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Climate Driven Evolutionary Dynamics of Fungi and the Emergence of Antifungal Resistance

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16 July 2026

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17 July 2026

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Abstract
Fungal infections are an increasingly important yet underrecognized global health threat. Climate change, environmental disruption, and intensified human–animal interactions are shifting fungal ecology, enabling pathogens to push beyond traditional geographic and thermal boundaries. Increasing temperature, shifting humidity, and extreme weather events have favoured the emergence and reemergence of fungal disease, as reflected in the rapid global dissemination of Candida auris, in a manner defying conventional models of pathogen spread. The environmental drive to fungal adaptation includes increased thermotolerance and survival under hostile conditions for the infection of endothermic hosts. At the human-animal-environment interface, the zoonotic spillover accelerates fungal evolution toward increased virulence and antifungal resistance. Resistance to all major classes of antifungal drugs is increasingly observed and “seriously challenges treatment, leading to persistent infections and a greater healthcare burden.” Despite advances in molecular diagnostics and genomic surveillance, significant gaps in our understanding of fungal transmission, host adaptation, and resistance mechanisms remain. This review focuses on climate-driven fungal emergence, its zoonotic potential, antifungal resistance, and current detection strategies that call for immediate action through integrated One Health surveillance and coordinated global responses.
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1. Introduction

Fungal diseases are an increasing, yet often ignored, global health issue (Rio et al., 2023; Anupama, 2024). The World Health Organization (WHO) released its first-ever fungal priority pathogens list (FPPL) in 2022, identifying 19 fungi that pose major risks to public health due to rising antifungal resistance and increasing incidence. (Figure 1) shows the global list of priority endemic pathogens. Once viewed mainly as opportunistic infections with little significance, fungal pathogens are now recognized as organisms that can quickly change, spread to new areas, and find new hosts (Corrêa-Junior et al., 2025; Kruithoff et al., 2023). The rising rates of invasive, superficial, and allergic mycoses worldwide show clear links to changes in climate, land use, urban development, medical practices, and global movement (Halak, 2025; Sztandera-Tymoczek, 2023; Petrucelli et al., 2020). These factors have shifted the ecological and evolutionary landscape of fungi. As a result, we need to pay more attention to how fungi spread and how new diseases emerge globally.
Recent years have revealed unusual global patterns of fungal emergence. These show the almost simultaneous appearance of different genetic lineages across various continents (Garcia-Bustos, 2024; Phan-Canh et al., 2024). Such trends challenge traditional outbreak models that focus only on local spread. A key example is Candida auris, which appears to have distinct clades emerging nearly at the same time due to strong environmental pressures (Garcia-Bustos, 2024; Phan-Canh et al., 2024). These findings highlight how ecological changes, environmental reservoirs, and adaptive evolution allow fungi to spread beyond typical geographic locations and host types.
Climate change is a major factor driving these trends. It affects fungal ecology by raising temperatures, changing humidity, and increasing extreme weather events (Anupama, 2024; Rio et al., 2023; Cuartero et al., 2024). These changes expand fungal habitats and promote the development of traits like heat tolerance and stress resistance, which help fungi thrive in animal hosts (Phan-Canh et al., 2024; Corrêa-Junior et al., 2025). This climate-driven adaptation lowers the usual barriers that restrict fungi’s ability to cause disease in humans and animals. As a result, there is a greater chance of new or returning fungal diseases.
At the same time, increasing interactions between humans, animals, and the environment have raised opportunities for zoonotic spillover and host adaptation (Gupta et al., 2025; Cabañes, 2000; Chang et al., 2022). Domestic animals, wildlife, and human-altered environments are becoming interconnected reservoirs under a One Health approach (Ganesan et al., 2025). Evidence of fungal infections in animals raises concerns about transmission between species, lasting reservoirs, and the potential increase in virulence or drug resistance through host switching (Gupta et al., 2025; Chang et al., 2022). These processes are not yet well understood, but they may play a key role in ongoing fungal transmission.
A troubling aspect of modern fungal epidemiology is the rapid rise of antifungal resistance. This has become a global problem affecting many types of fungi, making both first-choice and alternative treatments less effective (Kruithoff et al., 2023; Lass-Flörl & Cuenca-Estrella, 2017; Hwang et al., 2014). Several factors contribute to this crisis, including the limited number of antifungal drug classes, the widespread use of azole compounds in agriculture, inappropriate or long-term antifungal use in hospitals, and environmental stressors that promote genetic and epigenetic changes (Phan-Canh et al., 2024; Cuartero et al., 2024). Resistance occurs through various mechanisms, such as mutations at target sites, overexpression of efflux pumps, biofilm formation, and stress-induced genomic changes, allowing fungi to withstand both environmental pressures and treatments (Phan-Canh et al., 2024; Kruithoff et al., 2023).
The impact of antifungal resistance on human health is serious. Infections from drug-resistant fungi often lead to delayed diagnoses, treatment failures, ongoing colonization, longer hospital stays, and higher death rates (Lass-Flörl & Cuenca-Estrella, 2017; Anupama, 2024; Kruithoff et al., 2023). Invasive infections from resistant fungi particularly affect immunocompromised individuals, critically ill patients, and those needing long-term medical care. Additionally, resistance complicates efforts to control infections, raises healthcare costs, and limits treatment options, highlighting a significant gap in global readiness for fungal diseases.
Despite progress in molecular biology, we still face significant knowledge gaps in fungal epidemiology, genomics, and surveillance (Phan-Canh et al., 2024; Cuartero et al., 2024; García-Martín et al., 2024). Many areas lack standardized diagnostic procedures, routine antifungal susceptibility tests, and integrated genomic monitoring systems (Petrucelli et al., 2020; Kruithoff et al., 2023). Although tools like polymerase chain reaction tests, whole-genome sequencing, MALDI-TOF MS, and environmental metabarcoding have improved how we detect and study fungi, their use is inconsistent worldwide (Petrucelli et al., 2020; García-Martín et al., 2024; Amin & Bertelsen, 2025). Methodological issues such as underreporting, diagnostic uncertainty, incomplete reference databases, and a lack of integration of human, animal, and environmental data continue to obscure our understanding of transmission routes and the full scope of antifungal resistance.
This review brings together current evidence on global patterns of fungal transmission and geographic spread, the impact of climate change on fungal emergence, zoonotic spillover, host adaptation, and the growing issue of antifungal resistance, including its origins, mechanisms, and effects on human health. It also evaluates current detection methods and available protocols globally and identifies key methodological and knowledge gaps that must be addressed to improve surveillance, diagnosis, and management of fungal diseases during rapid environmental change.

2. Global Patterns of Fungal Transmission and Geographic Expansion

Global fungal transmission results from long-term ecological factors and modern human activities. Unlike fungi that only infect humans, these organisms can thrive without hosts. They can survive in soil, water, plant material, built environments, and animal reservoirs (Lass-Flörl et al., 2017; Vitasse et al., 2021; Corrêa-Junior et al., 2025). This ability allows fungi to quietly expand their geographic reach over long periods. Their endurance in the environment lets fungi cross political and ecological boundaries without direct human-to-human spread.
Recent phylogenomic studies indicate that fungal expansion usually occurs from multiple independent emergence events rather than a single source (Garcia-Bustos, 2024; Phan-Canh et al., 2024). The nearly simultaneous appearance of different strains of Candida auris across continents strongly supports this idea (Garcia-Bustos, 2024; Phan-Canh et al., 2024). We see similar patterns with dermatophytes, where migration, international travel, movement of people, and changes in hygiene and lifestyle have shifted which species dominate in various regions (Petrucelli et al., 2020; Belmokhtar et al., 2024; Kruithoff et al., 2023; Gupta et al., 2025).
Environmental sources like wastewater systems, hospital waste, swimming pools, and soil disrupted by urbanization connect clinical and environmental fungal populations (Garcia-Bustos, 2024; Cuartero et al., 2024; Amin & Bertelsen, 2025). Together, these findings suggest that we should view fungal transmission as a global ecological process and not just a clinical issue.

3. Rapid Emergence of Antifungal Resistance

Antifungal resistance has become a major global issue in medical and environmental mycology. It has fundamentally changed how we handle fungal diseases (Kruithoff et al., 2023; Lass-Flörl & Cuenca-Estrella, 2017; Hwang et al., 2014). Unlike bacterial pathogens, fungi have similar cellular and metabolic processes to humans. This limits the number of safe antifungal drug targets and reduces treatment options to a few drug classes, mainly azoles, echinocandins, and polyenes (Lass-Flörl & Cuenca-Estrella, 2017). Echinocandins (such as caspofungin, micafungin, and anidulafungin) have similar spectra and safety profiles but share susceptibility to the same resistance mechanisms. Amphotericin B, the only widely used polyene, is limited by significant toxicity. Although three drug classes are available, resistance to even one can substantially restrict therapeutic options, particularly in the presence of adverse effects or drug interactions (Logan et al., 2022). Reports show that resistance to one or more of these classes is now common among yeasts, dermatophytes, and filamentous fungi (Kruithoff et al., 2023; Lass-Flörl & Cuenca-Estrella, 2017; Gupta et al., 2025).
A key feature of antifungal resistance is that it often develops independently in different geographic areas (Garcia-Bustos, 2024; Hwang et al., 2014). Genomic studies suggest that resistant strains usually emerge locally due to selective pressure rather than spreading from a single ancestral strain (Garcia-Bustos, 2024; Phan-Canh et al., 2024). A clear example is Candida auris, where genetically distinct groups evolved independently on different continents. (Table 1) presents the antifungal resistance patterns and evolutionary trajectories of the major fungal pathogens.
The rise of antifungal resistance is driven by a combination of environmental, ecological, and clinical pressures (Kruithoff et al., 2023; Phan-Canh et al., 2024). The widespread use of azole fungicides in agriculture is a major environmental factor (Lass-Flörl & Cuenca-Estrella, 2017; Kruithoff et al., 2023). Climate change worsens this pressure by encouraging fungal growth, extending growth seasons, and increasing the use of antifungal chemicals in farming (Sztandera-Tymoczek, 2023; Halak, 2025). Environmental stresses like temperature changes, humidity shifts, chemical exposure, and nutrient shortages provoke adaptive genetic responses in fungi (Cuartero et al., 2024; Phan-Canh et al., 2024).
Clinical practices also significantly contribute to the development of resistance. Inappropriate prescribing of antifungals, prolonged or repeated treatments, empirical therapies without lab confirmation, and inadequate dosing promote the selection of resistant strains (Dogra & Narang, 2017; Kruithoff et al., 2023). Additionally, the lack of regular antifungal susceptibility testing and standardized monitoring systems in many areas adds to these problems (Petrucelli et al., 2020; Hwang et al., 2014).
Microbial resistance encompasses both primary resistances, in which strains exhibit intrinsic reduced susceptibility to a specific antifungal agent, and secondary resistance, where previously susceptible strains develop resistance following antifungal exposure (Cowen et al., 2014). On a molecular level, antifungal resistance occurs through various mechanisms (Phan-Canh et al., 2024; Kruithoff et al., 2023). These include point mutations in antifungal target genes, overexpression of efflux pumps, and biofilm formation as represented in (Figure 2). Fungi also show noteworthy genetic flexibility, such as aneuploidy and stress-induced chromosomal changes (Phan-Canh et al., 2024; Cuartero et al., 2024).

4. Effect of Antifungal Resistance

The impact of antifungal resistance extends beyond microbiological failure. It affects clinical outcomes, healthcare systems, and public health (Lass-Flörl & Cuenca-Estrella, 2017; Anupama, 2024; Kruithoff et al., 2023). Drug-resistant fungal infections often lead to treatment failures, prolonged colonization, repeated disease, and a higher risk of transmission (Dogra & Narang, 2017; Gupta et al., 2025). In cases of invasive fungal infections, resistance increases morbidity and mortality rates, especially among immunocompromised individuals (Anupama, 2024; Lass-Flörl & Cuenca-Estrella, 2017).
In superficial and chronic mycoses, antifungal resistance has turned manageable infections into ongoing and debilitating conditions (Dogra & Narang, 2017; Kruithoff et al., 2023). Patients often face extensive disease, chronic inflammation, relapses, and a significant decline in their quality of life. This frequently requires long or repeated courses of antifungal therapy. These clinical challenges create a large economic burden, including increased healthcare visits, repeated tests, longer treatment times, and the use of second-line drugs (Anupama, 2024; Kruithoff et al., 2023).
From a public health standpoint, antifungal resistance makes controlling outbreaks harder and skews disease burden estimates. The inconsistency between in vitro antifungal susceptibility testing and clinical outcomes adds to the difficulty of making treatment decisions and conducting surveillance (Dogra et al., 2017; Petrucelli et al., 2024). Furthermore, finding resistant fungal strains in the environment and animal hosts shows that resistance extends beyond healthcare facilities. It is part of larger ecological systems, which emphasizes the need for surveillance and intervention strategies based on a One Health approach (Garcia-Bustos, 2024; Chang et al., 2022).

5. Climate Change as a Driver of Emerging and Re-Emerging Fungal Diseases

Climate change plays a significant role in influencing fungal diversity, distribution, and their ability to cause disease (Anupama, 2024; Rio et al., 2023; Cuartero et al., 2024; Corrêa-Junior et al., 2025). Changes in global temperatures, humidity, rainfall patterns, and extreme weather events create constant pressure on fungal populations in the environment (Sztandera-Tymoczek, 2023; Halak, 2025; Amin & Bertelsen, 2025). This favors traits like heat tolerance, salt tolerance, resistance to oxidative stress, and adaptability (Phan-Canh et al., 2024; Corrêa-Junior et al., 2025). These traits are also essential for fungi to survive in mammals, indicating that climate change helps fungi that cause diseases to emerge (Phan-Canh et al., 2024; Anupama, 2024). The potential effects of climate change on different pathogenic fungi and fungal diseases are illustrated in (Figure 3).
Longer warm seasons and irregular rainfall extend the growth period for fungi, increasing human and animal exposure to them (Halak, 2025; Sztandera-Tymoczek, 2023). Research on airborne fungi shows that spores are appearing earlier in the year and lasting longer into fall (Halak, 2025). This disrupts traditional seasonal patterns and raises the risk of cumulative exposure. Extreme weather events like floods, storms, hurricanes, and dust storms can spread fungal spores over long distances, introducing them into areas that typically do not support these fungi (Sztandera-Tymoczek, 2023; Cuartero et al., 2024). These changes enable both harmful and allergenic fungi to expand their geographic range, even into temperate and high-altitude areas (Vitasse et al., 2021; Rio et al., 2023).
Climate change also affects the vulnerability of hosts (Anupama, 2024; Rio et al., 2023). Heat, food shortages, malnutrition, and environmental damage weaken the immune responses of humans and animals. This increases the risk of opportunistic fungal infections (Anupama, 2024). Rising respiratory diseases, damage to skin barriers, and ongoing health problems add to this vulnerability. Additionally, shifts in indoor environments, such as increased dampness, poor ventilation, and higher humidity, lead to more indoor fungal growth (Amin & Bertelsen, 2025). This further increases exposure to harmful molds.
In agricultural and environmental settings, climate change has heightened the threat from fungal plant diseases (Mawar & Saranya, 2023; Cuartero et al., 2024). This has resulted in more and longer use of azole fungicides (Kruithoff et al., 2023; Lass-Flörl & Cuenca-Estrella, 2017). These substances share structural and functional similarities with medical azoles, creating environmental sources of antifungal resistance that overlap with clinical antifungal treatments (Lass-Flörl & Cuenca-Estrella, 2017; Kruithoff et al., 2023). This connection highlights an ecological link between climate change, farming practices, and the rise of antifungal resistance that is crucial for health. Overall, these findings reveal that climate change is not just a background factor; it is a major driver of the emergence, adaptation, and resurgence of fungi that impact humans and animals (Anupama, 2024; Corrêa-Junior et al., 2025).

6. Zoonotic Spillover and Host Adaptation in Fungal Pathogens

Zoonotic spillover has gained attention as a key factor in the emergence and persistence of fungal pathogens (Gupta et al., 2025; Chang et al., 2022). Many fungi have great ecological flexibility and low host specificity. This allows them to infect humans, domestic animals, livestock, wildlife, and environmental sources such as soil and water (Cabañes et al., 2000; Chang et al., 2022; Gupta et al., 2025). Animals often act as silent carriers, keeping fungal populations alive over time and allowing unnoticed transmission between different host species and regions (Gupta et al., 2025; Cabañes et al., 2000). (Table 2) shows global annual incidence of zoonotic transfer of various fungal pathogens. Recent epidemiological surveillance according to Denning (2024) shows a sharp uptick in fungal “alerts” and incidence. According to ProMED data, fungal disease alerts increased from 1% to 7% of all recorded outbreaks between 1995 and 2024, with animal-to-human spillover events specifically rising by approximately 1.4%.
Fungi adapt to their hosts through a combination of phenotypic flexibility and quick genetic changes. Processes like morphogenetic switching, metabolic reprogramming, stress-response activation, and genomic rearrangements help fungi efficiently take advantage of new hosts and environments (Phan-Canh et al., 2024; Corrêa-Junior et al., 2025). For example, evidence of Candida auris colonizing dogs and reports of dermatophyte transmission from pets and livestock to humans suggest that fungi might cycle back and forth between humans and animals (Garcia-Bustos, 2024; Chang et al., 2022; Gupta et al., 2025). These cycles may support longer persistence, greater exposure to antifungal agents, and the selection of stress-resistant and drug-resistant traits (Gupta et al., 2025; Kruithoff et al., 2023).
Climate change increases the risk of zoonotic spillover by altering animal habitats, migration patterns, and population densities. This change leads to more interactions between humans and animals (Anupama, 2024; Ganesan et al., 2025). Thermal stress and environmental disruptions can weaken animal immune systems, making them more vulnerable to fungal colonization and shedding (Ganesan et al., 2025). In farming and peri-urban areas, intensified livestock production and close living conditions between humans and animals present more opportunities for fungal exchange. Wildlife moving due to habitat loss and extreme climate conditions might also introduce new fungal species into human-dominated areas, increasing the risk of host switching (Gupta et al., 2025). (Figure 4) shows a proposed scheme for the emergence of Candida auris, a multidrug-resistant, often fatal fungus identified by the WHO as a “critical” priority pathogen on its Fungal Priority Pathogens List (FPPL).
Despite growing evidence of zoonotic roles in fungal epidemiology, monitoring fungal pathogens in animal populations remains uneven (Gupta et al., 2025; Cabañes et al., 2000). Most monitoring systems focus on bacterial and viral zoonoses, leaving fungal spillover less recognized and reported. The absence of connected One Health monitoring frameworks makes it difficult to find new animal reservoirs, transmission routes, and key evolutionary areas (Gupta et al., 2025). Closing these gaps is crucial for understanding how host adaptation, zoonotic spillover, and environmental changes affect the future of fungal diseases.

7. Diagnostic Strategies and Standardized Protocols for Fungal Detection

Fungal detection and identification rely on a combination of conventional, molecular, and genomic methods. Each method has its own strengths and weaknesses (Petrucelli et al., 2020; García-Martín et al., 2024; Kruithoff et al., 2023). Direct microscopy and culture are the primary methods for diagnosing fungi worldwide because they are inexpensive and widely used (Petrucelli et al., 2020). However, these techniques often have low sensitivity, long turnaround times, and frequent false-negative results, especially in superficial and invasive fungal infections (Petrucelli et al., 2020; Dogra & Narang, 2017). Morphological similarities among different fungal species and slow growth make accurate identification more difficult (Petrucelli et al., 2020).
Histopathology uses stains like periodic acid-Schiff and Gomori methenamine silver to show tissue invasion. However, it usually does not help with identification at the species level (García-Martín et al., 2024). As a result, many diagnoses remain presumptive, which can delay specific treatments.
Molecular diagnostic techniques have greatly improved fungal detection (Petrucelli et al., 2020; Kruithoff et al., 2023). PCR-based tests, including conventional and real-time PCR focused on the internal transcribed spacer (ITS) regions, offer higher sensitivity and specificity. They also allow for quick species identification directly from clinical samples (Petrucelli et al., 2020). MALDI-TOF MS has become a useful tool for routine fungal identification in clinical labs, but its accuracy depends on having comprehensive reference spectral libraries, which are often limited for many fungal species (Petrucelli et al., 2020; Hwang et al., 2014).
Whole-genome sequencing (WGS) is the most complete method for identifying fungi, investigating outbreaks, analyzing relationships between species, and profiling antifungal resistance (Garcia-Bustos, 2024; Phan-Canh et al., 2024). WGS has helped reveal independent emergence events, clade structures, and resistance mechanisms in new fungi. However, its use is mostly confined to research and reference labs due to costs, required infrastructure, and bioinformatics expertise (Phan-Canh et al., 2024).
Environmental surveillance methods, such as DNA metabarcoding and wastewater monitoring, are becoming important for detecting fungal populations and giving early warnings about fungal circulation outside clinical settings (Cuartero et al., 2024; Amin & Bertelsen, 2025). These methods provide insights into environmental reservoirs and transmission patterns, but they are not yet standardized for regular public health use.
For antifungal resistance, international bodies like the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) provide standardized testing protocols (Kruithoff et al., 2023; Hwang et al., 2014). These protocols set reference methods and interpretive guidelines, but their consistent use varies worldwide, especially in low- and middle-income countries (Hwang et al., 2014). Furthermore, there is often little correlation between lab susceptibility results and patient outcomes, complicating interpretation and clinical decisions (Kruithoff et al., 2023).
In summary, while many diagnostic tools and protocols are available globally, unequal access, a lack of standardization, and limited integration across human, animal, and environmental sectors present significant challenges (García-Martín et al., 2024; Gupta et al., 2025). To improve global fungal detection, it is necessary to standardize protocols, expand reference databases, enhance lab capabilities, and create coordinated One Health surveillance systems. This approach will help ensure timely detection and an effective response to emerging fungal threats.

8. Current Knowledge Gaps and Methodological Limitations in Fungal Epidemiology and Genomics

Despite growing awareness of fungal diseases as a global health problem, significant gaps remain in our understanding of fungal epidemiology, surveillance, and genomics (Phan-Canh et al., 2024; Cuartero et al., 2024; García-Martín et al., 2024). One main limitation is the consistent underestimation of the burden of fungal diseases. This stems from underreporting, misdiagnosis, and inadequate routine surveillance in many areas (Gupta et al., 2025; Petrucelli et al., 2020). Unlike bacterial and viral infections, fungal diseases are often left out of national and international surveillance systems. This results in incomplete and fragmented epidemiological data (Anupama, 2024).
A significant knowledge gap exists regarding how fungi are transmitted and their sources in the environment (Cuartero et al., 2024; Amin & Bertelsen, 2025). While we are becoming more aware of environmental, animal, and healthcare-related sources, we still do not fully understand the significance of each pathway. Long-term data linking environmental fungal populations to clinical samples is limited. This restricts our understanding of how climate change, land use, and human actions contribute to the emergence and spread of these diseases (Rio et al., 2023). Additionally, the dynamics of zoonotic transmission have not been studied in depth. Fungal surveillance in animals rarely connects with human health data (Gupta et al., 2025).
From a genomic perspective, whole-genome sequencing has changed our understanding of fungal populations (Phan-Canh et al., 2024). However, the datasets we have are still mostly biased towards clinical samples from wealthy countries. Environmental and animal samples are often absent, which limits comparative studies and our understanding of how fungi evolve, adapt to hosts, and develop resistance (Cuartero et al., 2024; Gupta et al., 2025). Many studies mainly focus on describing genomic data. There is a lack of research validating genetic variants linked to virulence or resistance to antifungal treatments. This limits the practical applications of the research (Phan-Canh et al., 2024).
Methodological challenges also include the absence of standardized genomic and phenotypic measurements (García-Martín et al., 2024; Phan-Canh et al., 2024). Variability within species, epigenetic factors, and genomic changes make it difficult to link genotypes to phenotypes. This is particularly true when comparing samples from different regions and labs. The lack of universally accepted reference strains and consistent analytical methods complicates efforts to ensure reproducibility and comparability worldwide (Phan-Canh et al., 2024; Cuartero et al., 2024). Together, these issues hinder effective risk assessments, early detection of new pathogens, and predictions regarding resistance trends.

9. Conclusions

Fungal diseases are no longer rare or limited to specific areas. Fungi are increasingly spreading across different regions and hosts due to environmental change, human activity, and their own remarkable ability to adapt. The old view of fungal infections as opportunistic and localized is being replaced by a clearer understanding of fungi as dynamic pathogens influenced by global ecological factors. Climate change is a key factor in this shift. Rising temperatures, changed rainfall patterns, and extreme weather events create conditions that support fungal growth, persistence, and spread. These environmental changes also favor traits like heat tolerance and stress resistance, which help fungi survive in humans and animals. Changes in climate that affect host immunity and the increased use of antifungals in agriculture further link environmental change to the rise of hard-to-treat fungal infections. Zoonotic spillover adds more complexity. Many fungi can easily move between the environment, animals, and humans, often without causing clear disease in animal hosts. This silent circulation lets fungi persist, adapt, and sometimes return to humans in more resilient or resistant forms. Growing evidence of two-way transmission shows the importance of viewing fungal diseases through a One Health perspective.
One concerning trend is the rapid rise of antifungal resistance. With only a few classes of antifungal drugs available, resistance leads to serious issues. Resistant infections are harder to treat, tend to return, and result in higher rates of illness, death, and healthcare costs. The detection of resistant fungi outside hospitals indicates that this problem goes beyond clinical settings and is closely linked to larger environmental pressures. Despite progress in molecular diagnostics and genomics, there are significant gaps in how fungal diseases are detected, monitored, and understood globally. Limited surveillance, uneven access to diagnostic tools, and a lack of integrated human, animal, and environmental data mean that many fungal threats are recognized too late. Coordinated global surveillance, better antifungal management, and stronger One Health approaches will be crucial to reduce the impact of fungal diseases in a rapidly changing world.

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Figure 1. Global Priority Pathogens as per the WHO fungal priority pathogens list. Dots indicate where each pathogen appears on regional top 10 lists. Regional results are intended to inform deliberations and should not be read as regional priorities in themselves. ∗Cytomegalovirus results are provisional due to lack of systematic burden estimates. Reproduced from Hasso-Agopsowicz et al. licensed under CC BY 4.0.
Figure 1. Global Priority Pathogens as per the WHO fungal priority pathogens list. Dots indicate where each pathogen appears on regional top 10 lists. Regional results are intended to inform deliberations and should not be read as regional priorities in themselves. ∗Cytomegalovirus results are provisional due to lack of systematic burden estimates. Reproduced from Hasso-Agopsowicz et al. licensed under CC BY 4.0.
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Figure 2. Pictorial representation of mechanisms of antifungal resistance. Reproduced from Logan et al. with permission from Springer Nature.
Figure 2. Pictorial representation of mechanisms of antifungal resistance. Reproduced from Logan et al. with permission from Springer Nature.
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Figure 3. Potential effects of climate change on pathogenic fungi and fungal diseases. Reproduced from Nnadi and Carter licensed under CC BY 4.0.
Figure 3. Potential effects of climate change on pathogenic fungi and fungal diseases. Reproduced from Nnadi and Carter licensed under CC BY 4.0.
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Figure 4. Proposed scheme for the emergence of C. auris. Reproduced from Casadevall et al. licensed under CC BY 4.0.
Figure 4. Proposed scheme for the emergence of C. auris. Reproduced from Casadevall et al. licensed under CC BY 4.0.
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Table 1. Patterns of Antifungal Resistance and Evolutionary Dynamics of Major Fungal Pathogens, Source: Motta et al. (2025).
Table 1. Patterns of Antifungal Resistance and Evolutionary Dynamics of Major Fungal Pathogens, Source: Motta et al. (2025).
Species/Complex Resistance Pattern (Drug class) Key molecular mechanisms Evolutionary/Epidemiological Features Clinical & Public Health Implications
Candida parapsilosis FCZ: up to 63% (regional outbreaks) VCZ: cross-resistance (~44%) Emerging echinocandin resistance AmB: <3% resistance ERG11 mutations (Y132F, K143R) Silent T591C mutation Efflux pump overexpression FKS1 hotspot mutations (F652S, R658G, S656P) Natural P660A polymorphism Clonal nosocomial outbreaks Resistance without prior exposure Adaptive mutation + hospital persistence Persistent candidemia Reduced echinocandin efficacy AmB as salvage therapy Requires molecular surveillance
Candida tropicalis Azoles: ~10% resistance Echinocandins: ~0.4% AmB: highly active ERG11 mutations (Y132F, Y257H/N) FKS1 mutation (S659P) High genotypic diversity Environmental reservoirs (e.g., beach sand) Long-distance clonal spread (>1400 km) Potential unrecognized outbreaks Strong candidate for One Health surveillance
Nakaseomyces glabratus FCZ: 4–30% (variable regionally) Echinocandins: up to 10% Polyenes: rare resistance PDR1 mutations FKS1/FKS2 hotspot mutations Biofilm formation EPA adhesins High adaptability under drug pressure Prior echinocandin exposure selects mutants Intracellular persistence Multidrug resistance risk Elevated MICs compromise therapy AmB critical in salvage regimens
Pichia kudriavzevii Intrinsic FCZ resistance (~70%) VCZ: ~25% Echinocandins: <5% baseline AmB: >95% susceptible FKS1 hotspot mutations (treatment-emergent) Intrinsic azole resistance Resistance may emerge during therapy Regional variability Requires echinocandin first-line Transition to AmB in breakthrough infection
Candida haemulonii complex Multidrug resistance FCZ & AmB resistance common Not fully characterized Misidentification common Emerging invasive pathogen Frequently misidentified Hospital-associated Requires MALDI-TOF/molecular ID Surveillance essential
Candida duobushaemulonii Multidrug resistant Limited genomic data Likely shared mechanisms with haemulonii complex Underdiagnosed nosocomial spread Misidentified during surveillance Hidden burden Requires reference-lab confirmation
Meyerozyma guilliermondii complex Azole resistance: 40–70% Reports of AmB & echinocandin resistance Genetic diversity Clade-specific azole resistance High taxonomic complexity Clade spread (e.g., M. caribbica) Individualized therapy needed Strengthened molecular diagnostics required
Candida rugosa
FCZ resistance: ~65% VCZ reduced sensitivity AmB resistance reported Not fully defined Higher regional prevalence ICU-associated outbreaks Azoles unreliable Therapeutic risk with empirical treatment
Candidozyma auris FCZ: >90% (Clade IV) AmB: 30–60% Echinocandins: up to 5% MDR common ERG11 mutations (F126L, Y132F, K143R) TAC1B involvement FKS1 mutations Transcription factor mutations (e.g., FLO8 homolog S108N) Biofilm formation Independent clade emergence (I–IV) Local transmission foci Environmental persistence (marine, freshwater) Thermal adaptation hypothesis Nosocomial colonization High mortality (30–60%) Prolonged colonization Hospital outbreaks Requires mandatory reporting & genomic surveillance One Health relevance
Abbreviation: FCZ, Fluconazole; VCZ, Voriconazole; AmB, Amphotericin B; MIC, Minimum Inhibitory Concentration; ERG11, Gene encoding lanosterol 14-α-demethylase; FKS1 / FKS2, Genes encoding subunits of β-1,3-D-glucan synthase; PDR1, Pleotropic Drug Resistance 1 transcription factor; EPA, Epithelial Adhesin proteins.
Table 2. Global annual incidence of fungal spillover of various species. Source: Denning (2024).
Table 2. Global annual incidence of fungal spillover of various species. Source: Denning (2024).
Pathogen Category Global Annual Incidence Mortality Rate Primary Source/Reservoir
Invasive Fungal Infections ~6.5 Million ~58% Multi-environmental
Cryptococcal Meningitis ~194,000 ~75% Bird guano, Trees, Bats
Zoonotic Dermatophytosis >2.1 Billion (All types) Low (but rising resistance) Cats, Dogs, Livestock
Candida auris Rapidly Increasing 30% – 60% Environmental/Hospital
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