Clinical Mycology Today: Emerging Challenges and Opportunities

Abstract The Mycoses Study Group Education and Research Consortium is a collective of clinicians, researchers, and educators with the common goal to advance awareness, diagnosis, and management of invasive fungal diseases. Clinical Mycology Today, the Mycoses Study Group Education and Research Consortium's biennial meeting, is dedicated to discussing the most pressing contemporary issues facing the field of clinical mycology, promoting clinical, translational, and basic science collaborations, and mentoring the next generation of clinical mycologists. Here, we review the current opportunities and challenges facing the field of mycology that arose from discussions at the 2022 meeting, with emphasis on novel host risk factors, emerging resistant fungal pathogens, the evolving antifungal pipeline, and critical issues affecting the advancement of mycology research.

Invasive fungal diseases (IFDs) are associated with significant morbidity and mortality and pose a growing threat globally [1].The Mycoses Study Group Education and Research Consortium (MSGERC) is a collective of clinicians, researchers, and educators dedicated to advancing awareness, diagnosis, and management of IFDs.Clinical Mycology Today 2022, MSGERC's biennial meeting, was held September 7-9, 2022, in Albuquerque, New Mexico, and brought together stakeholders to review challenges and outline a vision for the field.All 40 presentations given at the meeting were recorded and are freely and openly available on the MSGERC's public YouTube channel (https://msgerc.org/2022-biennial-meeting/).The report here highlights salient themes to emerge from the meeting and attempts to expand on these discussions to highlight challenges and opportunities in clinical mycology for the next decade.
It is a dynamic time for the field of clinical mycology.Advances in medical therapies continue to lead to increased numbers of patients at risk of IFD.These include patients receiving solid organ and stem cell transplantation, chimeric antigen receptor (CAR) T-cell therapy, monoclonal antibodies, and small molecule targeted therapies.At the same time, virulent, highly transmissible, and/or resistant fungal pathogens have spread globally, challenging public health and infection prevention and control efforts.After years of stagnation in the development of antifungals, driven by challenges in trial execution and design as well as the lack of financial incentives to bring novel antimicrobials to market, promising new treatments are now on the horizon, including several new classes of antifungal therapies with novel mechanisms of action, as well as refinements in drugs from existing classes with improved tolerability, pharmacokinetics, and ease of administration.Despite this, there are major challenges anticipated, including anticipated shortfalls related to the number of clinicians and scientists with expertise and interest in fungal disease, limited research funding opportunities, and regulatory challenges related to clinical trial design execution.growth of biologics and small molecule agents, as well as cellular therapies has occurred since the 1990s [19,20].These therapies target specific immunologic pathways or immune cell subsets as opposed to the broader immunosuppressive activity of corticosteroids or cytotoxic chemotherapy [21][22][23].Despite this targeted approach, infections remain an important complication, and risk for individual pathogens can be difficult to predict based on mechanism.The speed with which these novel therapies are being developed and the lack of uniform attention to opportunistic infections in clinical trials has led to delayed identification of therapies that pose a risk for IFDs [24].In addition to the development of novel agents, older biologic therapies with well-known risk profiles are being applied in new settings such as combination monoclonal antibody and small molecule therapy for chronic lymphocytic leukemia, maintenance immunotherapy following allogeneic HCT or CAR T-cell therapy, and use of Janus kinase inhibitors or tumor necrosis factor-α (TNF-α) inhibitors for treatment of graft-versus-host disease [25][26][27][28][29][30][31][32].Longer durations of therapy are also being used, but the cumulative risk of infection over time has not been fully assessed in clinical trials.The risk of IFDs may be related to the patient's net state of immunosuppression more than to any individual agent and thus must continue to be reassessed with these new drug applications.Improved understanding of individual risk factors and the continued development of biomarkers and novel tools potentially harnessing the power of artificial intelligence to assess risk for IFDs in this population will be vital to prevent morbidity and mortality.

Monoclonal Antibodies and Small Molecule Therapies
Monoclonal antibodies (Mabs) target cell surface receptors or soluble cytokines and are among the first immunotherapies approved in the United States [20].Since the first MAbs approval in 1986, more than 100 products have surfaced across a multitude of fields [33,34].PD1/PDL1 immune checkpoint inhibitors, CD20 inhibitors, and TNF-α inhibitors constitute the most common targets.When assessing attributable risk for IFDs, it can be difficult to determine the impact of any individual therapy on a background of underlying disease, prior treatment regimens, and immunologic effects of combination therapy.In addition some agents, such as immune checkpoint inhibitors may be associated with acute toxicities that are in turn treated with additional immunosuppressive therapies such as corticosteroids, potentially increasing the risk of IFDs in those patients.Nonetheless, risk of IFDs appears to be low for these common Mabs [20,21,35,36].
TNF-α inhibitors represent a notable exception with an increased risk for opportunistic infections reported in large studies including a predisposition for endemic fungal infections such as histoplasmosis and coccidioidomycosis, leading to a black box warning for these products [37][38][39][40][41][42][43][44].Other less commonly used Mabs with clearly established risks for IFDs include CD52-targeted agents (alemtuzumab) and interleukin-17 (IL-17)-targeted agents (brodalumab, ixekizumab, and secukinumab) [21,45].Serious opportunistic infections including IFDs related to profound B-and T-cell depletion have been reported with alemtuzumab and routine Pneumocystis jirovecii pneumonia prophylaxis is recommended during use [46].IL-17-targeted agents are primarily used for the treatment of autoimmune and inflammatory diseases and have been associated with an increased risk of candidiasis, which is predicted given the association of chronic mucocutaneous candidiasis with mutations affecting the IL-17 pathway [47][48][49].Notably, invasive candidiasis appears to be uncommon and with these more mild mucosal infections, drug discontinuation is often unnecessary [49].Finally, emerging evidence suggests that there may be an increased risk for IFDs in patients receiving belatacept (CTLA-4 monoclonal antibody) in patients following solid organ transplantation, though confirmatory studies are needed.
Small molecules represent another class of rapidly expanding targeted immunotherapy [50].These agents typically act as intracellular secondary messengers and thus have a propensity for increased off-target effects including impaired pathogen response [20].Several small molecule agents have been associated with an increased risk for IFDs.Bruton's tyrosine kinase inhibitors are the most well-known example, where multiple postmarketing studies emerged suggesting an increased risk for fungal infections, in particular with increased rates of invasive mold infections involving the central nervous system [19,24,[51][52][53][54][55][56][57][58][59][60].The risk appears to be increased for patients with chronic lymphocytic leukemia following prior antineoplastic therapy or receiving combination therapy with corticosteroids, demonstrating the impacts of cumulative immunosuppression [60,61].
Phosphoinositide 3-kinase (PI3K) inhibitors are a second class of small molecule agents that have been associated with an increased risk for IFDs [22,62].These agents are primarily used for the treatment of hematologic malignancy, and multiple phase III studies have been halted because of high rates of death and serious adverse events that were primarily attributed to opportunistic infections including Pneumocystis jirovecii pneumonia [63][64][65].Given more recent trials indicating worse overall survival for patients receiving PI3K inhibitors as well as significant toxicity, increased scrutiny is being placed on this drug class with several withdrawals from the market [66].For patients receiving PI3K inhibitors, routine Pneumocystis prophylaxis is recommended and close surveillance for other opportunistic infections should be undertaken.

Cellular Therapies
Cellular therapies such as CD19-directed CAR T-cell therapy for the treatment of acute lymphoblastic leukemia and large B-cell lymphoma, as well as B-cell maturation antigen-directed CAR T-cell therapy for treatment of multiple myeloma have thus far demonstrated a low risk of IFDs in multiple studies [67][68][69].Cases have been reported and are often in the setting of advanced disease with extensive prior therapies including HCT or severe toxicities requiring treatment with high-dose corticosteroids [67,70,71].Further studies are needed to characterize specific risk factors for IFDs in this population and to delineate the optimal approach to antifungal prophylaxis and stewardship in this population.Furthermore, as we begin to see increasing numbers of patients who are treated with cellular therapies earlier in the course of disease, or for nononcologic diseases, the risks of IFDs may be even lower and it will be important to continue to assess these risks and modify prophylactic strategies as indicated [72,73].

Genetic Risk for Invasive Fungal Disease
Advances in the molecular and genetic tools for assessment of acquired immunodeficiency have resulted in enormous gains in understanding of host genetic risk factors for IFDs over recent years.Genetic mutations in CARD9, STAT1, STAT3, and AIRE, as well as IL-17 and IL-12 receptors have been associated with chronic mucocutaneous candidiasis and invasive candidiasis as well as other fungal infections [18,48,[74][75][76].Invasive mold infections such as aspergillosis have been associated with defects in phagocyte effector function due to nicotinamide adenine dinucleotide phosphate oxidase mutations, as well as GATA2 mutations [18,77,78].Finally, disruption of normal IL-12 and interferon-γ signaling appears to predispose patients to serious endemic or dimorphic fungal infections [17,76,79].These insights have aided in better understanding the impacts of targeted therapies that act on similar pathways.Advances in the field of immunogenetics over the coming years may help to define genetic or immunologic markers that indicate an increased risk for IFDs in patients without diagnosed immunodeficiency syndromes [76,80].

Fungal Infections Complicating Respiratory Viral Infections
Even before the arrival of COVID-19, influenza-associated fungal infections were increasingly reported, albeit with significant heterogeneity in the prevalence across geographic regions.For instance, in a seminal retrospective study, the Dutch-Belgian Mycoses Study Group reported that aspergillosis complicated nearly 1 in 5 intensive care unit admissions for severe influenza [81].COVID-19 has similarly introduced a large population of patients with localized and systemic immunological derangements that increase the likelihood of invasive fungal infection, even in persons without classic risk factors [82,83].Pulmonary aspergillosis is a serious complication that can compound morbidity and mortality of critically ill patients with COVID-19 and has been reported globally [83,84].In addition, in some geographic regions-most notably India-COVID-19 emerged as an important risk for rhino-orbital-cerebral and to a lesser extent pulmonary mucormycosis [85].The public health burden from mucormycosis was substantial, with tens of thousands of persons in India affected during the delta wave, before the widespread availability of vaccines [85].The most important risk factors for COVID-19-associated mucormycosis are poor glycemic control (often in persons with undiagnosed diabetes) worsened by receipt of corticosteroids [86].

Iatrogenic Outbreaks of Fungal Disease
Some fungal infections are primarily acquired from the hospital environment, with prototypical examples being colonization and disease with Candida auris, or pulmonary or cutaneous mold infections in intensive care units or hematology wards when engineering controls are absent or compromised.In recent years, health care-associated outbreaks have emerged involving contaminated injectable medication.A decade ago, intrathecal injection of methylprednisolone from contaminated vials led to hundreds of cases of fungal meningitis caused by Exserohilum rostratum [87].Far from being an isolated occurrence, there have been 2 recent outbreaks of iatrogenic fungal meningitis caused by Fusarium sonali linked to contaminated anaesthetics in Mexico [88,89].Prevention and containment of future national and international outbreaks will require ongoing cooperation between regulators, epidemiologists, laboratorians, and clinicians globally.

Mitigating Emerging Host Risks
The landscape of host risk factors for IFD is rapidly transforming.As outlined here, it can be exceedingly difficult to characterize the attributable risk of any single therapeutic agent when administered on a background of advanced underlying disease and heavy prior immunosuppression.Nevertheless, it remains critical that there is ongoing focus on evaluating novel therapies with improved surveillance for IFDs in clinical trials, as well as continued evaluation in a "real-world" setting following approval.New applications of old drugs should not be considered to have the same risk profile as previously shown for other indications, and the cumulative immunosuppressive effects of long-term therapies should be considered.

PATHOGENS: THE THREAT OF ANTIFUNGAL RESISTANCE
The landscape of fungal pathogens causing clinically important infections is diverse and dynamic.The most common and deadly pathogens have been collated and ranked by the World Health Organization in their first Fungal Priority Pathogen List, published soon after the meeting [1].In addition to these familiar foes that continue to cause disease in hospital and community settings, pathogens with new epidemiological or geographical associations such as COVID-associated fungal disease have arisen in recent years [82].In addition, fungal resistance patterns continue to shift with the emergence of drug-resistant fungal pathogens across multiple species and disease types [90].This ongoing evolution of fungal pathogens has important implications for individual clinical management and treatment as well as global public health efforts.

Drug-resistant Dermatophytes
Although not life-threatening, dermatophyte infections affect as many as 1 in 5 people around the world and can contribute to substantial morbidity through disfiguring and often painful or pruritic skin lesions [91].In this context, drug-resistant dermatophytosis is an emerging global health threat [92].Among Trichophyton species, the predominant agents of dermatophytosis in North America, Trichophyton indotineae (previously T mentagrophytes genotype VIII) has recently emerged as a novel strain with global spread, increasingly severe inflammatory lesions, and resistance to terbinafine and azole antifungals such as itraconazole and fluconazole, traditionally considered first-line treatments [93].Trichophyton rubrum is the most common cause of dermatophytosis and has also had increasing treatment-resistance documented globally and in the United States [92].Among dermatophytes referred to a U.S. reference laboratory in 2021-2022, Cañete-Gibas et al. reported that 18.6% were resistant to terbinafine, including isolates of T rubrum and T indotineae [93].Furthermore, the incidence of resistant isolates may be underestimated given the challenges in obtaining antifungal susceptibilities with many cases not obtaining a confirmed microbiologic diagnosis [94].These shifts in both the severity and susceptibility profiles of dermatophyte infections can significantly impact morbidity and have led to global outbreaks that are difficult to treat or control.Further studies are needed to better characterize the evolving epidemiology, transmission, host interactions, and outcomes of these challenging infections.

Drug-resistant Aspergillosis
In contrast to dermatophytosis, invasive mold infections are less common but carry high mortality rates, occurring predominantly among immunocompromised persons.The most common cause of invasive mold infections is Aspergillus fumigatus, and among this species, azole resistance has increased in recent years.In some parts of the world, azole resistance in A fumigatus is clearly linked to use of azole fungicides in horticulture and agriculture but can also be impacted by patient exposure to antifungals via broadly increased use of antifungal prophylaxis in immunosuppressed populations [90,95].In the Netherlands, for example, as many as 15% of A fumigatus clinical isolates in some years are azole-resistant [96].Rare cases of azole-resistant A fumigatus with telltale genetic mutations that bely this in-field mechanism of resistance acquisition have been reported in the United States, but clinical and environmental surveys have not identified rates of resistance that approach what is observed in the Netherlands [97].Nonetheless, azole-resistance A fumigatus remains a real threat, with the potential for increased toxicity related to non-azole antifungal therapy and increased mortality reported in multiple studies [98].
In addition to A fumigatus, other species with reduced susceptibility to antifungals may also be implicated in disease.For example, A terreus is frequently resistant to amphotericin B [99].In addition, cryptic species of Aspergillus with reduced susceptibility to antifungals can be overlooked by phenotypic identification methods.

Candida auris
Candida auris is a multidrug resistant yeast that is prone to environmental colonization leading to outbreaks in the healthcare setting that are difficult to contain [100,101].C auris emerged independently in multiple regions in 2009 and has continued to spread around the world and across North America [102].The COVID-19 pandemic "was like throwing a bit of lighter fluid on the fire" noted Centers for Disease Control and Prevention Mycotic Diseases Branch Chief, Dr. Tom Chiller, at the meeting.In the United States, clinical cases of C auris increased dramatically, with year-over-year increase of 95% between 2020 and 2021 [100].Major infection prevention and control challenges caused by C auris remain, including difficulty of disinfecting contaminated health care environments, and inability to effectively decolonize patients.

TREATMENT: NEW HOPE ON THE HORIZON
After years of stagnation, the antifungal development pipeline is flourishing [103,104].There are new antifungal agents with meaningful advantages in pharmacokinetic properties, safety profile, and/or route of administration compared to extant options from existing antifungal classes, as well as first-in-class antifungals with novel mechanisms of action that are in advanced stages of development (Table 1) [105].In addition, investigation of the potential benefits of immunotherapy or immune augmentation as an adjunctive approach to standard antifungal therapy in patients with IFDs is ongoing and may change the treatment paradigm in years to come [76,106].
Until now, treatment of invasive fungal infections has been limited to few classes of antifungals, namely the polyenes (amphotericin B), azoles, and echinocandins.Flucytosine is another antifungal with a limited role as part of combination therapy in some systemic and resistant mycoses (eg, in the central nervous system or urinary tract), and terbinafine is occasionally used in combination in difficult to treat mold infections.New agents among the azoles include oteseconazole, which specifically targets fungal ergosterol synthase, and is negligibly metabolized by mammalian CYP450 enzymes, resulting in a long half-life, fewer adverse effects, and avoidance of drug-drug interactions [107].It has already received Food and Drug Administration approval for treatment of recurrent vulvovaginal candidiasis in women who are not of child-bearing potential [108].Among the echinocandins, rezafungin has a longer half-life allowing once-weekly administration and has been approved for treatment of invasive candidiasis and candidemia [109].Ibrexafungerp is an oral triterpenoid antifungal that shares a mechanism of action with echinocandins (inhibition of 1,3-β-d-glucan synthase) and that has been approved by the Food and Drug Administration for treatment of vulvovaginal candidiasis [108] and is currently being evaluated for other indications.Encochleated amphotericin B is a novel reformulation of the polyene within a lipid bilayer rolled into a taquito-shaped nanocochleate, which improves bioavailability that enables oral administration and an improved safety profile [110].A third-generation renal-sparing polyene has also been developed and is undergoing preclinical evaluation [111].In addition to these, there are several first-in-class antifungals with novel mechanisms of action.These include olorofim, an orotomide, which works by blocking pyrimidine biosynthesis and has potent antifungal activity against Lomentospora, Scedosporium, and azole-resistant Aspergillus isolates, and some dimorphic fungi [112]; and fosmanogepix, the first gepix antifungal, which inhibits glycosylphosphatidylinositol synthesis by binding to Gwt1, and which shows promise for a wide spectrum that includes yeasts (including C auris) but that is most anticipated for potent activity against Lomentospora, Scedosporium, Fusarium, and Aspergillus [104].

Expanding the Scope of Clinical Trials
The development of new treatments for fungal diseases has forced into focus issues of clinical trial design to identify the optimal roles of these agents in our armamentarium.The development of clinical trials for the treatment and prevention of fungal infections must consider input from a range of stakeholders, including patients, physicians, pathologists, pharmaceutical companies, and government agencies.Most clinical trials evaluating mold-active therapies are conducted in the global north and focus primarily on hematological oncology patients, which may limit generalizability of results beyond these populations.Trials for treatment of cryptococcal meningitis are generated in resource-limited settings in the context of HIV, although HIV-seronegative persons comprise most affected patients in resource-rich countries.In general, there is a need to explore management of IFDs in patients with other risk factors, including emerging risks from new antineoplastic therapeutics outlined previously.Moreover, most clinical trials are conducted only in nonpregnant adults and exclude children.It is imperative to improve global representation and equity in clinical trials for IFDs and to focus on groups in highest need.

Clinical Trial Response Criteria: Opportunities for Improvement
Given the high associated mortality of IFD and its increased impact in populations of patients who are heavily immunosuppressed and often critically ill, the design and conduct of successful trials for novel antifungal therapeutics remains challenging [113][114][115].In particular, the current response criteria for invasive fungal disease have important limitations that have spurred efforts to expand the definition of treatment success, better understand attributable mortality resulting from IFDs, incorporate mycologic biomarkers, and work toward the use of patient-reported outcomes.

Where Clinical Trials Fall Short
Observational studies and the use of secondary data present new opportunities for mycology research because they can help answer questions that are difficult to address through randomized controlled trials.However, there are barriers to the acceptance and expertise needed to conduct adaptive trials in mycology.Cohort studies have gained traction in mycology, and the use of electronic data sources provides a wealth of data collected over many years, offering opportunities for exploring rare outcomes and exposures more rapidly than traditional methods.Although such data sources have been underused in mycology, they enable a wider range of research questions to be addressed in a timely manner.A tradeoff of using secondary data is that outcomes tend to be broad, but the benefits of this approach can be significant.

Workforce Challenges
The challenges and opportunities in clinical mycology demand a robust workforce of clinicians and scientists focused on these problems.However, there is a common agreement that there are too few mycologists around the world, and few investigators enter and are retained in the field.Among medically trained clinical mycologists, most are infectious diseases (ID) physicians, and, to an extent, challenges in ensuring a robust ID workforce are reverberated in the clinical mycology arena.Challenges in attracting trainees to the subspecialty are well documented.For instance, one quarter of U.S. training posts for ID went unfilled in the residency match of 2023 [116].Human Resources & Services Administration models suggest that there are at least 240 too few ID physicians in the United States, with shortfalls concentrated in rural areas [117]; in fact, an earlier study suggested that >200 million Americans live in counties with no or insufficient access to an ID physician [118].

CONCLUSIONS
Invasive fungal disease represents a worldwide public health threat and key opportunities and challenges are facing the field of mycology over the coming years.Improved understanding of host risk factors, epidemiologic surveillance of emerging resistant fungal pathogens, and expansion of the clinical and basic research pipelines in mycology are essential to improve patient outcomes.

Figure 1 .
Figure 1.Interplay of risks of fungal disease from novel therapies, traditional inherited or acquired host factors, and genetic risk factors.

Table 1 . New Antifungals Recently Approved or in Advanced Stages of Clinical Development
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