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### 217 Pathogenesis, Diagnosis, and Treatment of Fungal Infections

covers and a face shield and/or goggles. If available, N-95 or N-100 respi­
rators may be used to further limit infection risk. Positive-air-pressure 
respirators should be considered for high-risk medical procedures, 
such as intubation or suctioning. Medical equipment used in the care of 
an infected patient, such as gloves or syringes, should never be reused. 
Because filovirions are enveloped, disinfecting with detergents (e.g., 
1% sodium deoxycholate, diethyl ether, or phenolic compounds) is 
relatively straightforward. Bleach solutions are recommended at 1:100 
for surface disinfection and 1:10 for application to excreta or corpses. 
Whenever possible, potentially contaminated materials should be auto­
claved, irradiated, or destroyed.
Emerging from research conducted during the 2013–2016 EVD 
outbreak in Western Africa, a vaccine based on a recombinant vesicu­
lar stomatitis Indiana virus expressing EBOV GP1,2 (rVSV-ZEBOV/
Ervebo) was the first filovirid vaccine approved for use in the United 
States and the European Union (EU). It is now widely deployed in both 
a reactive-ring vaccination strategy, targeting close contacts and their 
contacts in EVD outbreak settings, and for the preexposure vaccination 
of health care workers in at-risk regions. More recently, a heterologous 
dose vaccine candidate incorporating EBOV GP1,2 into an adenovirus 
vector (Ad26.ZEBOV-GP/Zabdeno) followed by a vaccinia virus vec­
tor incorporating multiple filovirid antigens (MVA-BN-filo/Mvabea) 
has been shown to be safe and immunogenic in humans. Though 
evaluation of efficacy in a clinical trial has not been possible, immu­
nobridging data gained during nonhuman primate experimentation 
led to regulatory authorization in the EU under “exceptional circum­
stances”; the two-dose requirement likely limits current use to proac­
tive preexposure prevention in “peri-outbreak” settings rather than 
reactive “in-outbreak” reactive strategies. Development and evaluation 
of this and other vaccine candidates continue toward complementary 
preventive approaches for non-outbreak or peri-outbreak settings, 
with emphasis on the durability of immune responses and increases in 
preventive breadth toward other filovirids.
Even in the absence of high-level evidence, expert consensus informs 
the targeted use of EBOV-specific vaccine or postexposure prophylaxis 
(PEP) to prevent infection or disease in health care workers considered 
to have had a high-risk EBOV exposure (e.g., after needlestick injury). 
Evidence is needed to inform the use of PEP in high-risk contacts in 
the field outbreak setting. For male survivors, abstinence from sexual 
activity with a partner for at least 12 months after disappearance of 
clinical signs is recommended, unless testing proves semen to be free of 
filovirid RNA. (The use of condoms is generally recommended for all 
sexual activities.) Reproductive tract and CNS tissues, including ocular 
tissues and fluids from survivors, should be handled with appropriate 
precautions until demonstrated to be filovirid-RNA free. The role of 
filovirid-specific therapeutics in the prevention or treatment of filoviral 
persistence is unclear.
■
■FURTHER READING
Cnops L et al: Essentials of filoviral load quantification. Lancet Infect 
Dis 16:e134, 2016.
Crozier I et al: The evolution of medical countermeasures for Ebola 
virus disease: Lessons learned and next steps. Vaccines (Basel) 
10:1213, 2022.
Dudas G et al: Virus genomes reveal factors that spread and sustained 
the Ebola epidemic. Nature 544:309, 2017.
Hoenen T et al: Therapeutic strategies to target the Ebola virus life 
cycle. Nat Rev Microbiol 17:593, 2019.
Jacob ST et al: Ebola virus disease. Nat Rev Dis Primers 6:13, 2020.
Kuhn JH et al: Filoviridae, in Fields Virology, Vol 1, 7th ed, PM Howley 
et al (eds). Philadelphia, Wolters Kluwer/Lippincott Williams & 
Wilkins, 2020, pp 449–503.
Matz KM et al: Ebola vaccine trials: Progress in vaccine safety and 
immunogenicity. Expert Rev Vaccines 18:1229, 2019.
Mulangu S et al: A randomized, controlled trial of Ebola virus disease 
therapeutics. N Engl J Med 381:2293, 2019.
Regules JA et al: A recombinant vesicular stomatitis virus Ebola 
vaccine. N Engl J Med 376:330, 2017.

Section 16	Fungal Infections
Michail S. Lionakis, John E. Edwards, Jr.

Pathogenesis, Diagnosis, 

and Treatment of Fungal 
Infections
DEFINITION AND ETIOLOGY
In recent decades, human fungal infections have dramatically increased 
worldwide as a result of the AIDS pandemic, the widespread use of 
antibacterial agents, and the introduction of cytotoxic agents and 
precision medicine biologics for the treatment of autoimmune and 
neoplastic diseases and for use in patients undergoing solid organ 
transplantation or hematopoietic stem cell transplantation. Moreover, 
of great concern has been the recent rise in fungal infections caused 
by drug-resistant species, such as azole- and/or echinocandin-resistant 
Candida glabrata and Candida auris and azole-resistant Aspergillus 
fumigatus. Among the ~5 million fungal species, only a few cause 
human infections (Table 217-1).
Fungal infections are classified as mucocutaneous and deep organ 
infections on the basis of anatomic location and as endemic and opportu­
nistic infections on the basis of epidemiology. Mucocutaneous infections 
can cause serious morbidity but are rarely fatal. Deep organ infections 
cause severe illness and often carry a high mortality rate. The endemic 
mycoses are caused by fungi that are not part of the normal human 
microbiota but are environmentally acquired. The opportunistic myco­
ses are caused by fungi (Candida, Aspergillus) that often are components 
of the human microbiota and whose ubiquity in nature renders them 
easily acquired by immunosuppressed hosts (Table 217-1). Opportunis­
tic fungi cause serious infections when impaired host immune responses 
allow the organisms to transition from commensals to invasive patho­
gens. Endemic fungi typically cause self-limited disease in immunocom­
petent hosts but severe illness in immunosuppressed patients.
CHAPTER 217
Pathogenesis, Diagnosis, and Treatment of Fungal Infections 
Fungi are morphologically classified as yeast, mold, and dimorphic. 
Yeasts are seen as round single cells or budding organisms. Molds grow 
as filamentous forms called hyphae both at room temperature and in 
tissue. Aspergillus, Mucorales, and dermatophytes that infect skin and 
nails are mold fungi. Variations exist within this classification system. 
For instance, when Candida infects tissue, both yeasts and filamen­
tous forms (pseudohyphae) may be present (except in the cases of C. 
glabrata and C. auris, which form only yeasts in tissue); in contrast, 
Cryptococcus exists only in yeast form. Dimorphic is the term used to 
describe fungi that have two forms; they grow as yeasts or large spheri­
cal structures in tissue but as filamentous forms at room temperature 
in the environment (Table 217-1).
Patients acquire deep organ infection by molds and endemic 
dimorphic fungi via inhalation. Skin dermatophytes are primarily 
environmentally acquired, but human-to-human transmission may 
also occur. The commensal Candida invades deep tissues from sites of 
mucocutaneous colonization, usually in the gastrointestinal tract or the 
skin in the case of C. auris.
In this chapter, we outline general principles of immunology, diagno­
sis, and treatment related to the most common human fungal infections.
■
■PATHOGENESIS
In the past decade, our understanding of fungal recognition pathways 
and of tissue-specific innate and adaptive antifungal host defense 
mechanisms has markedly expanded. A major breakthrough has been 
the discovery and functional characterization of the C-type lectin recep­
tor/spleen tyrosine kinase/caspase recruitment domain–containing 

protein 9 (CLR/SYK/CARD9) signaling pathway, which mediates 
fungal polysaccharide recognition and orchestrates proinflamma­
tory mediator production, leukocyte recruitment, inflammasome

TABLE 217-1  Major Fungal Infections, Associated At-Risk Patient Populations, and Diagnostic Tests
INFECTION (MOST COMMON 
FUNGAL GENERA AND SPECIES)
CLINICAL SYNDROME(S)
RISK FACTOR(S)
DIAGNOSTIC TEST(S)
Mold (Filamentous) Fungi
Aspergillosis
(Aspergillus fumigatus, 

A. terreus, A. flavus, A. niger, 

A. nidulansa)
Pneumonia or 
disseminated infection
ABPA
Keratitis
Neutropenia, glucocorticoids, 
HSCT, post-influenza or 
COVID-19, BTK inhibition
Atopic individuals
Direct inoculation
Mucormycosis
(Rhizopus, Rhizomucor, 

Mucor, Cunninghamella, and 
Lichtheimia spp.)
Sinopulmonary infection
Rhinocerebral infection
Necrotizing skin infection
Neutropenia, HSCT
Diabetic ketoacidosis
Direct inoculation (e.g., 
tornado victims)
Fusariosis
(Fusarium solani, F. oxysporum)
Pneumonia or 
disseminated infection
Keratitis
Neutropenia
Direct inoculation
Scedosporiosis
(Scedosporium apiospermum)
Pneumonia or 
disseminated infection
Neutropenia, glucocorticoids, 
HSCT
Phaeohyphomycosis
(Cladophialophora, Alternaria, 
Phialophora, Rhinocladiella, 
Exophiala, and Exserohilum spp.)
Sinopulmonary, CNS, or 
disseminated infection
Skin infection
Allergic sinusitis
HSCT, neutropenia, 
glucocorticoids, healthy 
individuals (for CNS), TNF-α 
inhibition
Direct inoculation
Atopic individuals
Dermatophytosis
(Trichophyton, Microsporum, and 
Epidermophyton spp.)
Skin and nail infections
Healthy individuals
Culture or microscopic examination of scrapings or clippings: chains 
of arthrospores (diagnostic)
PART 5
Infectious Diseases
Eumycetoma
(Madurella mycetomatis)
Skin and subcutaneous 
infections
Healthy individuals
Culture and macroscopic and histologic examination of grains 
harvested from biopsy or aspiration
Yeast Fungi
Mucosal candidiasisc
Oropharyngeal or 
esophageal candidiasis
Vulvovaginal candidiasis
AIDS, glucocorticoids
Antibiotic use
(Candida albicans, C. glabrata)
Invasive candidiasisc
Candidemia
Disseminated infection 
(spleen, liver, kidney, eye, 
heart, CNS)
Critical illness (ICU)
Neutropenia, glucocorticoids
(C. albicans, C. glabrata, 

C. parapsilosis, C. tropicalis, 

C. auris)
Cryptococcosis
(Cryptococcus neoformans, 
C. gattii)
Pneumonia
Osteomyelitis
Meningoencephalitis
AIDS, glucocorticoids
Sarcoidosis
AIDS, AAbs to IFN-γ or 
GM-CSF, BTK or JAK inhibition
Trichosporonosisd
Superficial skin infection 
(white piedra)
Disseminated infection 
(skin, eye)
Healthy individuals
Neutropenia, glucocorticoids, 
HSCT, SOT
(Trichosporon asahii, 
T. mucoides, T. asteroides)
Endemic Dimorphic Fungi
Histoplasmosis
(Histoplasma capsulatum, 
H. duboisii [in Africa])
Self-limited pneumonia
Disseminated infection 
(liver, bone, bone marrow)
Fibrosing mediastinitis
Healthy individuals
AIDS, SOT, glucocorticoids, 
AAbs to IFN-γ, JAK or TNF-α 
inhibition
Blastomycosis
(Blastomyces dermatitidis, 
B. gilchristii)
Pneumonia
Disseminated infection 
(skin, bone, mucosal 
surfaces, genitourinary 
tract)
Healthy individuals
AIDS, glucocorticoids,
TNF-α inhibition
Coccidioidomycosis
(Coccidioides immitis, 
C. posadasii)
Self-limited pneumonia
Disseminated infection 
(CNS, bone)
Healthy individuals
AIDS, glucocorticoids,
TNF-α inhibition
Paracoccidioidomycosis
(Paracoccidioides brasiliensis, 
P. lutzii)
Pneumonia
Disseminated infection
(skin, bone, mucosal 
surfaces)
Healthy individuals
AIDS, glucocorticoids

Culture of BAL fluid: low sensitivity, nonspecific (colonization, 
contamination)
Histologic examination of tissueb: acute-angle septate hyphae
Biomarkers: GM (BAL > serum); serum BDG (nonspecific)
Culture of BAL fluid or sinus tissue: very low sensitivity
Histologic examination of tissue: ribbon-like aseptate hyphae
Biomarkers: Negative
Culture of tissue or blood: one of the few molds recovered from blood
Histologic examination of tissue: acute-angle septate hyphae
Biomarkers: GM can be positive; BDG (nonspecific)
Culture of BAL: low sensitivity, nonspecific (colonization, contamination)
Histologic examination of tissue: acute-angle septate hyphae
Biomarkers: BDG can be positive
Culture of ordinarily sterile site
Histologic examination of tissue: cell walls may appear dark brown or 
golden on H&E; Fontana-Masson may stain fungal melanin
Culture of mucosal surfaces
Histologic examination of esophageal tissue or wet preparation (10% 
KOH) of vaginal discharge: yeast and/or pseudohyphae
Culture of blood: low sensitivity
Histologic examination of tissue: yeast and/or pseudohyphae
Biomarkers/other tests: BDG (nonspecific); T2 magnetic resonance in 
whole blood
Culture of CSF, BAL fluid, blood
Microscopic examination of tissue or
CSF: encapsulated yeast (GMS, India ink, mucicarmine stain)
Biomarkers: Cryptococcus Ag (serum, CSF) is sensitive and specific
Culture of tissue or blood
Histologic examination of tissue: yeasts, hyphae, and arthroconidia
Biomarkers: BDG can be positive
Culture of blood or tissue: low sensitivity; weeks needed for growth
Histologic examination of tissue: yeast with narrow-based budding
Other tests: Histoplasma Ag (urine > serum > BAL); BDG can be 
positive; serology (CF) can be useful in non-AIDS patients
Culture of BAL or tissue: low sensitivity; weeks needed for growth
Histologic examination of tissue: yeast with broad-based budding
Other tests: serology (CF, ID) has low sensitivity; Blastomyces Ag test 
cross-reacts with other endemic fungi; GM can be positive
Culture is diagnostice
Histologic examination: spherules
Other tests: serology (CF, ID); Coccidioides Ag test can be useful in 
CNS infection; BDG can be positive
Culture of tissue: active disease; several weeks needed for growth
Histologic examination of KOH preparations or tissue: yeast with 
budding in steering-wheel pattern
Other tests: serology (ID, CF); Paracoccidioides Ag test
(Continued)

TABLE 217-1  Major Fungal Infections, Associated At-Risk Patient Populations, and Diagnostic Tests
INFECTION (MOST COMMON 
FUNGAL GENERA AND SPECIES)
CLINICAL SYNDROME(S)
RISK FACTOR(S)
DIAGNOSTIC TEST(S)
Sporotrichosis
(Sporothrix schenckii)
Lymphocutaneous 
infection (ascending 
lymphangitis)
Disseminated infection
Direct inoculation
AIDS, glucocorticoids
Talaromycosis
(Talaromyces marneffei)
Pneumonia
Disseminated infection
(skin, bone, mucosal 
surfaces)
Healthy individuals
AIDS, glucocorticoids, AAbs 
to IFN-γ
Adiaspiromycosis
(Emmonsia crescens, E. parva)
Pneumonia
Occupational dust exposure
Culture: nonculturable
Histologic examination: thick-walled adiaspore within granuloma
Emergomycosis
(Emergomyces africanus, 
E. pasteurianus)
Disseminated infection 
(lungs, skin)
AIDS, SOT
Culture of infected tissue
Histologic examination of tissue: yeast with narrow-based budding
Biomarkers: Histoplasma Ag can be positive
Chromoblastomycosis
(Fonsecaea pedrosoi, 
F. monophora)
Skin and subcutaneous 
tissue infections
Healthy individuals
Culture of infected tissue
Histologic examination of scrapings (KOH) or tissue (GMS): sclerotic 
bodies (pathognomonic)
Other Fungi   
Pneumocystosisf
Pneumonia
Disseminated infection 
(eye, CNS, skin, 
gastrointestinal tract)
AIDS, glucocorticoids, BTK 
inhibition
AIDS
(Pneumocystis jirovecii)
aA. nidulans is seen almost exclusively in chronic granulomatous disease. bGMS or PAS stains. cSome Candida species form pseudohyphae. dTrichosporon species are 
yeast-like fungi that also generate septate hyphae and arthroconidia. eCoccidioides is a laboratory hazard. It is important to notify the microbiology laboratory if this 
infection is suspected. fPneumocystis is present in cyst and trophozoite forms.
Abbreviations: AAbs, autoantibodies; ABPA, allergic bronchopulmonary aspergillosis; Ag, antigen; BAL, bronchoalveolar lavage; BDG, β-D-glucan; BTK, Bruton’s tyrosine kinase; 
CF, complement fixation; CNS, central nervous system; CSF, cerebrospinal fluid; GM, galactomannan; GM-CSF, granulocyte-macrophage colony-stimulating factor; GMS, Gomori 
methenamine silver; H&E, hematoxylin and eosin; HSCT, hematopoietic stem cell transplantation; ICU, intensive care unit; ID, immunodiffusion; IFN-γ, interferon γ; JAK, Janus 
kinase; KOH, potassium hydroxide; PAS, periodic acid–Schiff; PCR, polymerase chain reaction; SOT, solid organ transplantation; TNF-α, tumor necrosis factor α.
activation, and Th17 cell differentiation upon fungal invasion. Human 
inherited CARD9 deficiency causes severe mucocutaneous and inva­
sive fungal disease and is the only known primary immunodeficiency 
to feature fungus-specific infection susceptibility without a predispo­
sition to other infections, autoimmunity, allergy, or cancer. Notably, 
CARD9-deficient patients develop infections by certain fungi in cer­
tain tissues, including (1) chronic mucocutaneous candidiasis linked 
to defective interleukin (IL) 17 responses; (2) infections of the central 
nervous system (CNS) caused by Candida (but also by Aspergillus 
and phaeohyphomycetes) linked to impaired microglial-neutrophilic 
responses; and (3) deep dermatophytosis. Thus, the clinical use of SYK 
inhibitors for autoimmunity and cancer may cause opportunistic fun­
gal disease. Human inherited deficiency of Toll-like receptor (TLR) sig­
naling does not lead to spontaneous fungal disease, yet polymorphisms 
in TLR pathway molecules may increase the risk of fungal disease in 
critically ill or immunosuppressed persons, and TLR stimulation may 
boost protective CLR immunity, as has been shown with the TLR7 
agonist imiquimod in chromoblastomycosis.
The development of clinically relevant animal models of mycoses 
and the phenotypic characterization of fungal infections that develop 
in patients with primary immunodeficiencies and in recipients of 
immune pathway-targeting biologics have led to the delineation of 
fungus-, cell-, and tissue-specific requirements for antifungal host 
defense (Fig. 217-1).
At the mucosal interface, IL-17-producing lymphoid cells play a 
critical role in protection by driving epithelial cell production of anti­
microbial peptides that restrict mucosal Candida invasion. Indeed, 
AIDS patients are at risk for mucosal—but not invasive—candidiasis. 
Concordantly, inherited deficiency of IL-17 signaling caused by muta­
tions in IL17F, IL17RA, IL17RC, or TRAF3IP2 (encoding the IL-17 
receptor adaptor ACT1) or pharmacologic inhibition of IL-17 signal­
ing by biologics that target IL-12p40, IL-23p19, IL-17A, IL-17A/IL17F, or IL-17RA cause mucosal—but not invasive—candidiasis. Other 
conditions that underlie a predisposition to chronic mucocutaneous 

(Continued)
Culture of tissue (diagnostic)
Histologic examination: cigar-shaped yeast, often with surrounding 
asteroid body
Culture of tissue (diagnostic)
Histologic examination of tissue: yeasts with transverse septa
Biomarkers: GM is often positive
Culture: nonculturable
Histologic examination (gold standard): special (GMS, Diff-Quik) or 
immunofluorescence stains
Biomarkers/other tests: BDG (nonspecific); BAL fluid PCR (sensitive; 
can be positive in colonized individuals)
CHAPTER 217
Pathogenesis, Diagnosis, and Treatment of Fungal Infections 
candidiasis include primary immunodeficiencies due to mutations in 
STAT3, STAT1, DOCK8, JNK1, IRF8, RORC, and CARD9, all of which 
impair Th17 cells, as well as thymoma and autoimmune polyendocri­
nopathy–candidiasis–ectodermal dystrophy (APECED), which feature 
autoantibodies to IL-17A, IL-17F, and IL-22. In APECED, exacerbated 

T cell–derived interferon γ (IFN-γ)/STAT1 responses disrupt the integrity 
of the oral epithelial barrier, thereby promoting mucosal fungal inva­
sion and infection; remission of candidiasis can be achieved with JAK 
inhibition in APECED and STAT1 gain of function (GOF). Of note, 
vaginal candidiasis (unlike oropharyngeal and esophageal candidiasis) 
develops in the setting of antibiotic treatment, not AIDS or IL-17–targeted 
biologics; this observation underscores the role of the microbiota in 
fungal control at the vaginal—but not the oral—mucosa.
On the other hand, neutrophils—but not lymphocytes—are criti­
cal for control of invasive infections caused by Aspergillus (and other 
inhaled molds) and Candida (Fig. 217-1). Indeed, patients with che­
motherapy-induced neutropenia and patients undergoing allogeneic 
hematopoietic stem cell transplantation are at risk for invasive aspergil­
losis and candidiasis. Both oxidative and nonoxidative burst–dependent 
effector mechanisms are operational within neutrophils for fungal 
killing. Inherited deficiency in neutrophil superoxide generation due to 
mutations in the six subunits of the nicotinamide adenine dinucleotide 
phosphate (NADPH) oxidase complex causes chronic granulomatous 
disease, a prototypic primary immunodeficiency that carries a lifetime 
risk for invasive aspergillosis of ~40%; infrequently (i.e., in <5% of 
cases, mostly infants), chronic granulomatous disease predisposes to 
invasive candidiasis. The unexpected development of invasive mold 
infections in recipients of Bruton’s tyrosine kinase (BTK) inhibitors 
has recently uncovered the critical role of BTK in promoting myeloid 
phagocyte-dependent antifungal effector functions.
Host defenses against fungi that reside within macrophages, such as 
Cryptococcus, Pneumocystis, and endemic dimorphic fungi, depend on 
the interplay of IFN-γ–producing lymphoid cells and IL-12–producing 
macrophages that enable intramacrophagic fungal killing (Fig. 217-1).

IL6R
IL23R
Th17 cell
Th1 cell
Neutrophil
JAK2
TYK2
STAT3
JAK2
TYK2
RORγT
CXCL1
Nucleus
fc T cell
CXCR2
AAbs
NADPH
p22phox
gp91phox
IL-17A/IL-17F
AAbs
p67phox p47phox
p40phox
IL-17F
IL-17A
IL-22
IL-22R1
IL-10Rβ
IL-17RA
IL-17RC
NADP+
PART 5
Infectious Diseases
Candida
yeast and
pseudohyphae  
Multilobed
nucleus
STAT3
ACT1
Epithelial cells
Neutrophil
Lung
FIGURE 217-1  Host defense against fungi. Left: Production of IL-17A, IL-17F, and IL-22 by Th17 cells, Tc17 cells, γδ T cells, and innate lymphoid cells confers protection from 
mucosal Candida invasion. STAT3 promotes Th17 differentiation via RORγt induction. IL-17A and IL-17F bind to IL-17RA and IL-17RC on epithelial cells and signal via ACT1 
to produce antimicrobial peptides that inhibit fungal growth. IL-22 binds to its receptor on epithelial cells and activates STAT3 to mediate epithelial proliferation and repair. 
Middle: Activation of CXCR2+ neutrophils recruited from blood in the Aspergillus-infected lung enables assembly of the six subunits of NADPH oxidase and superoxide 
generation that promotes fungal killing. Production of reactive oxygen species by neutrophils is facilitated by recruited monocyte-derived and plasmacytoid dendritic 
cells via type I and type III IFNs and GM-CSF. Right: The interaction of Th1 cells with macrophages is protective against intramacrophagic endemic dimorphic fungi, 
Pneumocystis, and Cryptococcus. Upon fungal uptake, macrophages produce IL-12 that binds to its receptor on T cells and activates STAT4, with consequent release of IFNγ. IFN-γ binds to its receptor on macrophages and activates STAT1, thereby enabling fungal killing. TNF-α and GM-CSF are also critical for macrophage activation. AAbs, 
autoantibodies; IL, interleukin; IFN, interferon; JAK, Janus kinase; GM-CSF, granulocyte-macrophage colony-stimulating factor; NADPH, nicotinamide adenine dinucleotide 
phosphate; RORγt; RAR-related orphan receptor γ; SOD, superoxide dismutase; STAT, signal transducer and activator of transcription; TNF, tumor necrosis factor; TYK2, 
tyrosine kinase 2.
Indeed, AIDS patients and those receiving glucocorticoids, which affect 
lymphocytes and macrophages both quantitatively and qualitatively, are 
at risk for severe infections by these fungi. Accordingly, inherited impair­
ment of the IL-12/IFN-γ signaling axis caused by mutations in IL12RB1, 
IFNGR1, IFNGR2, STAT1, IRF8, or GATA2 underlies susceptibility to 
severe infection by intramacrophagic fungi (and other intramacrophagic 
pathogens, such as mycobacteria and salmonellae). In addition, the 
IFN-γ–targeting monoclonal antibody emapalumab, JAK inhibitors that 
block IFN-γ–dependent cellular responses, and autoantibodies to IFN-γ 
predispose to infection with intramacrophagic fungi, as do biologics 
targeting tumor necrosis factor α (TNF-α) and autoantibodies to gran­
ulocyte-macrophage colony-stimulating factor (GM-CSF). The latter 
predisposing factors reveal the central role of these two Th1-associated 
cytokines—TNF-α and GM-CSF—in macrophage activation.
Taken together, these observations show that the cellular and molec­
ular factors that drive protective antifungal immune responses vary 
greatly with the anatomic site of the infection, the offending fungus, 
and the patient population (Table 217-1). The growing body of data on 
human immunologic responses to fungi promises to inform precision 
medicine strategies for risk assessment, prophylaxis, immunotherapy, 
and vaccination of vulnerable patients.

Blood
IFNγ
CXCR2
Nucleus
STAT4
STAT4
CXCL2
TYK2
JAK2
GM-CSF
IL12Rβ1
IL12Rβ2
IFNγ
IFN-λ
Aspergillus
conidia
AAbs
IL-12
IFNγ
IFN-γR2
TNFα
IFN-γR1
e–
O2
–
JAK2
STAT1
SOD
JAK1
Phagosome
STAT1
Phagosome
H2O2
Yeast
(Histoplasma,
Cryptococcus)
Macrophage
IL-12
Nucleus
GM-CSF
■
■DIAGNOSIS
The diagnostic modalities used for various fungal infections are out­
lined in Table 217-1 and are detailed in the chapters on specific myco­
ses that follow in this section. Definitive diagnosis of a fungal infection 
requires histopathologic identification of the fungus invading tissue with 
parallel culture of the fungus from the specimen. Certain fungi have dis­
tinctive morphologic features that facilitate diagnosis (Table 217-1). The 
stains most often used to identify fungi are periodic acid–Schiff (PAS) 
and Gomori methenamine silver (GMS). Candida, unlike other fungi, 
is visible on Gram-stained tissue smears. Hematoxylin and eosin stains 
define accompanying histologic features of fungal disease (granuloma 
formation, angioinvasion, necrosis) but are insufficient to reliably 
identify fungi in tissue. A positive India ink stain of cerebrospinal fluid 
(CSF) is diagnostic for cryptococcosis. Most laboratories use calcofluor 
white staining coupled with fluorescence microscopy to identify fungi 
in fluid specimens. A positive fungal culture of blood or tissue may 
signify either patient colonization or lab contamination instead of 
true infection, with the most likely scenario depending on the fungus 
and the anatomic site. In blood, Candida can be detected with any 
of the widely used automated blood culture systems, but the lysiscentrifugation technique increases the sensitivity of blood cultures for

both Candida and other less common fungi (e.g., Histoplasma). Matrixassisted laser desorption/ionization time-of-flight mass spectrometry 
(MALDI-TOF-MS) is now used extensively for detection and specia­
tion of fungi recovered from culture.
The several available fungal-antigen and serologic tests vary in sen­
sitivity and specificity. The most reliable of these tests are the antibody 
to Coccidioides, Histoplasma antigen, and cryptococcal polysaccharide 
antigen. Serologic tests are also available for other endemic dimorphic 
fungi (Table 217-1). The galactomannan test—especially in the bron­
choalveolar lavage fluid—is useful for the diagnosis of aspergillosis; 
however, false-negative results are common, particularly in patients 
receiving antifungal prophylaxis, and false-positive results may occur 
with other fungal infections. The β-glucan test has a high negative pre­
dictive value for invasive candidiasis but lacks specificity. T2 magnetic 
resonance is now approved by the U.S. Food and Drug Administration 
(FDA) for detection of Candida in blood. Several polymerase chain 
reaction and nucleic acid hybridization assays exist for fungal detection 
but are not standardized and are not widely used in the clinic.
■
■ANTIFUNGAL DRUGS
This section provides a brief overview of available agents for the treat­
ment of fungal infections. Drug regimens and schedules are detailed 
in the chapters on specific mycoses that follow in this section. Since 
fungal organisms, like human cells, are eukaryotic, the identification 
of drugs that selectively kill or inhibit fungi but that are not toxic to 
human cells poses challenges. Indeed, far fewer antifungal than anti­
bacterial agents have been introduced into clinical medicine.
Early initiation of appropriate antifungal therapy is a critical determi­
nant of favorable outcome, as has been shown for candidemia, aspergil­
losis, and mucormycosis. In addition, source control of the infection is 
important—e.g., with removal of the central venous catheter in candi­
demia, drainage of abdominal abscesses in intraabdominal candidiasis, 
and surgical debridement of sinus tissue in mucormycosis. Moreover, an 
essential factor in a favorable prognosis in patients with opportunistic 
mycoses is the achievement of immune reconstitution—e.g., with neu­
trophil recovery, tapering of glucocorticoids or other immunosuppres­
sive drugs, or initiation of combination antiretroviral therapy in AIDS.
■
■AMPHOTERICIN B
The advent of amphotericin B (AmB) in the 1950s revolutionized the 
treatment of deep-seated mycoses. Before the availability of AmB, 
cryptococcal meningitis and other disseminated fungal infections were 
nearly always fatal. AmB remains the broadest-spectrum antifungal 
agent. Its fungicidal mechanism of action involves forming extramem­
branous sponge-like aggregates that extract fungal ergosterol from lipid 
bilayers. AmB remains the preferred antifungal agent for the treatment 
of mucormycosis and fusariosis and for induction therapy for cryptococ­
cal meningitis and disseminated infections caused by endemic dimor­
phic fungi. However, AmB has several limitations, including lack of a 
licensed oral formulation and significant toxicity from the intravenous 
preparations, primarily renal and infusion-related (fever, chills, throm­
bosis). The introduction of lipid AmB formulations has ameliorated 
these toxicities, and the lipid formulations have largely replaced the 
original deoxycholate formulation in resource-rich settings. In develop­
ing countries, AmB deoxycholate is still widely used because of the high 
cost of the lipid formulations. The two lipid formulations commonly 
used in the clinic are liposomal AmB and AmB lipid complex, which 
exhibit comparable efficacy, toxicity, and tissue penetration profiles.
■
■AZOLES
Azoles offer important advantages over AmB, such as the availability of 
oral and IV formulations and a lack of renal toxicity. The mechanism of 
action of azoles involves inhibition of lanosterol 14α-demethylase and 
ergosterol synthesis in the fungal cell membrane, with a consequent 
accumulation of toxic sterol intermediates and growth arrest. Unlike 
AmB, azoles are considered fungistatic.
Fluconazole 
Fluconazole plays an important role in the treatment 
of several fungal infections. Its major advantages are the availability of 
oral and IV formulations, a long half-life, penetration into most body 

fluids (ocular fluid, CSF, urine), and minimal toxicity. This drug rarely 
causes liver toxicity; high doses may result in alopecia, dry mouth, and 
a metallic taste. Notably, the administration of even low doses of fluco­
nazole to pregnant women for the treatment of vaginal candidiasis was 
recently linked to miscarriage and stillbirth. Fluconazole has no activ­
ity against molds and most endemic dimorphic fungi and is less active 
than the newer azoles against C. glabrata and C. krusei.

Fluconazole is the preferred agent for the treatment of coccidioidal 
meningitis, although relapses may occur despite therapy. Fluconazole 
is also used as consolidation and maintenance therapy for cryptococcal 
meningitis and for the treatment of mucosal candidiasis. It is used for 
treating candidemia in patients who are not critically ill or immuno­
suppressed; in these patients, fluconazole was found to be as effica­
cious as AmB. Because of increasing rates of azole-resistant Candida 
strains, echinocandin treatment is preferred, which is then replaced 
by fluconazole once a susceptible Candida species is recovered. Flu­
conazole is effective as prophylaxis in recipients of high-risk liver and 
allogeneic bone marrow transplants, although many centers now use 
posaconazole in neutropenic patients, given its added activity against 
molds. Fluconazole prophylaxis in leukemic patients, in AIDS patients 
with low CD4+ T-cell counts, and in patients on surgical intensive care 
units is controversial.
Itraconazole 
Itraconazole is available in oral (capsule, suspension) 
and IV formulations and has broader antifungal activity—i.e., against 
molds and endemic dimorphic fungi—than fluconazole. Itraconazole 
is the drug of choice for mild to moderate histoplasmosis and blasto­
mycosis and has also been used to treat chronic coccidioidomycosis, 
phaeohyphomycosis, sporotrichosis, and mucocutaneous mycoses 
such as oropharyngeal candidiasis, tinea versicolor, tinea capitis, and 
onychomycosis. Although it is approved by the FDA for use in febrile 
neutropenic patients, most centers now use newer azoles in such 
patients. Disadvantages of itraconazole include its poor CSF penetra­
tion, the use of cyclodextrin in its oral suspension and IV formulation, 
and its variable level of absorption in the capsule form, which requires 
monitoring of blood levels in patients receiving capsules for dis­
seminated mycoses. A new formulation of itraconazole, called SUBAitraconazole (for “super-bioavailability”), which results in improved 
absorption and less variable plasma levels, has recently been approved 
by the FDA. Itraconazole is a potent CYP3A4 inhibitor; this character­
istic leads to significant drug interactions. The drug causes hepatotox­
icity and cardiac toxicity that may manifest as congestive heart failure.
CHAPTER 217
Pathogenesis, Diagnosis, and Treatment of Fungal Infections 
Voriconazole 
Voriconazole is also available in oral and IV formula­
tions, has far broader antifungal activity than fluconazole (including 

C. glabrata, C. krusei, Aspergillus, Scedosporium, and endemic dimorphic 
fungi—but not Mucorales), and penetrates into most body fluids (ocular 
fluid, CSF). It is the preferred agent for the treatment of aspergillosis and 
also has been used to treat scedosporiosis and as step-down (but not pri­
mary) therapy for coccidioidomycosis, blastomycosis, and histoplasmo­
sis. Voriconazole is considerably more expensive than fluconazole, and as 
with itraconazole, its use is associated with numerous interactions with 
drugs typically used in patients at risk for fungal infections. Hepatotoxic­
ity, visual disturbances, and skin rashes (including photosensitivity) are 
relatively common, and long-term use requires skin cancer surveillance. 
A unique toxicity of voriconazole among azoles is fluorosis-associated 
periostitis. It is crucial to monitor drug levels because (1) voriconazole 
is metabolized in the liver by CYP2C9, CYP3A4, and CYP2C19; and (2) 
human genetic variation in CYP2C19 activity exists and can lead to sig­
nificant interpatient variability in drug levels. Dosages should be reduced 
in patients with hepatic, but not renal, failure; however, because the IV 
formulation is prepared in cyclodextrin, it should be given with caution 
to patients with severe renal failure.
Posaconazole 
Posaconazole has broader activity than voricon­
azole, including activity against Mucorales. Both oral (suspension, tablet) 
and IV formulations are available. Posaconazole is approved by the 
FDA for antifungal prophylaxis in neutropenic leukemic patients and 
allogeneic hematopoietic stem cell transplant recipients as well as for 
treatment of oropharyngeal candidiasis, including infections refractory