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gonorrhea based on positive Gram-stained smears or nonculture
tests if the specimen has been adequately maintained. However,
culture is not optimal in all circumstances due to the tenuous
viability of the organism during storage and transport, which is
what led to the development of nonculture tests for the detection of gonorrhea.79 Occasionally, susceptibility testing is performed on N gonorrhoeae isolates, especially in patients with
suspected or documented treatment failure, to guide the choice
of antibiotic therapy, as well as for epidemiologic purposes.78 In
either case, patients are typically given empiric therapy with an
antibiotic that demonstrates excellent activity against gonorrhea,
keeping in mind that the incidence of β-lactamase-producing,
penicillin-resistant gonococci is increasing.
In many clinical settings, nonculture tests for the detection
of N gonorrhoeae have replaced traditional culture. Nonculture
tests include NAATs, which are able to amplify organism-specic
DNA sequences, and the NA hybridization (probe) test, which
hybridizes any complementary rRNA that is present in the specimen (cannot dierentiate organisms).
78,79
Several NAATs for the
detection of N gonorrhoeae are commercially available and have
been designed to detect RNA or DNA sequences using amplication techniques (even on nonviable organisms). ese tests
have been FDA-approved for the detection of N gonorrhoeae in
endocervical and vaginal swabs from women, urethral swabs
from men, and urine samples from men and women; because
the tests are dierent, the product information for each individual test should be consulted to dictate the collection methods and clinical specimen type that is suitable for each test.
78,79
ese tests are also useful for the detection of N gonorrhoeae
from clinical specimens that have not been adequately maintained during transport or for collection for culture methods to
be used. e major drawback of nonculture techniques for the
detection of gonorrhea is that they cannot provide information
on antibiotic susceptibility of the organism.
81
Chlamydia
Chlamydia trachomatis is the most frequently reported infectious disease in the United States, with >1.3 million cases
reported to the Centers for Disease Control and Prevention in
78,79
2010.
municable disease in the United States, with the highest prevalence in persons aged ≤24 years.78 C trachomatis can cause a
number of infections, including cervicitis, endometritis, and
PID in women; and urethritis, epididymo-orchitis, prostatitis,
and proctitis (via receptive anal intercourse) in men.78 Infection with C trachomatis is also thought to contribute to female
infertility and ectopic pregnancies. It is estimated that more than
$500 million is spent annually on the direct costs associated with
the management of C trachomatis infections.
so screening is necessary to detect the presence of the organism.
thought that the current rates of reporting underestimate the
true incidence of infection due to this organism. Chlamydia
screening is now recommended annually in all sexually active
women aged <25 years and other women at increased risk for
infection (eg, new sexual partner, multiple sexual partners,
Infection with C trachomatis is now a reportable com-
79
Most patients with chlamydial infections are asymptomatic,
78,79
Because of the asymptomatic nature of chlamydia, it is
sexual partner with an STD).78 In addition, chlamydia screening is also recommended in patients with other STDs because
chlamydia oen coexists with other STD pathogens.
Culture and nonculture methods are available for the detection of chlamydia. Culture involves the inoculation of the biologic specimen onto a conuent monolayer of cells that support
the growth of C trachomatis. e culture is evaluated at 24 to
72hours for the presence of intracellular inclusions using a uorescent monoclonal antibody stain, which occur as a result of
C trachomatis infection.79 Cell culture is not routinely used by
most laboratories because of lack of standardization, technical diculty, cost, and length of time to yield results (at least
48 hours). erefore, other nonculture approaches for the laboratory diagnosis of chlamydia have been developed, including
the direct uorescent antibody (DFA) test and NAATs.
Direct uorescent antibody testing involves the staining of a
biologic specimen with a uorescein-labeled monoclonal antibody that binds to C trachomatis-specic antigens (elementary
bodies).80 If the patient is infected with C trachomatis, the anti-
bodies will react with the elementary bodies of the chlamydia in
the secretions to produce uorescence. DFA tests require signicant technologist time for performance, so they are typically only
used as a conrmatory test to other antigen detection tests.
e other nonculture test used for the detection of C tracho-
matis is the NAAT, which has largely replaced tissue culture and
DFA testing because of greater sensitivity and specicity.
Several commercially available NAATs for the detection of C tra-
chomatis have been designed to detect RNA or DNA sequences
using PCR, ligase chain reaction, and various amplication techniques. ese tests have been FDA approved for the detection
of C trachomatis in endocervical or vaginal swabs from women,
urethral swabs from men, and rectal swab or rst catch urine
samples from men and women.
78,79
Syphilis
e spirochete T pallidum is the causative pathogen of an STD
known as syphilis. ere are a number of clinical manifestations
and stages of syphilis that are based primarily on presenting
symptoms and the natural history of the infection
1.
Primary syphilis: characterized by painless ulcers called
chancres that are typically located at the site of inoculation
or initial infection (usually in genital area) and spontaneously
resolve over 1 to 8 weeks.
2.
Secondary syphilis: characterized by systemic symptoms,
including fever, weight loss, malaise, headache, lymphade-
nopathy, and a mucocutaneous skin rash (generalized or
localized, oen involving the palms or the soles of the feet)
resulting from hematogenous or lymphatic spread of the
organism. If untreated, the manifestations resolve within 4
to 10 weeks.
3.
Latent syphilis: occurs aer secondary syphilis, in which the
organism is still present, but the patient is without symptoms.
Latent syphilis acquired within the preceding year is catego-
rized as early latent syphilis, whereas syphilis acquired more
than 1 year ago or of unknown duration is categorized as late
latent syphilis. is subclinical infection can be detected only
by serologic tests.
46,78,81
80
80
78,79,81
:
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 437
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4.
Late/tertiary syphilis and neurosyphilis: occurs in approximately 35% of untreated patients up to 10 to 25 years aer
initial infection; clinical manifestations are caused by progressive inammatory disease that can involve the CNS (categorized as neurosyphilis) or outside the CNS (referred to as
tertiary syphilis) including cardiovascular lesions (ascending aorta) and granuloma-like lesions (gummas) in the skin,
bone, or visceral organs.
T pallidum cannot be grown in culture; therefore, the diagnosis of syphilis involves the direct detection of the spirochete
in biologic specimens by microscopy or the detection of treponemal-specic antibodies using serologic testing.
Direct detection methods can be performed on appropriate clinical specimens obtained from suspicious genital or skin
lesions, including lesion exudate or tissue. e direct detection
of T pallidum using dark-eld microscopy involves the immediate examination (within 20 minutes of collection) of the biologic specimen under a microscope with a dark-eld condenser,
looking for the presence of motile spirochetes, where T pallidum
appears as 8- to 10-µm spiral-shaped organisms.
4,46,81
Another
test for the direct detection of T pallidum is the direct uorescent antibody (DFA-TP) test in which the biologic specimen is
combined with uorescein-labeled monoclonal or polyclonal
antibodies specic for T pallidum and examined by uorescence microscopy.
46,78
e interaction between the antibodies
and treponemal-specic antigens produces uorescence that can
be visualized using microscopy.
ere are two types of serologic tests that are used for the
diagnosis of syphilis – nontreponemal and treponemal antibody
tests. e use of only one type of serologic test is not sucient
for the diagnosis of syphilis (may result in false-negative or falsepositive diagnoses), so persons with a reactive nontreponemal
test result should undergo treponemal antibody testing to conrm the diagnosis.
78
e nontreponemal antibody tests include the Venereal Disease Research Laboratory (VDRL) test and the rapid plasma
reagin (RPR) test.
46,81
Both the VDRL and RPR measure the
presence of reagin, an antibody-like protein produced in patients
with syphilis. However, reaginic antibodies are also produced
in patients with other infections and conditions including autoimmune diseases, leprosy, TB, malaria, pregnancy, and injection
drug use, so false-positive RPR results may occur.
46,81
Both the
RPR and VDRL tests are occulation tests in which visible clumps
are produced in the presence of the reagin antibody (T pallidum)
in the submitted specimen. For the VDRL test, the biologic specimen (serum, CSF) is combined with cardiolipin-lecithin coated
cholesterol particles on a glass slide and examined microscopically.46 If the reagin antibody is present in the biologic specimen,
visual clumping occurs and is reported as reactive (medium and
large clumps). e VDRL can be performed on serum and CSF as
e RPR test is a modication of the VDRL test and is commercially available as a reaction card. Serum from the patient
is placed on the reaction card and observed for clumping. e
RPR result is quantied by evaluating dilutions of the biologic
specimen for reactivity, with the highest dilution that produces
a fully reactive result being reported as the RPR titer (eg, 1:8 or
1:32). e RPR titer is also used to monitor a patient’s response
to therapy, where a 4-fold decline in titer 6 to 12 months aer
therapy would be suggestive of response. e RPR is easier to
perform than the VDRL and is used by many laboratories and
blood banks for routine syphilis screening. However, the RPR
should not be used for the analysis of CSF specimens.
e nontreponemal antibody detection tests are nonspecic,
so they are most useful for screening for the presence of syphi-
46,81
lis.
Because it takes several weeks for the development of
reagin antibodies aer exposure to syphilis, false-negative results
(up to 25% of patients with primary syphilis) can occur in the
early stages of the disease. In addition, false-positive results (up
to 1% to 2%) can also occur because of the numerous other
conditions where reagin antibodies are produced.
3,46
erefore,
a positive RPR or VDRL test result should be conrmed with
the uorescent treponemal antibody absorption (FTA-ABS) or
the microhemagglutination T pallidum (MHA-TP) test, both of
which measure the presence of treponemal-specic antibodies.
e other type of serologic test measures the presence of
treponemal antibodies and includes the FTA-ABS test and the
MHA-TP test.
46,78,81
In the FTA-ABS test, the patient’s serum or
CSF is initially absorbed with non-T pallidum antigens to reduce
cross-reactivity and then applied to a slide on which T pallidum
organisms have been xed followed by addition of a uorescein-conjugated antihuman antibody for detection of specic
antitreponemal antibodies. e amount of uorescence is subjectively measured by the laboratory technician and reported as
reactive, minimally reactive, or nonreactive. erefore, this test
is dicult to standardize among dierent laboratories. Because
this test is also fairly expensive, it is primarily used to verify
the results of a positive VDRL or RPR, rather than as a routine
screening tool.
46,81
e FTA-ABS test can detect antibodies earlier in the course of syphilis than nontreponemal tests and, once
positive, remains positive for the life of the patient.
e MHA-TP test is performed using erythrocytes from a
turkey, sheep, or other mammal that have been coated with
treponemal antigens. ese erythrocytes are then mixed with
the patient’s serum and observed for agglutination, which signies the presence of antibodies directed against T pallidum. e
results are reported as reactive (positive) or nonreactive (negative). Lastly, EIA tests and PCR-based tests for the detection of
T pallidum are being evaluated as screening or conrmatory
tests for the diagnosis of syphilis, especially for patients in whom
serologic testing is not reliable.
46,81
a quantitative test in which dilutions of the biologic specimen can
be evaluated for reactivity; the dilution that produces a fully reactive result is reported as the VDRL titer (eg, 1:8 or 1:32). erefore, the VDRL titer can be used to monitor a patient’s response
to therapy. e high titers present in untreated disease (eg, 1:32)
traditionally decrease 4-fold within 6 to 12 months of treatment
and become undetectable in 1 to 2 years.
Trichomonas
Infection caused by the protozoan T vaginalis is the most common, nonviral STD in the United States, aecting 3.7 million
people.78 T. vaginalis is typically diagnosed through detection
of actively motile organisms during microscopic examination of wet mount preparations of vaginal secretions, urethral
438 BASIC SKILLS IN INTERPRETING LABORATORY DATA
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discharge, prostatic uid, or urine sediment.
61,78,81
Because the
sensitivity of the wet mount preparation is 50% to 80%, other
diagnostic tests have been developed for the detection of T vagi-
nalis to enhance diagnostic yield, sensitivity, and specicity.
78,81
Culture using Diamond’s medium is considered the diagnostic gold standard test because it is associated with >80% sensitivity; however, culture methods require proper collection and
rapid inoculation for best results, so it is not routinely performed
by most laboratories.81 Several rapid antigen detection methods are commercially available for the diagnosis of infection
caused by T vaginalis that are easy to perform and employ different assays (IFA and capillary ow ICA).61 Lastly, NA detection
methods are highly sensitive and specic tests for the detection
of Trichomonas and include direct DNA probe Arm VPIII
(BD) and the APTIMA T vaginalis Assay (Hologic-GenProbe,
SanDiego, CA).
61,78
Assessing Sterile Body Fluids for
Presence of Infection
Sterile body uids such as pericardial uid (pericarditis), pleural uid (empyema), synovial uid (septic arthritis), and peritoneal uid (peritonitis) can be analyzed for the presence of
infection. e specimens should be aseptically obtained by needle aspiration, placed in sterile collection tubes, and immediately transported to the laboratory for uid analysis and culture.
Approximately 1 to 5 mL of uid should be obtained when analyzing pericardial, pleural, or synovial uid, while up to 10 mL
of peritoneal uid is required for the diagnosis of peritonitis.82
All sterile uids should be processed for cell count (establishing the presence of WBCs with dierential), chemistry (protein
and glucose), direct microscopic examination including Gram
stain (presence of bacteria), and culture. For pleural and synovial uids, specic criteria are available to aid in the diagnosis of infection (Tables18-13 and 18-14).
82-88
Peritoneal uid
characteristics that may be suggestive of peritonitis include a
WBC of >250 cells/mm3, a lactate concentration >25 mg/dL,
apH <7.35, a uid/blood glucose ratio of <0.7 (in TB peritonitis), and an elevated protein concentration (except in patients
with cirrhosis).
89,90
e diagnosis of infection in each of these
sites should be established based on the presence of WBCs and
other characteristic chemistry abnormalities in the sterile uid
specimen, the growth of a pathogenic organism from the cultured material, and the characteristic signs and symptoms of
infection at that site.
ACUTE PHASE REACTANTS
ANDINFECTION
Chapters16 and 20 provide information on the background,
normal range, and clinical use of acute phase reactants such
as the ESR, CRP, and procalcitonin in the diagnosis of inammatory diseases. e ESR and CRP may also be elevated in the
presence of infection.
not dierentiate between inammatory or infectious processes
because they increase in response to tissue injury of any cause.
However, the ESR and CRP are oen elevated in the presence
of infection, with increased levels reported in bacterial otitis
media, osteomyelitis, endocarditis, PID, septic arthritis, prosthetic joint infections, and infections in transplant patients, and
they may serve as an adjunctive modality to aid in the diagnosis
91-96
Elevations in the ESR and CRP do
TABLE 18-13. Pleural Fluid Findings and Interpretation
EXUDATIVE
(SUGGESTIVE OF INFECTION
TRANSUDATIVE (SUGGESTIVE
OF CONGESTIVE HEART FAILURE,
CIRRHOSIS)
Appearance
pH
3
)
Source: References 82–85.
>7.2 <7.2
<200 ≥200
<0.6 >0.6
<3 >3
<0.5 >0.5
>60 (same as serum) <40–60
<10,000 >10,000
<
SUCH AS EMPYEMA, MALIGNANCY,
PANCREATITIS WITH ESOPHAGEAL
PERFORATION, SLE)
If infectious, depends on pathogen
CHAPTER 18 • InfECTIous DIsEAsEs: BACTERIA 439
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TABLE 18-14.
PURULENT
NORMAL
3
)
<150–200 <2,000
NONINFLAMMATORY
(OSTEOARTHRITIS,
TRAUMA, AVASCULAR
NECROSIS, SLE,
EARLY RHEUMATOID
ARTHRITIS)
INFLAMMATORY
(RHEUMATOID ARTHRITIS,
SPONDYLOARTHROPATHIES,
VIRAL ARTHRITIS, CRYSTALINDUCED ARTHRITIS)
2,000–50,000
(BACTERIAL
INFECTION,
TUBERCULOUS
INFECTION,
FUNGAL
INFECTION)
>50,000
No predominance
1.3–1.8 3–3.5
< > >
>3.5 >3.5
Normal Normal 70–90
Source: References 86–88.
of these infections.
91-96
ESR levels of >100 mm/hr have a high
specicity for the presence of infection, malignancy, or arteritis.92 Serial measurement of the ESR, and especially the CRP, may
also be useful in assessing the response to antibiotic therapy in
the treatment of deep-seated infections such as endocarditis or
osteomyelitis.
91-96
Procalcitonin is the precursor of calcitonin, a calcium regu-
in the CNS, infectious complications of burns and pancreatitis,
and polytrauma.
in diagnostic accuracy, usefulness in guiding antibiotic discontinuation, and cost eectiveness. Additional research is needed
to further dene the role of procalcitonin in the diagnosis and
management of dierent patient types, infections, and clinical
settings.
latory hormone, which is also an acute phase reactant that is
produced in response to systemic inammation.
91,97-99
During
SUMMARY
infection, the metabolism of procalcitonin is altered in response
to toxins and cytokines from bacteria, malaria, and some fungi
(not viruses).
97-100
As procalcitonin accumulates, its levels
become detectable within 2 to 4 hours of infection and peak at
6 to 24 hours, with the extent of production correlating with bacterial load and severity of infection.
97,98
It was originally believed
that procalcitonin levels increased in response to tissue injury
or sepsis induced only by infection; however, levels of procalcitonin may be elevated in other inammatory diseases or situations, such as autoimmune diseases, severe trauma, cirrhosis,
pancreatitis, burns, cardiac surgery, cardiac arrest, certain types
of cancer, receipt of some conditioning agents prior to stem cell
transplantation, and hypotension during surgery.
91,92,97-100
e use of procalcitonin in the diagnosis of infection has
been evaluated in numerous studies involving dierent patient
types, infections, and clinical settings, with several procalcitonin-based algorithms being developed to (1) determine the
presence of infection/guide initiation of antibiotic therapy,
(2) evaluate the ecacy of empiric antibiotic therapy, and
(3)determine when antibiotic therapy can be deescalated or
discontinued during the treatment of an infection.
97,98
Procalcitonin levels that correlate with the presence of infection have
not been clearly dened for all infection types and clinical settings, but it does appear as if procalcitonin levels <0.1 mcg/L
(eg, undetectable) exclude the presence of infection.98 In the past
decade, the role of procalcitonin has been studied in the context
of sepsis and critically ill patients, lower respiratory tract infections, chronic obstructive pulmonary disease, acute infections
Although infectious disease is a rapidly changing eld because
of new challenges and technological advances, the diagnosis of
infection is highly dependent on the proper performance and
interpretation of numerous laboratory tests. For example, the
Gram stain is a readily available, invaluable tool for examining
clinical specimens for the presence of bacteria. Culture of clinical
specimens using appropriate growth media allows for the cultivation and identication of many infecting bacteria, which oen
takes 24 to 48 hours. Numerous rapid diagnostic tests are now
available for the identication of bacteria directly from clinical
specimens, such as blood, stool, respiratory secretions, or body
uids, which substantially decrease the time to organism identication when compared with traditional bacterial culture and
identication methods.3 Susceptibility tests for rapidly growing
aerobic bacteria are commonly performed using an automated
microdilution or a manual disk diusion method. Bacterial
susceptibilities to various antimicrobial agents are reported as
S, I, and R. National standards for susceptibility testing are available and help guide the performance of the tests, the choice
of antimicrobial agents to evaluate for susceptibility, and the
reporting procedures of susceptibility tests by the clinical microbiology laboratory. Empiric antimicrobial therapy is typically
chosen based on the suspected site and subsequent potential
causative organisms of infection (using local or regional susceptibility information). Once the results of bacterial culture
and susceptibility testing are available, antimicrobial therapy is
de-escalated, if possible, to a more targeted (directed) regimen
97-99
<40–50
101
ese studies demonstrate a wide variability
440 BASIC SKILLS IN INTERPRETING LABORATORY DATA
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based on the susceptibility prole of the infecting organism in
conjunction with patient-specic (eg, clinical condition, site of
infection, drug allergies, and renal function) and infection-specic information.
Lastly, several infection types (eg, meningitis, UTIs) and
certain pathogens (eg, B burgdorferi and L pneumophila) oen
require specialized laboratory testing to aid in the identication
of the infecting organism. e clinician should be aware of the
diagnostic tests currently available for these infections.
LEARNING POINTS
1.
What methods for antimicrobial susceptibility testing are used by most microbiology laboratories in the
United States, and how is this information conveyed to
the clinician?
ANSWER:-
ods for antimicrobial susceptibility testing to accurately determine the activity of antibiotics against many different types of
bacteria (eg, aerobic, anaerobic, and fastidious). However, most
laboratories predominantly use automated broth microdilution
pared, disposable microtiter trays or cassettes for antimicrobial
susceptibility testing that can test the susceptibility of multiple antibiotics simultaneously while decreasing cost and labor.
Although many microbiology laboratories perform rapid diag-
of pertinent resistant gene markers, antimicrobial susceptibility
testing (using automated microdilution methods) is still being
results for each bacteria are compiled in a report that contains
(especially with automated broth microdilution methods), and
located in the patient’s medical chart (electronic or paper) and in
2. Is the antibiotic with the lowest MIC on an individual sus-
ceptibility report always the best antibiotic choice in the
treatment of an infection?
ANSWER:
susceptibility report may not always be the best choice for the
tion of the in vitro activity of the antibiotic against an organism,
other issues must be considered when choosing an antibiotic once
susceptibility results have returned (these are the same consid
-
age range, resulting in unique serum and site concentrations. An
antibiotic might display potent in vitro active against a particular organism but may be ineffective in vivo because of poor penetration to the site of infection. Thus, both the site of infection
Other things that should also be considered when selecting an
antibiotic include the pharmacodynamic parameter that corretionship for each antibiotic-organism combination as well as the
population pharmacokinetic data of the antibiotic and bacteria
percentage of time the antibiotic will achieve adequate pharmacodynamic indices for the treatment of that organism in a simulated population), if available, should be reviewed to determine if
patients with clinical success versus clinical failure? Lastly, other
factors, such as patient characteristics (eg, pregnancy, comorbidities, allergies), drug characteristics (eg, administration schedule,
lary, should also be considered when selecting an antibiotic.
3.
What are the major laboratory tests that are used in the
diagnosis of UTIs, meningitis, pneumonia, and septic
arthritis?
ANSWER: In patients with signs and symptoms suggestive of a
eterized specimen, suprapubic aspiration) is usually sent to the
laboratory for microscopic analysis (urinalysis) and culture. In
patients with signs and symptoms suggestive of meningitis, a
general appearance, glucose concentration, protein concentra-
addition, depending on the medical history of the patient, spe-
signs and symptoms suggestive of pneumonia, a sputum sam
adequacy evaluation, Gram stain and culture, and, occasionally,
S. pneumoniae urinary antigen. In patients with suspected septic
of bacteria), and culture. Patients with septic arthritis may also
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Infectious Diseases: Fungi, Viruses,
https://t.me/med1917
and Mycobacteria
19
OBJECTIVES
After completing this chapter, the
reader should be able to
•
Describe the basic methods that may
be used in the diagnosis of invasive
fungal infections
•
Discuss the laboratory tests that
are commonly used in the diagnosis
of common viral infections such
syncytial virus
•
Discuss the laboratory tests that
are commonly used in the diagnosis
describe the laboratory tests that are
commonly used in the assessment
infection
•
Discuss the laboratory tests that
are commonly used in the diagnosis
of infections due to Mycobacterium
tuberculosis and nontuberculous
mycobacteria
DOI 10.37573/9781585286423.019
Rodrigo M. Burgos, Sharon M. Erdman,
and Keith A. Rodvold
e assessment, diagnosis, and treatment of a patient with a fungal, viral, or mycobacterial infection can be challenging tasks for most clinicians. is may be partly due
to the nonspecic presentation and clinical recognition of infectious processes; the
continuously changing taxonomy and diagnostic procedures of infecting organisms;
the emergence of multidrug resistant pathogens such as Candida auris and Aspergil-
lus tanneri; the understanding of drug resistance mechanisms and interpretation of
susceptibility characteristics; and the recognition of the potential role of older and
newer therapeutic agents in the prevention and/or treatment of these infections.
It is important to note that diagnostic tests for many infectious diseases, particularly
the diagnosis of COVID-19 caused by a coronavirus (ie, SARS-CoV-2) and human
immunodeciency virus (HIV) infection, are continuously evolving to reect technological advances in laboratory procedures.
sequencing- based identication methods, and/or proteomics (eg, matrix- assisted
laser desorption/ionization- time- of- ight mass spectroscopy [MALDI-TOF MS])
are transforming diagnostic microbiology and becoming rapidly accepted detection
techniques of fungal, viral, and mycobacterial pathogens.
is chapter describes the laboratory tests commonly used in the diagnosis of
common infections due to fungi, mycobacteria, and viruses. Laboratory tests used
in the diagnosis of viral hepatitis are addressed in Chapter15.
8,9
Nucleic acid amplication test (NAAT),
10-13
FUNGI
Fungi are classied as one of the six kingdoms of life. ere are approximately 500
named species of fungi that are known to cause infection in humans and other vertebrate animals.14 Approximately 50 fungal species are associated with infections in
healthy subjects and most fungal infections occur in immunocompromised or debilitated patients by organisms that are part of the normal human ora. However, an
increasing number of serious and life- threatening opportunistic infections are being
caused by ubiquitous environmental molds.
Some of the most challenging and frustrating aspects of diagnostic medical mycology are the terminology, taxonomy, classication, and nomenclature of fungi.
example, the correct name for a species of fungi is that which was published earliest and
met the requirements in the International Code of Botanical Nomenclature for algae,
fungi, and plants (http://www.iapt- taxon.org/nomen/main.php). Since January 1, 2013,
the concept of “One Fungus/One Name” has been applied, eliminating the use of dual
names (eg, anamorph and teleomorph names of fungal species). All subsequent names
are considered synonyms; however, exceptions do exist, particularly when a later name
is more commonly used than the earlier name or if research requires a species to be
transferred to a dierent genus. Changes have occurred within the kingdom fungi (eg,
the phylum Zygomycota is no longer recommended because of polyphyletic characteristics). Because of these issues, the reader is referred to the latest editions of standard
microbiology textbooks and reference manuals (eg, Manual of Clinical Microbiology,
American Society for Microbiology Press) and the following links (http://www.myco
bank.org/; https://mycology.adelaide.edu.au/; http://www.indexfungorum.org/names
/names.asp; https://www.fungaltaxonomy.org/; http://www.clinicalfungi.org) for more
detailed information and updates on taxonomy and classications of fungi.
tion, a glossary of common mycological terms is oen included.
14,15
14,15
For
In addi-
1-8
445
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