nature reviews microbiology https://doi.org/10.1038/s41579-025-01180-z Review article Check for updates Aspergillus fumigatus biology, immunopathogenicity and drug resistance Frank L. van de Veerdonk 1,2 , Agostinho Carvalho , Joost Wauters 3,4 , George Chamilos 5 6,7 & Paul E. Verweij2,8 Abstract Sections Aspergillus fumigatus is a saprophytic fungus prevalent in the environment and capable of causing severe invasive infection in humans. This organism can use strategies such as molecule masking, immune response manipulation and gene expression alteration to evade host defences. Understanding these mechanisms is essential for developing effective diagnostics and therapies to improve patient outcomes in Aspergillus-related diseases. In this Review, we explore the biology and pathogenesis of A. fumigatus in the context of host biology and disease, highlighting virus-associated pulmonary aspergillosis, a newly identified condition that arises in patients with severe pulmonary viral infections. In the post-pandemic landscape, in which immunotherapy is gaining attention for managing severe infections, we examine the host immune responses that are critical for controlling invasive aspergillosis and how A. fumigatus circumvents these defences. Additionally, we address the emerging issue of azole resistance in A. fumigatus, emphasizing the urgent need for greater understanding in an era marked by increasing antimicrobial resistance. This Review provides timely insights necessary for developing new immunotherapeutic strategies against invasive aspergillosis. Introduction Department of Internal Medicine, Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands. 2Radboudumc/CWZ Center of Expertise in Mycology (RCEM), Radboud University Medical Center, Nijmegen, The Netherlands. 3Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal. 4ICVS/3B’s–PT Government Associate Laboratory, Braga, Portugal. 5Medical Intensive Care, University Hospitals Leuven and Department for Clinical Infectious and Inflammatory Disorders, University Leuven, Leuven, Belgium. 6Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece. 7School of Medicine, University of Crete, Heraklion, Greece. 8Department of Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands. e-mail: frank.vandeveerdonk@ radboudumc.nl 1 Nature Reviews Microbiology Aspergillus fumigatus biology Host defence against Aspergillus fumigatus Virus-associated invasive aspergillosis Strategies to survive azole exposure Conclusions and outlook Review article Introduction Aspergillus species are saprotrophic fungi widely present in soil, where they play a vital role in carbon and nitrogen recycling by thriving on decaying vegetation. While Aspergillus fumigatus typically does not cause infection in immunocompetent hosts, it can lead to severe invasive disease in immunocompromised individuals. Traditionally, this susceptibility has been observed in patients undergoing chemotherapy or those with rare immunodeficiencies (Box 1). However, the landscape is changing: new drugs in oncology and rheumatology have broadened the population at risk for invasive aspergillosis. The COVID-19 pandemic has brought to light a new clinical entity known as virus-associated pulmonary aspergillosis (VAPA), highlighting the evolving nature of these infections. To improve clinical outcomes in Aspergillus-related infections, experts believe that a combination of antifungal therapy and immunomodulatory treatments is needed. A thorough understanding of the interactions between Aspergillus spp. and the host is crucial for developing new effective treatment strategies. This Review will provide timely updates on recent progress in host–pathogen interactions, detailing how A. fumigatus evades host defences and adapts to the host environment and subsequently what mechanisms are used by the host to control and eliminate invasive infection. This will be discussed in the context of the new clinical entity VAPA and the emergence of antifungal drug resistance, underscoring the timely nature of this Review. Aspergillus fumigatus biology The life cycle of A. fumigatus begins with the germination of spores (Fig. 1). These spores are typically formed in specialized structures called conidiophores, which are often found in large numbers on the surface of the fungal colony. Aspergillus species produce vast quantities of asexual spores known as conidia, which are small unicellular structures that are highly resistant to environmental stressors, allowing them to survive in a wide range of conditions. Recent studies have shown heterogeneity in the conidial population produced on a single conidiophore, which results in different germination behaviours upon exit of quiescence1,2. Once the conidia are released into the environment, they can be dispersed by various means such as air currents, water or animal vectors3. This enables A. fumigatus to colonize new substrates and environments. When favourable conditions are encountered, the conidia can germinate and initiate the growth of new colonies. Germination is triggered by environmental factors such as moisture, temperature and nutrient availability. Upon germination, the conidium swells and gives rise to a specialized hyphal structure known as the germ tube. The germ tube elongates and branches, forming a network of hyphae that infiltrates the substrate. The hyphae secrete enzymes and absorb nutrients from the environment, enabling the fungus to grow and expand its mycelium. As the mycelium develops, it forms a complex network of hyphae that penetrate the substrate, facilitating the decomposition of organic matter and nutrient acquisition. Under certain conditions, such as the presence of specific mating types or stress factors, A. fumigatus can undergo sexual reproduction4, which involves the fusion of two compatible mating types with the consequent formation of sexual spores called ascospores that are enclosed within protective structures, known as ascus4. The ascospores are released from the ascus and can be dispersed in a similar manner to asexual conidia. These sexual spores have the potential to contribute to genetic diversity and adaptation, making sexual reproduction an important aspect of the A. fumigatus life cycle5. It is worth noting that while sexual reproduction occurs in some Aspergillus species, many others are predominantly asexual and rely on the production and dispersal of conidia for their survival and propagation. Although the sexual reproduction is not directly involved in disease, understanding the biology of Aspergillus spp. life cycle is important for studying its ecology, and can be helpful to develop effective control measures against pathogenic species6. Further research into the molecular mechanisms and regulatory factors involved in each Box 1 | Host genetics and Aspergillus fumigatus infections While virulence mechanisms contribute to infection, studies in patients with rare mutations and high-risk cohorts have unveiled the contribution of heritable host factors to the development and clinical course of aspergillosis. Diseases such as chronic granulomatous disease caused by mutations in components of the nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase complex, caspase recruitment domain 9 (CARD9) deficiency and mutations in signal transducer and activator of transcription 3 (STAT3) lead to hyper IgE syndrome. This predisposes individuals to severe Aspergillus fumigatus infections and has substantially contributed to the understanding of host defence against this pathogen186. SNPs in the long pentraxin 3 (PTX3) remain the most robust genetic markers identified thus far187. A haplotype in PTX3 was reported to influence the development of invasive pulmonary aspergillosis (IPA) after stem cell transplantation60,179, but also after solid organ transplantation188,189 and in chronic obstructive pulmonary disease190. This association was also observed in patients with acute myeloid leukaemia, but only in the absence of pre-existing neutropenia191, a finding confirming the detrimental consequences of PTX3 SNPs to the antifungal effector functions of neutrophils60. Because of its role in activating phagocytosis by neutrophils, SNPs Nature Reviews Microbiology in another pentraxin family member, the serum amyloid P, also predisposed to IPA192. Individuals carrying an early stop codon SNP in dectin-1, which truncates the receptor at the recognition domain and impairs cytokine production, displayed heightened susceptibility to IPA across different studies110,178,179. More recently, a SNP in the MelLec receptor that presumably affects signal transduction was also found to impair cytokine production and predispose to IPA193. In line with its role as a negative regulator of dectin-1 during A. fumigatus infection, SNPs in the nucleotide-binding oligomerization domain 2 (NOD2) were instead reported to confer resistance to IPA194. Besides fungal recognition, genetic variants that affect processes of immune cell activation and functional activity have also been implicated in the risk of aspergillosis. Relevant examples include SNPs that affect phagosome maturation and the activation of LC3-associated phagocytosis82,118,195, post-translational modification of proteins196 and cytokine secretion182,183,197. More recently, functional genomics approaches that combine genome information and immunological screenings were used to pinpoint variants that influenced immune cell metabolism198 and ROS production199, and that ultimately predisposed to IPA. Review article Habitat or niche a b Lung cavity (chronic pulmonary aspergillosis) Plant waste Airways (tracheobronchitis) Reproduction mode and cycle c Swollen conidia Conidia Asexual Germlings Mycelium Vesicle Conidiophore Hyphae Hyphae d Fig. 1 | Habitats and life cycles of Aspergillus fumigatus. a, The lung can be infected by inhaled conidia, leading to Aspergillus fumigatus infection in susceptible hosts. A. fumigatus can cause a range of conditions, from allergic to invasive diseases. The figure highlights two disease spectra that have become increasingly difficult to treat in recent years and that are associated with specific predisposing factors. The first is chronic pulmonary aspergillosis, in which A. fumigatus infects a lung cavity caused by tuberculosis, sarcoidosis or other underlying structural lung diseases. The other is invasive tracheobronchitis, an acute and often lethal infection in the airways, especially seen in influenzaassociated aspergillosis. b, Plant waste deposits are habitats where A. fumigatus can reproduce sexually and asexually and are environmental niches that can substantially contribute to the genetic diversity of A. fumigatus and the development of azole resistance. c, Asexual reproduction occurs through hyphae called conidiophores. The tip of the conidiophore swells up into a head called vesicle, which forms many radially arranged tubular outgrowths. From these structures, the conidia are released into the environment, where they swell and germinate (germlings) originating a germ tube that subsequently becomes septated, branched and forms a mycelium. d, Sexual reproduction is rare and occurs with the formation of a male sex organ (antheridium) and a female sex organ (ascogonium) from the mycelium. When in close proximity, these two sex organs can merge and the nuclei can fuse and divide and eventually form an ascus that contains 8 haploid nuclei. These asci are present in the cleisthotecium and the ascospores can be released from these asci into the environment. Ascospores can form germlings that will grow and develop into mycelium. Ascogonium Ascogonium Antheridium Antheridium Sexual Ascospore Ascus Ascospores Carbon and nitrogen recycling Cleistothecium Germlings stage of the life cycle will deepen our knowledge and will help to pave the way for innovative strategies to manage Aspergillus-related diseases. A. fumigatus is a highly adaptable pathogen capable of adopting several molecular mechanisms to cope with host-induced and drug-induced stresses. In this section, we summarize the main molecular aspects of nutrient recycling and cation sequestration, hypoxia adaptation and biofilm formation by A. fumigatus, which contribute to its adaptation to the host and fungal pathogenicity (Fig. 2). A. fumigatus is highly efficient at recycling carbon and nitrogen and can adapt to a wide range of substrates for its metabolic needs7. To counter nutritional restrictions during infection, A. fumigatus utilizes organic compounds and essential metals derived from host tissue degradation. It expresses several proteases and enzymes (for example, serine proteases, metalloproteinases and aspartic proteases), which upon secretion, digest host macromolecules into organic components that can be metabolized. Besides nutrient acquisition, these proteases target host mechanisms Nature Reviews Microbiology to modulate the immune response. Some examples include the alkaline protease 1 (Alp1) that can damage junctions of bronchiolar epithelial club cells and incites eosinophilia and inflammation during fungal allergy8; the metalloproteinase Mep1p, which can inactivate host complement proteins to restrain conidial opsonization and phagocytosis; and fungal proteases that can cleave the dectin-1 receptor to dampen phagocytosis and cytokine production9. Although many other examples exist and are being discovered, the ones mentioned here underscore the complex and extensive interactions between proteases and the host in the context of Aspergillus-related diseases. In the presence of different carbon sources, A. fumigatus uses carbon catabolite repression to favour the utilization of selected substrates. While this mechanism appears dispensable for initiation of infection, the limited nutrient and oxygen availability at the site of infection favours glucose utilization instead of alternative carbon sources, which contributes to disease progression10. This implies that the variety of usable carbon sources may differentially impact fungal fitness in vivo. For example, the utilization of acetate affects cell wall composition and resistance to oxidative stress, antifungal drugs and neutrophil-mediated killing, while the deletion of the transcription factor facB that controls acetate utilization impairs fungal virulence11. The relevance of nitrogen acquisition to fungal survival within the host is illustrated by the attenuated virulence of a deletion mutant in CpcA, the transcriptional activator of the cross-pathway control system of amino acid biosynthesis12. Moreover, deletion strains in genes involved in the biosynthesis of histidine, lysine, tyrosine, tryptophan, isoleucine/valine, methionine, cysteine and alanine also exhibit impaired virulence13. In certain conditions, A. fumigatus can also degrade amino acids, such as tryptophan, to produce immunoregulatory molecules required to maintain lung immune homeostasis14. The fact that environmental strains can be distinguished from clinical isolates based on genome enrichment in genes involved in carbohydrate and amino acid metabolism15, and on Review article a Carbon and nitrogen recycling b Cation acquisition Tissue degradation Aspergillus Proteases Fe FsC TAFC Zn Cu MirD MirB Fe CccA ZrfA–C Fe Acquisition of nutrients FC CtrA2 CtrC Vacuole Metabolic processes Inhibition of neutrophil function Antifungal drug resistance c Adaptation to hypoxia Haem biosynthesis Hypoxia d Biofilm formation Carbohydrate metabolism Hypervirulent conidia Glucans Galactosaminogalactan Hyphae Conidia Galactomannan SrbA Nitrate assimilation Ergosterol biosynthesis Antifungal resistance Resistance to oxidative stress Oxygen tension Cell wall remodelling Fig. 2 | Mechanisms of Aspergillus fumigatus adaptation to the host. a, During infection, Aspergillus fumigatus undergoes substantial rearrangements of its metabolic pathways to cope with limited nutrient availability and survive within the host. This metabolic plasticity is essential for cell wall remodelling, resistance to oxidative stress, inhibition of neutrophil functions and antifungal drug resistance. b, During infection, A. fumigatus expresses efficient molecular machineries involved in the acquisition of nutrients and cations (iron, copper, zinc, calcium), such as siderophore-mediated iron acquisition from the infected tissues. c, In these conditions, hypoxia regulates the activation of the SrbA transcription factor, which in turn coordinates fungal virulence and contributes to processes such as carbohydrate metabolism, haem and ergosterol biosynthesis, and nitrate assimilation. d, Hypoxia is also a crucial process involved in the transcriptional regulation of fungal biofilm formation and composition, contributing to antifungal resistance and activating molecular programmes that enhance virulence. The extracellular matrix of A. fumigatus biofilms is mainly composed of glucans, galactosaminogalactan and galactomannan. profiles of metabolic reactions associated with nitrogen, amino acid and nucleotide metabolism16, further highlights the importance of these pathways to fungal fitness in vivo. whereas HapX can activate vacuolar iron storage20. Recently, AtrR, a transcription factor involved in ergosterol biosynthesis, azole resistance and adaptation to hypoxia, was also implicated in iron acquisition, including siderophore biosynthesis and uptake21. Zinc is acquired from the host through the transporters ZrfA, ZrfB and ZrfC22, whose expression is regulated by the transcription factor ZafA23. ZafA also appears to influence genes involved in iron uptake24. The copper-responsive transcription factors, AceA and MacA, coordinate copper import and export, ensuring an adequate supply for copper-dependent processes while mitigating its toxic effects25. Recently, small molecules produced by A. fumigatus termed isocyanides were also found to bind copper and partake in its homeostasis26. Calcium is essential for multiple biological functions in A. fumigatus due to its role as an intracellular signalling molecule. The calcium-responsive calcineurin–CrzA pathway influences cell morphology, cell wall composition, virulence and echinocandin resistance, and its disruption hinders virulence27,28. Several transcription factors besides CrzA have also been reported to promote Cation acquisition Several cations such as iron and zinc are essential for the growth of A. fumigatus. Although iron is an abundant trace metal, in the host it is mostly bound to proteins such as haem and transferrin. To acquire iron, A. fumigatus uses reductive iron assimilation and siderophore-mediated iron acquisition, with the latter widely implicated in virulence. The siderophore system consists of two secreted siderophores for iron uptake (fusarinin C and triacetylfusarinin C) and two intracellular siderophores for iron storage (ferricrocin and hydroxyferricrocin)17. The transcription factors SreA and HapX regulate iron homeostasis and siderophore production, although only HapX was found to affect pathogenicity18,19. Under toxic iron concentrations, and to inhibit its utilization, SreA can repress iron uptake through the siderophore system18, Nature Reviews Microbiology Review article tolerance to calcium stress, but only ZipD has thus far been linked to reduced virulence in vivo29. Adaptation to hypoxia Being an obligate aerobe, oxygen is essential for A. fumigatus. However, the restricted oxygen availability during infection implies the need for adaptation to these conditions30,31. The inflammatory response to infection also sustains hypoxia due to tissue degradation and obstruction of blood vessels. Moreover, the secreted secondary metabolite gliotoxin inhibits the neovascularization of damaged tissues to further restrain oxygen availability32. By downregulating the inflammatory response, local tissue hypoxia decreases and improves outcomes after experimental aspergillosis33. Adaptation to low oxygen is correlated with virulence and exposure to chronic hypoxia can restore the virulence of fungal strains that have reduced fitness under low oxygen conditions34. The sterol regulatory element-binding protein SrbA is required for hypoxia adaptation and the loss of SrbA function disrupts ergosterol biosynthesis, resistance to azoles, cell polarity and the ability to cause disease35. Moreover, SrbA also contributes to hypoxia fitness by regulating nitrate assimilation and haem biosynthesis36. The adaptation to oxygen stress also relies on the redirection of fungal metabolism towards mitochondrial respiration31 and activation of the AlcC alcohol dehydrogenase30. Biofilm formation Within the lung, A. fumigatus can form biofilms that enhance resistance to antifungals and immune defences. The presence of an extracellular matrix in biofilms mediates surface adherence and confers resistance to antifungals and immune defences. This matrix is composed mainly of extracellular DNA, polyols, proteins, lipids and exopolysaccharides including α-glucans, galactomannan and galactosaminogalactan (GAG), with the latter being a good example how complex the biology of biofilm in Aspergillus spp. is37 and how important these biofilm components can be for driving pathology in Aspergillus-related diseases38. GAG is critical for the formation of adherent biofilms as the deletion of Uge3, which encodes a UDP-glucose epimerase required for GAG production, impairs the production of the extracellular matrix39. Deacetylation of GAG mediated by Agd3 is also required for its adhesive properties and biofilm formation40, whereas GAG digestion by the endo-α-1,4-galactosaminidase Ega3 disrupts biofilm formation41. Biofilm formation also interplays with fungal metabolism. The alanine aminotransferase AlaA, which participates in alanine catabolism, is required for the maturation of GAG and biofilm adherence, with an important role in resistance to echinocandins42. Besides GAG, the role of other polysaccharides in biofilm formation has not been detailed. The structural properties of fungal biofilms can be influenced by environmental factors, such as oxygen tension43. The decreasing oxygen gradient towards the base of biofilms is linked to antifungal drug resistance44. Hypoxia drives the expression of a subtelomeric gene cluster (hrmA-associated gene cluster, HAC) associated with the putative transcriptional regulator hrmA, which modifies the hyphal surface and hinders their interactions to disrupt biofilm formation45. The increased virulence resulting from this morphotype promotes inflammation, as well as disease progression and mortality in vivo. The biofilm architecture factor A (BafA) within the HAC cluster is sufficient to generate the hypoxia-associated morphotype associated with altered biofilm structure46. Moreover, the loss of SrbA entirely disrupts biofilm maturation, while the loss of SrbB affects biofilm structure and reduces biofilm biomass44. Nature Reviews Microbiology Host defence against Aspergillus fumigatus Genetic predisposition to invasive aspergillosis in humans has revealed many crucial mechanisms that are important for A. fumigatus antifungal host defence (Box 1). This has directed the field of fungal immunology towards the study of several key mechanisms that defend against the invasion of A. fumigatus, illustrated in Fig. 3. Here, we will provide a basic background on the innate and adaptive immune responses elicited by A. fumigatus and provide an update and more detail of new insights made in recent years. Innate immunity Inhaled A. fumigatus conidia interact with local immune defences of the respiratory tract on a daily basis. Lung immune homeostasis during fungal infection is conferred through a tightly coordinated inflammatory response. Crosstalk of alveolar epithelia with alveolar macrophages via calcium signals47 promotes timely phagocytosis of inhaled pathogens by alveolar macrophages and restricts inflammatory neutrophil influx48. Lung tissue-resident phagocytes, including alveolar macrophages and dendritic cells, express pattern recognition receptors (PRRs) that recognize specific components of A. fumigatus cell wall, such as β-glucans and galactomannans49. Toll-like receptors (TLRs) and C-type lectin receptors (CLRs) are examples of PRRs involved in this recognition process50. A. fumigatus conidia that escape phagocytosis by patrolling alveolar macrophages activate alveolar epithelia and innate immune cells to release pro-inflammatory cytokines such as tumour necrosis factor (TNF) and chemokines51. These cytokines attract and activate other immune cells, including neutrophils inflammatory monocytes, which are recruited to the site of infection52. Neutrophil recruitment in the lung occurs in distinct phases. The activation of interleukin-1α (IL-1α), C-X-C motif chemokine ligand 1 (CXCL1)–CXCL5 signalling in alveolar epithelia induces early neutrophil chemotaxis53,54. A second wave of neutrophil influx is regulated by other myeloid phagocytes via caspase recruitment domain-containing protein 9 (CARD9)–CXCL2 signalling53,55. IL-1 signalling and type III interferons also activate surfactant-producing alveolar epithelial to release granulocyte–macrophage colony-stimulating factor (GM-CSF), which enhances antifungal activity of neutrophils at the infection site56. Autocrine and paracrine release of leukotriene B4 (LTB4)57 and C5a anaphylatoxin58 further amplify neutrophil responses. Opsonization of A. fumigatus conidia by PTX3 via complement activation59,60 has a crucial role in their uptake by phagocytes. Additionally, innate B1a lymphocytes produce natural IgG antibodies that can opsonize A. fumigatus conidia and promote neutrophil killing61. CCR2+ inflammatory monocytes phagocytose A. fumigatus conidia62, enhance neutrophils activity62 and initiate an adaptive immune response upon differentiation to monocyte-derived dendritic cells (mo-DCs)63. Mo-DCs and neutrophils promote the recruitment of plasmacytoid-derived dendritic cells (pDCs) via the release of CXCR3 ligands. pDCs64 and type I and type III interferon signalling65 are essential for optimal antifungal effector activity of neutrophils via STAT-1 induced transcriptional activation of the cybb (NOX-2) subunit of NAPDH oxidase complex66. The sensing of cell wall polysaccharides via the reciprocal crosstalk of soluble, membrane-bound and cytosolic PRRs, shapes physiological immunity against A. fumigatus. β-glucan-mediated activation of dectin-1 signalling regulates type I and type III interferon responses against A. fumigatus in the lung67. A. fumigatus galactomannan can also trigger the release of pro-inflammatory cytokine via dectin-2–Syk signalling68, which could serve as an important compensatory host defence mechanism when β-glucan masking occurs due to lactate or echinocandins69,70. Review article Conidia AM IL-1R–MyD88 CXCL1 CXCL5 CARD9 signalling Alveolar epithelium Fungal killing by AMs • NADPH–ROS-induced LAP • Nutritional immunity Elimination of germinating fungal cells • Lateral transfer (metaphorosis) GM-CSF NETosis, swarming NADPH–ROS-dependent killing PTX3, C5a, LTB4 Chemotaxis of myeloid phagocytes CXCL2 Ly6Chi monocytes Neutrophil CXCL9/10 Type I and III interferons pDC recruitment ↑ ROS pDC ↑ ROS Fungal killing by PMNs • NADPH–ROS-induced apoptosis • Antimicrobial peptides • Nutritional immunity Fig. 3 | Physiological innate immune response to Aspergillus fumigatus infection. Inhaled Aspergillus fumigatus conidia are constantly phagocytosed by alveolar macrophages (AMs) (brown). Recruited neutrophils (red) and inflammatory Ly6Chi monocytes (yellow) eliminate conidia and germinating A. fumigatus hyphae that escape from immune surveillance by AMs. Neutrophil chemotaxis is regulated by sequential waves of chemokine release by epithelia via interleukin-1 receptor (IL-1R)–MyD88 signalling and myeloid-derived cells via caspase recruitment domain-containing protein 9 (CARD9) signalling. Opsonization of fungal conidia by pentraxin 3 (PTX3) and other humoral immunity effectors such as C-X-C motif chemokine ligand 1 (CXCL1) and CXCL5, C5a and leukotriene B4 (LTB4), facilitates their uptake by phagocytes. Plasmacytoid dendritic cells (pDCs) (grey), type I and type III interferons and granulocyte–macrophage colony-stimulating factor (GM-CSF) released by alveolar epithelia augment reactive oxygen species (ROS)-dependent mechanisms of A. fumigatus killing by polymorphonuclear neutrophils (PMNs). Germinating A. fumigatus conidia that evade phagocytosis are eliminated by NETosis and coordinated PMN clustering (swarming), which are both regulated by NADPH oxidase-dependent ROS. ROS-dependent activation of LC3-associated phagocytosis (LAP) controls the killing of phagocytosed conidia in AMs. Nutritional immunity further promotes the inhibition of fungal growth. Furthermore, lateral cell-to-cell transfer (metaphorosis) of germinating intracellular A. fumigatus conidia is an alternative host defence mechanism to control invasive fungal growth by alveolar macrophages. GAG, a signature polysaccharide of A. fumigatus produced during germination, triggers a variety of immune responses that are specific to different cell types. On the one hand, GAG has potent anti-inflammatory properties mediated by the release of IL-1 receptor antagonist, which promotes fungal pathogenicity during pulmonary infection in immunocompromised mice39,71. On the other hand, GAG induces robust CD56mediated natural killer cell activation that restricts fungal growth and promotes antifungal responses of neutrophils72. GAG also binds to ribosomal proteins and activates the NLRP3 inflammasome by inhibiting protein translation in macrophages, thereby conferring protective immunity against disseminated infection73. Of interest, PTX3, released by tissue-resident macrophages and infiltering neutrophils, specifically binds GAG on germinating hyphae, as well as surfactant protein D (SP-D) and the complement proteins C1q and C3b on opsonized conidia74. This activates a balanced anti-inflammatory response and promotes infection resolution in the lung. Similarly, serum opsonization of A. fumigatus cell wall chitin shapes the coordinated activation of pro-inflammatory and anti-inflammatory responses in human peripheral blood mononuclear cells through the activation of the Fcγ receptor–SyK–PI3K signalling pathway75. From the pathogen perspective, A. fumigatus inhibits the activation of inflammatory signalling pathways by masking cell wall polysaccharides with its hydrophobic rodlet protein layer76. The release of surface-associated proteins on A. fumigatus conidia, including a putative glycosylasparaginase, dampens pro-inflammatory cytokine responses and promote evasion from the immune system77. The elimination of fungal conidia is largely dependent on the activation of the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex and the production of reactive oxygen species (ROS) by phagocytes78. ROS have direct antifungal activity against A. fumigatus conidia79 and exhibit pleiotropic actions in immune cells, which remains unexplored at the molecular level. Recently, bruton tyrosine kinase (BTK) was identified as a new regulator of NADPH oxidase complex assembly via the phosphorylation of p40phox cytoplasmic subunit and the activation of the GTPAse Rac2 (ref. 80). These studies provide a mechanistic explanation on the development of invasive aspergillosis in patients with B cell lymphoid malignancies treated with BTK inhibitors81. Apart from acting as antifungal effectors, ROS promote nutritional immunity via copper-mediated cytotoxicity in the phagosome25. Furthermore, ROS activate LC3-associated phagocytosis (LAP), a pathway that promotes phagosome maturation and fungal killing82–85. Nature Reviews Microbiology Phagosome biology Following phagocytosis of A. fumigatus conidia, phagolysosome fusion occurs rapidly, within one hour of infection. In contrast, phagosome Review article acidification and killing of intracellular conidia occurs with significant delay, only after 4 to 6 hours of infection86. Importantly, intracellular swelling of A. fumigatus is a prerequisite for conidial killing. The exposure of β-glucan and other immunostimulatory polysaccharides during intracellular germination activates potent inflammatory responses via C-type lectin receptor–Syk kinase signalling76,87, to promote phagolysosome fusion88 and fungal clearance89. LAP is a pathway mechanistically distinct from classic (macro)autophagy90. Activation of LAP results in single membrane LC3 lipidation on the phagosome membrane and has an important role in immunity against A. fumigatus82–84. Recent studies reveal that the vacuolar-type ATPase (V-ATPase) is a master regulator of all single membrane LC3 lipidation processes, including LAP90–92. Proton imbalance induced by proton consumption during NADPH oxidase-mediated ROS production in the phagosome lumen recruits V-ATPase on the phagosome to promote LAP90. The specific V-ATPase inhibitor Bafilomycin completely abrogates the killing of A. fumigatus conidia inside alveolar macrophages86. Intercellular crosstalk facilitates the elimination of germinating hyphae of A. fumigatus through various pathways, including the lateral transfer of conidia between alveolar macrophages via calcineurin signalling93, the release of neutrophil extracellular traps (NETs)94 and the coordinated clustering (swarming) of neutrophil through the autocrine release of LTB495,96. The killing of hyphae is largely mediated by ROS-dependent mechanisms through the activation of NADPH oxidase and myeloperoxidase96,97. Interestingly, the deletion of the C-type lectin inhibitory receptor MICL, which directly recognizes DNA in NETs, resulted in protective immunity against disseminated aspergillosis through increased ROS–protein arginine deiminase 4 (PAD4) production, which in turn triggers NETs formation98. Nutritional immunity via calprotectin-mediated zinc and manganese chelation facilitates the inhibition of hyphal growth99. Iron acquisition during germination has a crucial role in the pathogenicity of A. fumigatus and is mediated via the siderophore ferricrocin100, which is an appealing therapeutic target101. Accordingly, iron overload is a well-established risk factor for invasive aspergillosis101,102. In an animal model of corneal fungal infection, dectin-1-mediated IL-6 production orchestrated hepcidin release and contributed to nutritional immunity against A. fumigatus. At the molecular level, the release of lipocalin-1 by neutrophils neutralizes the activity of A. fumigatus siderophores101. Nonetheless, the mechanisms that regulate iron limitation in A. fumigatus phagosome remain unexplored. Importantly, A. fumigatus can evade neutrophil-killing mechanisms by producing certain enzymes and toxins that impair neutrophil function78,103. Clinical observations in patients with congenital immunodeficiencies104 (Box 1) and experiments in mice devoid of lymphoid cells (Rag2−/− Fcγ−/−) suggest that protective immunity against A. fumigatus is largely conferred by professional phagocytes65. However, the substantial role of adaptive immunity and intercellular crosstalk in fine-tuning phagocyte activity has become increasingly recognized105. Adaptive immunity T cell-mediated immunity could play an important role in immunity against A. fumigatus immunity against, especially in patients with complex acquired immune defects61,106–108. Upon activation, CD4+ T cells differentiate into subsets such as T helper (TH) 1, TH2 and TH17 cells, which produce different cytokines and play distinct roles in the immune response109. TH1 cells produce interferon-γ (IFNγ) and help activate macrophages to kill the fungus110. TH2 cells produce cytokines like IL-4 and IL-13, promoting allergic responses111. TH17 cells produce IL-17 and IL-22, which are involved in recruiting and activating Nature Reviews Microbiology neutrophils112. On the other hand, a causative role of exuberant inflammatory immune responses mediated by overactive T cells or neutralizing auto-antibodies produced by B cells has been demonstrated in various forms of fungal disease113,114. Evasion of host immunity A. fumigatus conidia have evolved several immune evasion and immune adaptation strategies for surviving in the human host. Here, we will highlight two examples including escape from the phagosome and the production of toxins by A. fumigatus. The conidial surface comprises components such as hydrophobin76,89 and melanin115, which mask immunogenic features of the cell wall from immune recognition. Moreover, melanin was found to deplete selected chemokines from the extracellular space to suppress the inflammatory response116. Melanin also interferes with the production of antifungal ROS by inhibiting Ca2+–calmodulin signalling and regulating NADPH oxidase complex activation83. This in turn blocks phagosome maturation117 and inhibits LC3-associated phagocytosis that is required for the intracellular killing of conidia by myeloid phagocytes84. Conidial susceptibility to NADPH oxidase-dependent killing was found to rely also on the expression and activity of fungal BIR1, an anti-apoptotic protein that hinders the activation of programmed cell death pathways in engulfed conidia to promote virulence79. More recently, the HscA protein in the conidial surface was found to anchor to host p11(S100A10) on phagosomes and drive the sorting of ingested conidia to the non-degradative pathway, allowing fungal escape and transfer between cells118. Comparison of the conidial surface proteome of A. fumigatus with that of two closely related non-pathogenic species has revealed additional proteins involved in fungal evasion and modulation of host immunity, including a putative glycosylasparaginase capable of modulating IL-1β secretion77. The growth of A. fumigatus is also associated with the release of soluble GAG, which in addition to its adhesive properties, can also induce neutrophil apoptosis119 and mediate resistance to NETs120. The secondary metabolism of A. fumigatus is also responsible for secreting several other molecules that subvert the immune response, such as the toxic metabolites gliotoxin, fumagillin, endocrocin, fumigaclavines, fumiquinazolines, trypacidin and helvolic acid, among others121. Different mechanisms have been proposed by which these metabolites impact interactions with the immune system and disease. Among the most relevant are the inhibition of phagocytosis, the production of pro-inflammatory cytokines and neutrophil chemotaxis122. Gliotoxin can impair the function, proliferation and survival of multiple immune cell types, including neutrophils and macrophages123, with its production relying on the immune status of the host124. More specifically, gliotoxin was recently shown to exhibit immunomodulatory properties in macrophages by either selectively suppressing the production of the lipid mediator leukotriene (LT)B4 in activated cells or by priming them to drive prostaglandin biosynthesis125. Deletion of GliP, which catalyses the initial step in gliotoxin biosynthesis, was found to decrease fungal virulence in non-neutropenic mice, an observation that pinpoints neutrophils as a major cellular target of gliotoxin124. Given its toxic nature, A. fumigatus has evolved mechanisms to withstand gliotoxin and transcription factors such as RglT and GliT have recently emerged as master regulators of genes involved in gliotoxin synthesis126. The mitogen-activated protein kinase MpkA has been shown to be essential for gliotoxin production and self-protection127. It achieves this by physically interacting with GliT and the GtmA methyltransferase, and regulating the cellular compartmentalization of gliotoxin to prevent cell damage. Besides gliotoxin, fumagillin is a monoterpenoid toxin that Review article stimulates germination and hyphal branching of A. fumigatus, and that is also required for virulence in vivo128. Oxylipins, a large group of oxidized fatty acids and their derivatives, are also secreted by A. fumigatus and function as signalling molecules in developmental processes and virulence129. One such fungal oxylipin, 5,8-diHODE, has been found to induce hyphal branching and cellular differentiation130. More recently, an oxylipin signal mediated by the synthesis of 5,8-diHODE through the fungal oxygenase PpoA and dependent on the transcription factor ZfpA was shown to confer protection against tip lysis by echinocandins131. Importantly, fungal oxylipins such as 8-HODE and 5,8-diHODE share structural similarities with other lipid mediators known to act as ligands of the host G-protein-coupled receptor G2A132. Although the involvement of fungal oxylipins in G2A activity remains unexplored, G2A-deficient mice exhibit improved survival during experimental aspergillosis due to enhanced neutrophil recruitment and increased production of inflammatory mediators132. Collectively, these observations suggest that conserved oxylipin-directed signals play a pivotal role in protecting against echinocandin damage and possibly in modulating host immunity. Virus-associated invasive aspergillosis Invasive pulmonary aspergillosis typically occurs in severely immunocompromised patients, such as those with prolonged severe neutropenia, those taking immunosuppressants, or with specific inherited errors of immunity133,134. However, following the 2009 H1N1 pandemic, influenza-associated pulmonary aspergillosis (IAPA) was recognized as a viral–fungal co-infection in patients with supposedly normal pre-existing immunity135,136. During the pandemic, COVID-19-associated pulmonary aspergillosis (CAPA) was also identified in critically ill patients with COVID-19 (ref. 137). Immune dysregulation in IAPA and CAPA is a complex phenomenon that involves interactions between the virus, A. fumigatus, the microbiome and the host138 (Fig. 4). Although the underlying host pathology and interactions with the virus seem to differ139, it has been proposed in both IAPA and CAPA that the virus and its associated immunopathology leads to defects in antifungal immunity140,141. Moreover, a recent in vitro model showed that the influenza virus and A. fumigatus directly interact142. Although this interaction is currently under investigation, it is tempting to speculate that it involves sialic acids interactions, similar to the way host immune cell– A. fumigatus interactions occur through sialic acids expressed by A. fumigatus, neuraminidases present in influenza and the host receptor Siglec-15 (ref. 143). In addition, reduced expression of pro-inflammatory and interferon pathways in the bronchoalveolar lavage fluid of patients with IAPA or CAPA was observed, underscoring the altered immune response in IAPA and CAPA144. Respiratory viral infection leads to epithelial damage, creating an environment favourable for A. fumigatus to become tissue-invasive, as shown both in murine lung pathology and human tracheobronchial biopsies144. Moreover, epithelial damage also leads to impaired mucociliary clearance and decreased epithelial production of chemokines and pro-inflammatory mediators, increasing the susceptibility to a higher burden of A. fumigatus spores in the lower respiratory tract53. In the lungs of patients with severe viral pneumonia, immune cells playing a role in phagocytosis and killing of conidia can be negatively affected. Alveolar macrophages are depleted and the influx of hyperinflammatory monocytes that do not completely differentiate into well-functioning macrophages leads to reduced phagocytosis of fungal conidia145–147. Transcriptional immuno-metabolic disturbances, which suggests potential defects in killing conidia, have been observed in monocytes and macrophages from the bronchoalveolar lavage fluid Nature Reviews Microbiology of patients with CAPA, compared with patients with COVID-19 but without CAPA107. Reduced immune cell responses to IFNγ observed in patients with IAPA and CAPA, and impaired phagolysosomal maturation observed in mice with IAPA, might further affect the conidial killing capacity of phagocytes144,148. On the other hand, partial or complete genetic ablation of early, robust influenza-induced IFNγ production protected influenza mice from early VAPA by restoring a defective TH17 immune response and LAP-dependent killing of conidia, highlighting the need to maintain a balanced immune response during an infection149. The exact role of neutrophils in VAPA remains to be determined. Autopsy from patients with IAPA and CAPA revealed that neutrophils are abundant in human lung lavages and that neutrophilic necrotizing inflammation colocalizes with impeded fungal growth, whereas areas without neutrophils showed high fungal burden150. Recent animal data showed that both ROS-dependent and ROS-independent pathways of the fungal host response are impaired by viral infection148,151. In line, impaired neutrophil degranulation and LC3-phagolysosome-associated transcriptional changes in critically ill patients with IAPA were identified144. Patients with CAPA also show significantly increased production of NETs compared with patients with COVID-19 and without aspergillosis, and patients with CAPA that present high NET levels have a significantly lower mortality107. Several polymorphisms have been associated with VAPA and might provide new opportunities for diagnostics and therapeutic strategies for VAPA (Table 1). In observational studies, in which the fraction of all included patients who received bronchoalveolar lavage sampling is higher than 50%, the reported incidence of VAPA is approximately 20% with a large worldwide variation139,152. While various reasons may underlie the variations in reported VAPA incidence, numerous VAPA cases are likely to go undetected and, therefore, untreated. Clear data on the mortality rate attributable to VAPA is lacking. However, it is suggested that when antifungal therapy initiation is delayed the mortality is higher, implying that VAPA should be detected early and treated promptly153. The cornerstone for the management of VAPA is the combination of an early, aggressive diagnostic approach and the administration of effective and safe antifungals. Although prevention of VAPA using antifungal prophylaxis is an appealing approach, there are major caveats. A multicentric international pilot randomized controlled trial, which randomized patients with severe influenza to receive posaconazole prophylaxis upon admission in the intensive care unit (ICU) versus standard of care, found no significant difference in the incidence of IAPA in the prophylaxis group154. IAPA develops early and is often present upon ICU admission, making prophylaxis too late for most patients who are likely to develop the disease154. CAPA is different, as it presents with a delay of approximately one week between ICU admission and its diagnosis. Several observational studies have pointed out a potential benefit of antifungal prophylaxis in CAPA, especially for patients who are deeply immunocompromised, such as patients with solid organ transplant and who are admitted to the ICU with severe viral pneumonia155,156. VAPA is a new entity which needs more attention and research to improve its high morbidity and mortality. Lung bacterial communities also play a critical role in aspergillosis. For example, immunocompromised patients with invasive pulmonary aspergillosis were recently found to exhibit a markedly decreased bacterial diversity in the lower airways, which influenced local immune profiles and disease outcomes157. However, despite its clinical relevance, the potential of the lung microbiota as a diagnostic and therapeutic target in aspergillosis remains largely unexplored. Review article CAPA IAPA • Late in ICU stay • Corticosteroids • NETosis important • Tissue-invasion • Early in ICU stay • Decreased IFNγ signalling and LAP • Hampered neutrophil functions • Tissue-invasion and angio-invasion NET production Conidia Neutrophil Hyphae Alveolar macrophage Alveolar space Alveolar epithelium Interstitial space Blood vessel Angioinvasion Fig. 4 | Influenza-associated and COVID-19-associated pulmonary aspergillosis. Influenza-associated pulmonary aspergillosis (IAPA) and COVID19-associated pulmonary aspergillosis (CAPA) share similarities but are also distinct in several features. Incidences probably lie around 10–20% in critically ill patients and, despite antifungal therapy, both conditions are associated with an overall mortality rate of approximately 50%, being double compared with patients with severe viral pneumonia without virus-associated pulmonary aspergillosis (VAPA). While IAPA occurs within the first few days after intensive care unit (ICU) admission or even at the time of ICU admission, CAPA tends to occur later, typically between 3 and 9 days after ICU admission. Angioinvasion of Aspergillus fumigatus hyphae, reflected by positivity of serum galactomannan, is rarely detected in VAPA, but more often in IAPA than in CAPA. CAPA incidence is associated with the use of corticosteroids and tocilizumab as a treatment for COVID-19, while in influenza patients, prolonged use of corticosteroids Strategies to survive azole exposure Similar to host genetics and different host responses to infection, there are also many strains of A. fumigatus with diverse genetics and differing induced responses, which can impact the course of the disease. In this section, we will focus on strains in the context of antifungal therapy. A. fumigatus may persist in the host in the presence of antifungal azoles (Fig. 5). The formation of biofilms may enhance the resistance to Nature Reviews Microbiology before ICU admission has also been linked to an increased incidence of IAPA. The pathophysiology of VAPA is complex and involves interactions between the virus, A. fumigatus, the microbiome and the host, again showing similar but also distinct features between IAPA and CAPA. Interestingly, CAPA patients show higher neutrophil extracellular traps (NET) production in the lungs compared with COVID-19 patients without CAPA, while CAPA patients with lower bronchioalveolar lavage (BAL) NET levels had a reduced 90-day survival. On the other hand, several genes linked to LC3-associated phagocytosis (LAP), a noncanonical form of autophagy implied in phagolysosomal fusion and subsequent killing of A. fumigatus conidia, were downregulated in BAL fluid of IAPA patients compared with patients presenting only influenza. Moreover, transcription of genes related to neutrophil degranulation was significantly downregulated in BAL fluid of patients with IAPA compared with patients with influenza only, but this was not the case in patients with COVID-19. IFNγ, interferon-γ. antifungals. Other mechanisms may include metabolic quiescent cells that survive antifungal exposure by not metabolizing the drug158 or the development of a stress response involving the upregulation of multiple pathways that allow the fungus to survive. These pathways may involve sterol metabolism, siderophore-mediated iron acquisition and ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transmembrane transporters, which increase efflux of cytotoxic Review article Table 1 | Single-nucleotide polymorphisms in immunity genes associated with viral-associated pulmonary aspergillosis Gene SNP(s) Association with IPA Major evidence linking gene and/or SNP to VAPA Refs. CLEC7A rs16910526 (p.Y238X) Yes Lower BAL expression of CLEC7A is associated with increased mortality after IAPA 177–180 CXCL10 rs1554013, rs3921, rs4859588 Yes Patients with IAPA have lower expression of CXCL10 than those with influenza alone 144,181 IFNG rs2069705 Yes Downregulation of IFNγ signalling in patients with IAPA and CAPA compared with those with the viral infection alone The rs2069705 SNP enhanced cytokine production and the fungicidal activity of macrophages 144,182 IL1B rs16944 Yes Patients with IAPA exhibit a blunted transcriptional response to IL-1β compared with those with influenza alone 144,183 LGALS3 ? Not reported Patients with IAPA have lower expression of LGALS3 than those with influenza alone Lower BAL expression is associated with increased mortality after IAPA 144,180 PTX3 rs2305619 rs3816527 (p.D48A) Yes PTX3 coordinates the interaction between neutrophils and B1a cells towards the production of natural antibodies Neutrophils regulate the production of natural IgG against Aspergillus fumigatus by B1a cells in IAPA SIGLEC15 rs2919643 (p. F273I) Not reported Lower BAL expression of SIGLEC15 is associated with increased mortality after IAPA Antifungal activity of immune cells is dampened by SIGLEC15 silencing The F273I SNP impairs cytokine production after fungal stimulation 143,180 TLR2 rs5743708 (p.R753Q) Yes Patients with IAPA have lower expression of TLR2 than those with influenza alone 144,185 60,61,184 BAL, bronchoalveolar lavage; CAPA, COVID-19-associated pulmonary aspergillosis; CXCL10, C-X-C motif chemokine ligand 10; IAPA, influenza-associated pulmonary aspergillosis; IFNγ, interferon-γ; IL-1β, interleukin-1β; IPA, invasive pulmonary aspergillosis; PTX3, pentraxin-related 3 protein; TLR2, Toll-like receptor 2; VAPA, virus-associated pulmonary aspergillosis. compounds159. These stress responses are typically observed in a small fraction of cells within a population and may be transient158. Antifungal drug resistance can also arise from stable or inherited point mutations, as well as insertions or deletions in target genes. Mutations that confer antifungal drug resistance arise spontaneously within a population of cells. When the population is exposed to an antifungal, the mutated resistant cells will survive better than those cells without the mutation (wild-type population), becoming dominant in the population160. This process of resistance selection may occur in any environment that supports the growth and reproduction of A. fumigatus, although the ability to generate genetic variation depends on the reproduction mode. A study reported the role of sexual reproduction in the environment in the development of multidrug-resistant haplotypes in the Cyp51A gene5,161. Sexual reproduction is highly unlikely to take place in the human host due to the requirement of opposing mating types and the relatively long time needed to develop cleistothecia (closed fruit bodies that contain sexual ascospores). Parasexual recombination is another mechanism for fungi to transfer genetic material, without the need to develop specific structures. Following the fusion of compatible hyphae, a heterokaryon is formed with a diploid nucleus, which enables mitotic recombination162. Parasexual recombination was shown to occur in people with cystic fibrosis, where A. fumigatus genotypes may persist over many years in the lung163. Diploid formation was associated with increased frequency of SNPs in persistent A. fumigatus isolates and preceded the recovery of a voriconazole-resistant isolate, suggesting a possible role in resistance development. A third reproduction mode is asexual reproduction, characterized by mitotic mutations and replication slippage or unequal sister chromatid recombination at low frequency. This reproduction mode is abundantly present in the environment and may occur in human hosts when specific conditions are present164. Sporulation may occur in cavitary pulmonary disease (aspergilloma) or during invasive A. fumigatus tracheobronchitis, Nature Reviews Microbiology where the infection mainly affects the airways. Spontaneous mutations, some of which may confer azole resistance, are likely to occur when the population size is high. During antifungal therapy, host azole resistance selection affects a single host, as A. fumigatus diseases rarely spread from human to human. This contrasts with environmental resistance selection, where exposure to azole fungicides active against A. fumigatus has been found to migrate globally165. Various environmental hotspots for resistance selection, where resistant spores accumulate, have been identified166. The Cyp51A gene is the most common target for resistance mutations, including SNPs sometimes combined with tandem repeats (TR) in the gene promoter, such as TR34/L98H and TR46/Y121F/T289A167. These mutations confer resistance to azole fungicides, but show cross-resistance to the medical azoles, including itraconazole, voriconazole, posaconazole and isavuconazole168. Ambient air was shown to contain ~4% of tebuconazole-resistant A. fumigatus spores, indicating that people inhale a mixture of azole-susceptible and azole-resistant spores169. Although most spores originate through asexual recombination and are clonal, airborne spores are likely to arise from multiple sources resulting in a genetically highly diverse population. Linking patient cases to environmental sources using genotyping has proven very difficult, even during hospital outbreaks. As a consequence, pulmonary invasive aspergillosis may present with genetically mixed infection, including azole-resistant A. fumigatus diseases in azole-naïve patients170. Pulmonary lesions may have developed from an azole-susceptible spore, while other lesions may have originated from azole-resistant conidia. Azole resistance is associated with treatment failure and mortality, both in patients with chronic pulmonary aspergillosis and those with invasive pulmonary aspergillosis. Survival estimates of 7 clinical trials evaluating first-line voriconazole for invasive aspergillosis were 71.8–80% at 6 weeks and 59–70.2% at 12 weeks171–173. However, the survival of patients with voriconazole-resistant invasive aspergillosis was 53–57.7% at 6 weeks Review article and 42.3–43% at 12 weeks. lower compared with the survival of patients with voriconazole-susceptible invasive aspergillosis and in the range of rates observed in the pre-voriconazole era174,175. This demonstrates that voriconazole resistance has major implications for patient survival and requires immediate treatment adjustment when diagnosed. Managing the dual use of antifungal compounds with the same modes of action in both agriculture and medicine is a key goal for compounds with new modes of action. Improving the diagnosis and surveillance of resistance, as well as antifungal stewardship in agriculture, horticulture and clinical settings, remain critical to manage and reduce azole resistance selection in A. fumigatus. Conclusions and outlook This review describes the mechanisms by which A. fumigatus evades and adapts to the hostile environment presented by its host. Through Genetic variation Occurrence strategies such as molecule masking, immune response manipulation and modulation of gene expression, A. fumigatus effectively circumvents host defences, posing notable challenges to infection treatment and control. To expand the arsenal of antifungal drugs, it is crucial to understand these evasion tactics, especially in the human host, in order to develop effective targets for treating A. fumigatus infections. Another key component to advance the treatment of invasive aspergillosis is the elucidation of the immune response required to combat the infection. A deeper understanding of specialized phagosome responses, which play a pivotal role in controlling the intracellular growth of the fungus, is needed. This includes understanding the role of WD40-mediated single membrane LC3 lipidation in A. fumigatus immunity and how we can modulate this process during infection176. We argue that by targeting specific evasion strategies and modulating host immune responses with host-directed therapy, clinicians will be able to enhance treatment Genetic variation Predominant mutations in Cyp51A Selection sites Asexual reproduction Azole fungicide TR34 and TR46 Hotspot Conidia Medical azole Spontaneous mutation SNPs (e.g., G54, P216 and M220) Cavity Conidiophore Parasexual reproduction ? Hyphal fusion Diploidisation via nuclear fusion Sexual reproduction mat 1-1 Haploidisation following mitotic recombination Unknown Azole fungicide TR34 and TR46 Biofilm Ascospore mat 1-2 Mating types Medical azole Hotspot Meiotic recombination Cleistothecium Fig. 5 | Ability of Aspergillus fumigatus to generate genetic variation according to the reproduction mode, frequency and potential sites for resistance selection. The figure shows three modes of reproduction. Asexual reproduction is very frequent in the environment, but as the offspring is clonal, the genetic variation is low. Asexual reproduction occurs abundantly in the environment, and may also occur in human infection, especially when a cavity is present. Mutations in the Cyp51A gene, which encodes for a 14-α sterol demethylase involved in ergosterol synthesis for the fungal cell membrane, commonly include the TR34 and TR46 resistance mutations. In the human host, asexual reproduction can occur in cavitary lesions and selection of resistance may arise from long-term treatment with medical azoles. Resistance mutations commonly involve SNPs such as G54, M220 and P216. Parasexual reproduction requires two compatible hyphae to fuse, and therefore the Nature Reviews Microbiology variation achieved through this reproduction mode is limited. The occurrence and frequency in nature are unknown, but it has been shown to occur in patients with chronic A. fumigatus lung disease (chronic pulmonary aspergillosis) and colonization (cystic fibrosis). In these conditions, A. fumigatus exists mainly as hyphae in a biofilm and mitotic recombination enables the fungus to adapt to environmental stress and persist in the host environment. Thus far, there are no specific resistance mutations associated with this reproduction mode. Sexual reproduction requires opposing mating types and takes several weeks to complete, which makes it highly unlikely that this reproduction mode occurs in the human host. As two genetically parent strains are involved, this is the most effective way for A. fumigatus to generate genetic variation, as each ascospore will contain genetic information from each of the parents. Review article efficacy and improve patient outcomes in A. fumigatus-related diseases in the near future. Although these concepts have been studied over the last decades and substantial progress has been made, as reviewed here, new challenges are on the rise. A notable highlight of this review is the exploration of VAPA, a critical condition where A. fumigatus infection complicates severe pulmonary viral infections. This emerging phenomenon underscores the complex interplay between viral and fungal pathogens, necessitating a nuanced understanding for effective management. But many questions remain unanswered. How exactly do viral infections predispose to aspergillosis? Will vaccination against viral infection lower the incidence of VAPA? Why is there a difference in the incidence of VAPA between different countries? Is this due to differences in the environment? In this review, we discussed the alarming rise of azole resistance in A. fumigatus, a trend with serious implications for treatment outcomes. By shedding light on this evolving challenge, we underline the urgency of developing alternative strategies to combat drug-resistant strains. 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We thank Simon Feys for helping with Fig. 3 and Matthaios Sertedakis for helping with Fig. 2. Author contributions All authors contributed equally to the preparation of this manuscript. Competing interests The authors declare no competing interests. Additional information Peer review information Nature Reviews Microbiology thanks Gustavo Goldman, Jean-Paul Latge and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. © Springer Nature Limited 2025
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