods are used for specimen collection, urine travels through
the urethra and may inadvertently collect bacteria while passing through this nonsterile environment. erefore, diagnostic
criteria have been developed to discriminate between infection, bacterial colonization, or bacterial contamination based
on quantitative bacterial colony counts from urine cultures and
the presence of inammatory cells and epithelial cells in the
urinalysis.
Urine samples for urinalysis and culture can be collected
several ways. e most common method involves the collection of a clean-catch, midstream urine sample. Before obtaining
the sample, the patient should be instructed to clean and rinse
the periurethral area with a mild detergent and then retract the
labial folds or penile foreskin when beginning to urinate. e
patient should attempt to collect the urine in a sterile cup at the
midpoint of the urine stream, collecting the urine sample a few
seconds aer the start of urination.
Other methods for specimen collection involve invasive
procedures, such as obtaining urine via bladder catheterization
(straight catheter) or via suprapubic bladder aspiration. Both of
these methods avoid the potential contamination of the urine
specimen by the urethra because the urine is collected directly
from the bladder. In hospitalized patients with short-term
indwelling urinary catheters, urine specimens should be collected directly from the urinary catheter by aspirating the catheter port or tubing (representing freshly voided urine) rather than
obtaining the specimen from the collection bag (urine collected
over a period of time).
ing urinary catheters, the catheter should be exchanged with the
urine sample collected upon insertion of the new catheter.76 In
all cases, urine samples should be immediately transported to
the laboratory for processing.
Urine samples from women with acute uncomplicated cystitis are usually only evaluated using screening tests because the
results are rapidly available and are useful at excluding the presence of a UTI.72 e most common rapid screening tests include
commercially available reagent test strips, or urine dipsticks, that
72-74
72-75
UTIs are especially common in female
73,76
4,72,73,76
In patients with long-term indwell-
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 435
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contain the leukocyte esterase test and the nitrate reductase test,
and provide a negative predictive value of 98%.
72,73
e leukocyte
esterase test detects the presence of leukocyte esterase, which
is an enzyme found in neutrophils. e nitrate reductase test
detects the presence of urinary nitrite produced by the reduction
of nitrate by nitrate-reducing enzymes of common urinary tract
pathogens (primarily Enterobacterales).
72-74
Positive results from
either the leukocyte esterase test or nitrate reducatase test lead
to initiation of treatment for a UTI without the need for urine
culture in women with symptoms suggesting acute uncomplicated cystitis.
e urine from patients with recurrent UTIs, complicated/
upper tract UTIs, or catheter-associated UTIs is typically evaluated using a urinalysis (microscopic examination) and urine
culture. e urinalysis is a rapid test that involves the macroscopic and microscopic examination of the urine sample for
color, clarity, specic gravity, and the presence of protein, glucose, RBCs, WBCs, bacteria, and epithelial cells. e urinalysis is
performed either manually or with automated instruments. Urinalysis ndings suggestive of a UTI include specimen cloudiness
and the presence of pyuria (>10 WBC/mm3).
72-74
e detection
of pyuria, hematuria, proteinuria, or bacteriuria in the urinalysis may be an indication of infection, but none of these alone is
specic for infection. e presence of squamous epithelial cells
(>2 to 5 epithelial cells/mm3) in a urine sample suggests poor
specimen collection and possible contamination.
e urine culture remains the hallmark laboratory test for
the diagnosis of UTIs, with quantitative cultures providing the
most useful data for determining the clinical signicance of
isolated bacteria. To establish the diagnosis of a UTI, urine cultures from midstream urine samples should display >105 CFU
/mL of a single potential uropathogen with concomitant pyuria
on urinalysis; however, some women with symptomatic cystitis
may have lower colony counts of bacteria (103).73 Colony counts of
>103 CFU/mL with pyuria are considered clinically relevant in
urine specimens from patients with indwelling urethral catheters or intermittent catheterization, from men, or from chil-
72,75
dren.
Urine specimens obtained by suprapubic aspiration
that display >102 CFU/mL with pyuria are indicative of the
presence of infection.
72,73,76
Prostatitis
Bacterial prostatitis can present as an acute or chronic infection
that typically occurs in men >30 years of age.74 e diagnosis of
acute bacterial prostatitis is oen based on clinical presentation and the presence of bacteria in a urine specimen. Digital
palpation of the prostate and prostatic massage to express purulent secretions are not recommended for the diagnosis of acute
bacterial prostatitis because it may induce bacteremia. Conversely, the diagnosis of chronic bacterial prostatitis oen cannot be established based on clinical grounds alone because the
symptoms are nonspecic and the prostate is oen not acutely
inamed. erefore, the diagnosis of chronic prostatitis is classically established through the analysis of sequential urine and
prostatic uid cultures.
obtained for culture—one sample on initiation of urination
(VB-1) and one sample obtained at midstream (VB-2). Next,
74,77
Initially, two samples of urine are
prostate uid is obtained for culture by massaging the prostate
to produce expressed prostatic secretions. Lastly, a urine sample
(VB-3) is obtained aer prostatic secretions have been obtained
and sent for culture. e diagnosis of chronic bacterial prostati
tis is made when the expressed prostatic secretion sample contains > 10 times the quantity of bacteria cultured from VB-1 or
VB-2 or if the VB-3 contains 10 times the quantity of bacteria
cultured from VB-1 or VB-2.
74,77
Sexually Transmitted Diseases
Gonorrhea
Infection due to N gonorrhoeae is the second most common
notiable sexually transmitted disease (STD) reported in the
United States, with most infections involving the mucosa of the
cervix, the urethra, the rectum, and the pharynx.
caused by N gonorrhoeae include localized, uncomplicated, or
complicated genital infections (eg, urethritis, cervicitis, endo
metritis, pelvic inammatory disease [PID] in women, and urethritis or epididymitis in men), pharyngitis, anorectal infections,
and disseminated infection (eg, septic arthritis and meningitis)
in both men and women.
78,79
Women with genital tract infection
and patients with pharyngeal infection are oen asymptomatic,
while men with urethritis oen display symptoms of dysuria and
urethral discharge. In addition, patients with N gonorrhoeae are
oen coinfected with other STDs, such as Chlamydia trachoma-
tis, syphilis, or Trichomonas vaginalis; therefore, the diagnosis
and treatment of all possible STDs in the patient and their sexual partners are important public health considerations in the
control of STDs.
78
e diagnosis of infection due to N gonorrhoeae can be established using Gram-stained smears, culture, or nonculture techniques detecting cellular components (only NA amplication
tests [NAATs] are currently recommended for routine use; EIA
and DNA probe tests are no longer recommended) of urethral,
endocervical, or urine specimens (NAAT only) that detect cellular components of N gonorrhoeae.
4,78-81
A presumptive diagnosis of gonorrhea can be made using direct
microscopic examination of a clinical specimen using a Gram stain
and oxidase test, in which gram-negative, oxidase-positive diplococci are demonstrated.
78-81
In addition, the presence of neutrophils on a Gram stain of a urethral specimen is also helpful in
establishing the presumptive diagnosis of urethritis.79 e Gram
stain is both sensitive and specic for the presumptive diagnosis
of N gonorrhoeae as a point-of-care test for symptomatic men with
urethral discharge but is not as useful as a single diagnostic test
in asymptomatic men or when evaluating endocervical or pharyngeal specimens.
78,79
Additional tests, such as culture, should be
performed to conrm the identication of the organism.
Culture on selective media remains the diagnostic standard
for the identication of N gonorrhoeae.
79,80
mended for the diagnosis of gonorrhea from urethral, endocervical, vaginal, pharyngeal, or rectal swab (plastic or wire shas
with rayon, Dacron, or calcium alginate tips) specimens and
should be performed on specimens from all patients (and sexual partners) with suspected gonococcal infections.79 Culture is
also used as a conrmatory test in patients who have suspected
78,79
Infections
Culture is recom-
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