Introduction

Cryptococcal meningitis is a highly fatal central nervous system (CNS) infection commonly caused by the intracellular facultative basidiomycete Cryptococcus neoformans and, in a few instances, Cryptococcus gatti.1Cryptococcus neoformans is ubiquitous within the environment, habitually identified in soil rich in pigeon guano owing to the high levels of creatinine2 and uric acid3 required for growth and survival. It typically causes meningitis among persons diagnosed with advanced human immunodeficiency virus (HIV) disease.4Cryptococcus gatti, on the other hand, has been reported to cause meningitis in Australia, the Americas and some parts of Asia, commonly among HIV-uninfected persons.5 As we strive to achieve zero deaths from HIV-related cryptococcal meningitis by 2030,6 there is a critical need to understand the risk factors and factors influencing outcomes of this fatal central nervous system disease in the post-antiretroviral therapy era. The scope of this review is limited to Cryptococcus neoformans-related meningitis since it is the most commonly isolated pathogen in individuals diagnosed with HIV-related meningitis. It is responsible for approximately 19% of advanced HIV-related deaths, which translated to 112,000 deaths in 2020.7 As a result of the high associated mortality rate, in 2022 Cryptococcus neoformans was added to the WHO priority fungal pathogen list as a critical pathogen.8 In this review, we discuss the pathogenesis of HIV-related cryptococcal meningitis following Cryptococcus neoformans infection, and discuss the clinical-, immunological-, genetic- and pathogen-related risk factors of this highly fatal CNS disease.

Infection and Pathogenesis

With regard to the pathogenesis of cryptococcal disease, there is no evidence of human-to-human transmission of Cryptococcus. Infection from the environment happens after inhalation of basidiospores or desiccated yeasts that are less than 2µm, a size small enough for the cryptococcus to evade the mucocilliary defense of the bronchial tree.9,10 Infection with Cryptococcus can occur as early as childhood and the infected persons may never develop disease in their lifetime.11 Whether a person will develop disease following Cryptococcus infection is heavily reliant on the integrity of the host (infected person’s) immune response. Cryptococcus may clear from the lungs or be contained within a lung granuloma as a latent infection in immune competent individuals.12 In individuals with suppressed immunity as commonly observed among those diagnosed with advanced HIV disease (a peripheral CD4 count of <200 cells/µL),13Cryptococcus through its numerous virulence factors14–21 (Table 1) will evade the effector immune response in the lungs and disseminate throughout the host (human body).22 This results in any one of the epidemiologically significant clinical presentations of the cryptococcal disease spectrum ranging from pneumonia, asymptomatic cryptococcal antigenemia, symptomatic cryptococcal antigenemia, meningitis, and cryptococcomas (Figure 1). In this review, we discuss the clinical, immunological and genetic risk factors of HIV-related cryptococcal meningitis in humans and review how these risk factors influence clinical outcomes in persons living with HIV who are diagnosed with cryptococcal meningitis.

Table 1 Summarizing the Virulence Factors of Cryptococcus neoformans

Figure 1 Illustrating the spectrum of cryptococcal disease presentation in terms of clinical disease entity, cryptococcal antigen status and body compartment among individuals with advanced HIV disease.

Without Pre-Emptive Antifungal Treatment, Cryptococcal Antigenemia Progresses to Cryptococcal Meningitis

Cryptococcal antigenemia is a clinical entity along the cryptococcal disease spectrum whereby cryptococcus antigen becomes detectable in the peripheral blood following dissemination from the lungs. Cryptococcus in peripheral blood is identified based on a capsular antigen commonly using the bedside cryptococcal antigen (CrAg) lateral flow assay (LFA; Immuno-Mycologics Inc., Norman, OK), which has a high sensitivity and specificity.23 Individuals with advanced HIV disease and asymptomatic cryptococcal antigenemia will typically have a positive serum CrAg LFA test, negative cerebrospinal fluid CrAg LFA test and negative CSF fungal culture. Overall, individuals diagnosed with HIV-related cryptococcal antigenemia have a two-fold risk of death compared to their counterparts without cryptococcal antigenemia.24 These individuals may be asymptomatic or symptomatic with headache, neck pain and altered mentation.25 Cryptococcal antigenemia is an independent risk factor for HIV-related cryptococcal meningitis and death.26,27 In the absence of pre-emptive antifungal therapy, one study found that individuals with HIV-related cryptococcal antigenemia progress to cryptococcal meningitis in a median of 22 days following intermittent sampling.28 In a Tanzanian study, pre-emptive fluconazole reduced mortality among individuals with HIV-related cryptococcal antigenemia by 28%.29 However, even with pre-emptive fluconazole, 25% of individuals with HIV-related cryptococcal antigenemia develop meningitis or die by six months.26 Serum cryptococcal antigen titer—a measure of the fungal burden in serum—predicts the risk of developing cryptococcal meningitis or death following cryptococcal antigenemia diagnosis. A serum CrAg titer greater than >1:160 was associated with failure of pre-emptive fluconazole in a cohort of persons with HIV-related cryptococcal antigenemia.30 From a clinical perspective, serum CrAg titers are useful in risk stratifying HIV-related cryptococcal antigenemia into low- and high-risk groups using a titer of 1:160 as a cut off. Currently there are two ongoing randomized clinical trials with the goal of identifying an antifungal regimen that is superior to fluconazole alone as pre-emptive therapy for cryptococcal antigenemia. The first is using liposomal amphotericin B 10mg/kg as a single-dose combined with standard fluconazole to improve survival in persons diagnosed with HIV-related cryptococcal antigenemia (ACACIA trial: NCT03945448) that is recruiting individuals with a high CrAg titer (>1:160). The second trial is the treatment of cryptococcal antigen-positive patients identified through screening using a combination of flucytosine and fluconazole (EFFECT trial: ISRCTN30579828).

A high serum CrAg titer is not the only risk factor for failure of pre-emptive fluconazole prophylaxis. A high C-reactive protein level, depending on the cryptococcal antigen titer, was associated with not only failure of fluconazole pre-emptive therapy but also mortality.31 Similarly, C-reactive protein level was associated with mortality in HIV-related cryptococcal meningitis. Persons with a >49.5mg/L level were sicker and had a four-fold higher two-week mortality rate compared to those with a level of <29.0mg/L.32

Certain Clinical Characteristics at Cryptococcal Meningitis Diagnosis Including Coinfections Have Been Associated with an Increased Risk of Mortality

Older age, male sex at birth, seizures, altered mental status, mid-upper-arm circumference less than 22 cm, high CSF fungal burden, anemia and peripheral leukocytosis at the time of HIV-related cryptococcal meningitis diagnosis have been associated with an increased risk of mortality.33–35 For every 1000 cells/mm3 increase in peripheral neutrophil count, the risk of mortality increases by 10%.36 Similarly, a peripheral leukocyte count of >10,000 cells/mm3 was associated with an almost nine-fold risk of mortality compared to a leukocyte count of <10,000 cells/mm.3,33 These hematological observations may be a result of coinfections, which can be either hospital acquired or opportunistic in nature. Indeed, the incidence of blood stream infections, confirmed by blood culture, ranges from 3.5–15% among individuals hospitalized with HIV-related cryptococcal meningitis; such infections have been associated with a 50% increased risk of mortality at 10 weeks.37 Tuberculosis (TB) and cytomegalovirus (CMV) are increasingly gaining recognition as opportunistic co-infections among individuals hospitalized following HIV-related cryptococcal meningitis diagnosis. TB and CMV co-infections are associated with 75%38 and 45%39 increased risk of 18-week mortality among patients diagnosed with HIV-related meningitis, respectively. Interestingly, CMV viremia itself has been associated with poor outcomes in HIV-related cryptococcal meningitis, with a Ugandan study demonstrating a three-fold higher mortality rate (adjusted hazard ratio = 3.25; 95% CI: 1.49–7.10; P = 0.003) over the course of 10 weeks despite similar CD4 counts and receipt of the same antifungal treatment.40

Finally, at the time of cryptococcal meningitis diagnosis, the fungal burden in cerebrospinal fluid obtained by CSF fungal culture positively correlates with mortality. Higher mortality has been observed in individuals with a high fungal burden (≥100,000 colony forming units/mL) compared to those with a low fungal burden in CSF.33 These individuals typically have higher CSF opening pressure, seizures, and hyponatremia, which are independently associated with mortality.41–43

During Management of HIV-Related Cryptococcal Meningitis, Choice of Antifungal Regimen During the Induction Phase Is Crucial

Following diagnosis, the treatment of HIV-related cryptococcal meningitis is divided into three phases: first, a two-week induction phase, aiming to rapidly clear Cryptococcus from cerebrospinal fluid using combination antifungal therapy; second, an eight-week consolidation phase using high dose fluconazole (800mg daily); and third, a maintenance or secondary prophylaxis phase involving use of low dose fluconazole (200mg daily) for a minimum of 18 months after initiation of antifungal treatment.44 The rate at which Cryptococcus is cleared from CSF during the two-week induction phase by an antifungal drug is known as the early fungicidal activity (EFA) of that drug. An EFA of <0.2 log10 colony forming units/mL/day was associated with a 50% all-cause mortality rate at 18 weeks among individuals diagnosed with HIV-related cryptococcal meningitis compared to a 37% all-cause mortality rate with an EFA of >0.2 log10 colony forming units/mL/day.45 This implies that antifungal agents that can penetrate the blood–brain barrier to reach the CNS compartment and a faster reduction in the CSF fungal load are associated with better 18-week survival.

Overall, amphotericin B with or without flucytosine on a backbone of fluconazole is associated with better outcomes compared to fluconazole monotherapy during the induction phase. Mortality from HIV-related cryptococcal meningitis has been reported to be as high as 50% in settings where fluconazole monotherapy is used for induction therapy.46 Moreover, for the two-week induction phase, flucytosine-containing regimens have better outcomes compared to non-flucytosine regimens. In the ACTA trial, one week of amphotericin B deoxycholate (1mg/kg/day) with flucytosine (100mg/kg/day) followed by fluconazole 1200mg/day for one week and two weeks of flucytosine (100mg/kg/day) and fluconazole 1200mg/day had 10-week mortality rates of 36.2% and 35.1%, respectively compared to two weeks of amphotericin B deoxycholate (1mg/kg) and fluconazole 1200mg/day, which had a 10-week mortality rate of 39.7%.47

Amphotericin B is highly nephrotoxic and the risk of realizing its dose-dependent side effects, including anemia, hypokalemia and hypomagnesemia, increases with every subsequent dose.48 Of the two widely available amphotericin B formulations, liposomal amphotericin B is associated with fewer side effects compared to amphotericin B deoxycholate.49 The AMBITION-cm regimen of single-dose liposomal amphotericin B (10mg/kg) followed by two weeks of flucytosine and fluconazole was non-inferior, cheaper and associated with fewer adverse events of anemia, hypokalemia and thrombophlebitis compared to the ACTA trial involving one week of amphotericin B deoxycholate (1mg/kg/day) and flucytosine (100mg/kg/day), followed by one week of fluconazole (1200mg).50 Thus, this became the World Health Organization recommended regimen in low- and middle-income countries for the treatment of HIV-related cryptococcal meningitis during the two-week induction phase.44

Therapeutic Lumbar Punctures are as Important as the Choice of Antifungal Regimen and the Two are Complementary

Elevated intracranial pressure is one of the hallmarks of cryptococcal meningitis. It is thought to result from mechanical obstruction of the arachnoid villi, deposits in the brain parenchyma and perivascular spaces by the fungus and its shed capsule antigen.51 Mechanical obstruction of the arachnoid villi results in failure of CSF re-absorption giving rise to hydrocephalus.52 Elevated intracranial pressure in persons diagnosed with HIV-related cryptococcal meningitis presents with a CSF opening pressure of >20cmH2O. Symptoms of elevated intracranial pressure include headache, blurring of vision, cranial nerve VI palsies (which manifests as double vision), hearing loss, nausea, vomiting, seizures and altered mental status.53 In addition to the choice of antifungal regimen, managing elevated intracranial pressure by performing scheduled lumbar punctures confers a survival benefit among individuals diagnosed with HIV-related cryptococcal meningitis. Therapeutic lumbar punctures after diagnosis of cryptococcal meningitis are associated with a 69% relative reduction in mortality during the initial two weeks of treatment.54 Surprisingly even among persons with normal CSF opening pressure (<20cmH2O), an additional lumbar puncture has a 30-day mortality benefit.55

Immune Reconstitution Inflammatory Syndrome is Detrimental Among Individuals Diagnosed with HIV-Related Cryptococcal Meningitis

Cryptococcal meningitis immune reconstitution inflammatory syndrome (IRIS) can be classified as: (1) unmasking, whereby an individual living with HIV presents with symptoms and signs of cryptococcal meningitis following the initiation of antiretroviral therapy (ART); or (2) paradoxical, whereby an individual previously diagnosed with HIV-related cryptococcal meningitis clinically deteriorates, with recurrence of symptoms and signs of cryptococcal meningitis, despite successful antifungal therapy after initiation of ART.

A low peripheral CD4 T cell count, lack of CSF inflammatory cells at cryptococcal meningitis diagnosis and high initial CSF fungal burden prior to initiation of antiretroviral therapy are recognized as risk factors for paradoxical IRIS.56,57 Both unmasking58 and paradoxical cryptococcal meningitis59 IRIS have high mortality rates, which is why WHO recommends initiation of ART in individuals diagnosed with HIV-related cryptococcal meningitis after four weeks of antifungal therapy when the CSF fungal culture is sterile.44

Impaired Cell Immunity is Common in Persons with HIV-Related Cryptococcal Disease and is Not Only a Risk Factor for Disease but Also Has a Bearing on Outcome

Mononuclear cells (ie, macrophages, CD4 T cells, CD8 T cells and NK cells) are the main effector cells against Cryptococcus. Following the actin dependent phagocytosis of Cryptococcus, which occurs in the presence of complement-mediated16 and anti-cryptococcal capsule antibodies from B cells,60 macrophages depend on proinflammatory cytokines such as interferon-gamma from differentiated CD4 T-helper 1 lymphocytes to successfully contain and or kill intracellular cryptococcus in the phagolysosome.61

In the absence of ART, as observed among individuals recently diagnosed with HIV or those who have not adhered to ART treatment, long standing HIV infection causes both a qualitative and quantitative decline in CD4 T cells.62 As with other opportunistic infections, the prevalence of cryptococcal antigenemia in individuals with advanced HIV disease increases with declining peripheral CD4 T cell count63 (Figure 2). Similar to cryptococcal antigenemia, as the CD4 T cell count declines, the prevalence of cryptococcal meningitis increases among individuals with advanced HIV disease. In a Ugandan study, of the 736 patients who presented with first-episode HIV-related cryptococcal meningitis, only 9% had a CD4 T cell count greater than 100 cells/µL, with nearly three-quarters having a CD4 T cell count of less than 50 cells/µL. Compared to patients with CD4 T cell counts between 50–99 cells/µL, mortality was high in both extremes.64 A qualitative decline in the CD4 T cell function contributing to mortality in HIV-related cryptococcal meningitis was reported by Jarvis et al, who noted a high two-week mortality rate among individuals diagnosed with HIV-related cryptococcal meningitis with reduced or absent proinflammatory interferon-gamma and tumor necrosis factor-alpha compared to their counterparts with preserved CD4 T-helper 1 responses.65 Unlike the CD4 T- helper 1 response that is aimed at pathogen clearance or control, CD4 T-helper 2 responses result in abating the inflammatory response so that the tissue repair process can take place. A predominant CD4 T-helper 2 response in the presence of an invading pathogen usually results in dissemination of the pathogen from one body compartment to another and ultimately poor outcomes. In a South African cohort, inappropriate CD4 T-helper 2 anti-inflammatory cytokine signature, that is predominated by interleukin-10 and reduced human leukocyte antigen-DR expression (surface marker of cellular activation) on the peripheral monocytes in the presence of high levels of the fungal capsule glucuronoxylomannan (GXM) was observed in patients who died early on during hospitalization compared to survivors.66

Figure 2 Bar chart summarizing the prevalence of cryptococcal antigen positivity relative to peripheral CD4 T cell count among individuals with advanced HIV disease in Tanzania.

In some individuals with advanced HIV and cryptococcal infection, Cryptococcus antigenseg GXM influence the host naïve CD4 T cells to overwhelmingly differentiate into either CD4 T-helper 2 phenotype or CD4 T-helper 1 phenotype; however, the reasons for this observation remain unclear. A hypothesis for this observation is the differences in genetic variations of the same strain of Cryptococcus. Indeed, certain genetic variations of Cryptococcus neoformans var. grubii are associated with a CD4 T-helper 2 cytokine signature and consequently a higher mortality rate compared to others. Using multilocus sequence typing, the burst group 1 clonal cluster, which included Sequence Type 93 and other closely related genetic strains, was associated with a higher CSF cryptococcal capsule shedding (CSF CrAg titer), prominent CD4 T-helper 2 cytokine signature in cerebrospinal fluid and higher mortality compared to the burst group 3 clonal cluster.67 The findings of this translational clinical study imply that pathogen variation may be equally important as other host factors, such as CD4 T cell count, in predicting outcomes of HIV-related meningitis.

In a healthy host, activated CD4 T cells, following interaction with Cryptococcus antigen from antigen presenting cells, stimulate accessory cells, including macrophages, to release interleukin-15 that triggers granulysin production and release from CD8 T cells to kill Cryptococcus.68 However, exhausted or terminally differentiated CD8 T cells, as evidenced by a high proportion of surface programmed cell death (PD)-1 expression, have poor effector function.69 Previously, we have shown that a high proportion of surface PD-1 expression was observed on cerebrospinal fluid CD8 T cells of individuals who died within two weeks of HIV-related cryptococcal meningitis diagnosis compared to those who survived and were alive at one year.70 Whether the high proportion of PD-1 expression on the CSF CD8 T lymphocytes is a result of the Cryptococcus infection or chronic uncontrolled HIV infection is unclear and warrants further investigation.

Beyond a Low Peripheral CD4 T Cell Count (<200 Cell/mm3), There Seems to Be a Genetic Predisposition to Cryptococcal Disease

Despite universal exposure to Cryptococcus, not all individuals with advanced HIV disease have been observed to develop disseminated cryptococcal disease,71 leaving room for the possibility of host factors beyond the pathogen and HIV-related abnormalities on CD4 T cells. Genetic polymorphism of the Fc gamma receptors through the FCGR3A 158V allele is associated with a 20-fold risk of cryptococcal disease among Caucasian persons with HIV disease.72 In this condition, there is an increased affinity of macrophages for cryptococcal yeast that have been opsonized by immunoglobin G-mediated Fc-receptor dependent pathways. The increased uptake and stuffing of the macrophage with cryptococcus yeast is thought to paradoxically allow replication beyond the macrophage’s intracellular killing potential. As a result, borrowing from the trojan horse hypothesis,73Cryptococcus is able to disseminate quickly from the site of uptake to another body compartment, in this case, the CNS, to cause meningitis. It is important to note that the association of this macrophage Fc gamma receptor polymorphism and cryptococcal disease has only been reported in Caucasians with HIV and no other ethnic group.

The other human genetic risk factor for cryptococcal disease is polymorphisms of macrophage colony stimulating factor 1. The macrophage colony stimulating factor 1 is essential for the survival, chemotaxis, proliferation and activation of monocytes.74 In a South African study, a cluster of regulatory single nucleotide polymorphisms near the macrophage colony stimulating factor 1 locus was found to influence susceptibility to cryptococcal disease.75 In this study, five single nucleotide polymorphisms in the regulator region and one single nucleotide polymorphism in the enhancer region of the colony stimulating factor 1 gene encoding for the macrophage colony stimulating factor resulted in increased phagocytosis of cryptococcus and reduced intracellular killing of the fungus by the monocytes. This allows for Cryptococcus to be loaded and trafficked from the site of initial inflammatory response to another compartment by the monocytes.

Memory B Cells Among Individuals with HIV-Related Cryptococcal Antigenemia Has Been Implicated in the Development and Outcome of Meningitis

As earlier elaborated, infection with cryptococcus occurs as early as childhood. Following activation, B cells not only offer protection against cryptococcus through production of opsonizing antibodies during the initial infection but also differentiate to form memory B cells that offer protection against future cryptococcus infection. In one retrospective study, a reduced reservoir of circulating IgM producing memory B cells in blood was observed in HIV-infected individuals who either had a history of or active cryptococcal disease compared to HIV-infected individuals without cryptococcal disease or healthy controls without HIV, suggesting a possibility of a reduced reservoir of this B cell subtype contributing to the development of cryptococcal disease.76 It is unclear, however, whether this observation is as a result of abnormalities in T cell lymphocytes that are commonly seen in these high-risk individuals with advanced HIV disease.

Upcoming NIH Funded Research Looking into the Risk Factors and Factors and Outcomes of HIV-Related Cryptococcal Disease

Considerable effort has been dedicated to demonstrating what we now know as risk factors of cryptococcal disease, and how these factors impact the outcomes of HIV-related cryptococcal meningitis in humans. Ongoing work (Table 2) will further illuminate our understanding of the interactions between a human host and cryptococcus that result in failure of the initial protective response, describe the burden of cryptococcal disease including its sequalae and highlight newer antifungal drugs and adjuvant therapies.

Table 2 Ongoing Research into Risk Factors and Outcomes of HIV-Related Cryptococcal Meningitis from NIH Reporter, May 2026

Table 2 summarizes on-going research into the risk factors and outcomes of HIV-related cryptococcal meningitis from NIH reporter as of May 2026.

Conclusion

In this review we have highlighted that, in individuals with advanced HIV disease, there are both pathogen and host genetic and immunological risk factors that lead to cryptococcal antigenemia, which precedes the development of meningitis following pulmonary infection with Cryptococcus commonly occurring in childhood. Once meningitis develops, which may or may not as a result of pre-emptive antifungal treatment failure of cryptococcal antigenemia, the outcome relies on a number of factors, including individuals’ clinical characteristics, choice of antifungals used in the induction phase, therapeutic lumbar puncture strategy and immunological response following initiation of ART, acting independently or in concert.

Acknowledgments

This work is supported by NIH D43 training grants D43TW012266,NIH NINDS K23NS137968 and 5R01NS118538-07

Disclosure

The authors report no conflicts of interest in this work.

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