Tackling emerging fungal threats to animal health, food security and ecosystem resilience: The state of the art

The two pathogenic species of Cryptococci, Cryptococcus neoformans and C. gattii, share a remarkable ability to evade the innate immune system and disseminate throughout the body. This is thought, in large part, to be the result of natural selection through environmental amoebae, since virulence traits that the fungus has evolved to survive within such predators typically work just as effectively within human phagocytes.

In this talk I will discuss our recent work in probing the cryptococcal/macrophage interaction. In particular, I will discuss what we have learned about the molecular basis of “vomocytosis”, a phenomenon that the pathogen uses to exit from phagocytic cells. In addition, we are also interested in the genetic changes that drive hypervirulent outbreaks of cryptococcosis in otherwise healthy individuals and I will attempt to “compare and contrast” these disease situations and speculate on what they tell us about the innate immune response to fungal pathogens more generally.

Fungal infections with the cutaneous fungus Batrachochytrium dendrobatidis (Bd), that caused the collapse of amphibian assemblages and species extinctions elsewhere, appear to exert a rather localised impact on European amphibian communities. Introduction of Bd in different populations of the same European species may result in scenarios ranging from mass die offs and population declines to the establishment of apparent host-pathogen co-existence in the absence of obvious mortality and declines, but with potentially far reaching impact on amphibian fitness. Although the mechanisms underpinning these scenarios are not well understood, the importance of environmental drivers is increasingly being recognized, which opens opportunities for future in situ conservation measures. The emergence of a previously unknown chytrid fungus, B. salamandrivorans (Bs), has even further complicated the story of chytridiomycosis in Europe. This novel pathogen probably spilled over from captive, Asiatic urodelans to wild populations through the pet trade. Bsal has driven several European salamander populations to the edge of extinction in three European countries and has shown the potential to kill most European salamander and newt species in lab experiments. Bsal range expansion would pose an imminent threat to western Palearctic urodelan diversity, calling for urgent policy actions.

Zymoseptoria tritici is a major fungal pathogen on wheat, causing Septoria tritici blotch. The fungus is considered to be dimorphic, with non-infectious yeast-like macropygnidiospores and a filamentous infectious stage. Macropygnidiospores grow in plant debris and are distributed by rain splash, but have the ability to turn into hyphae that invades the stomata of wheat leaves. We recently developed a large range of molecular tools for working with Z. tritici, including GFP-labelled cellular markers and inducible/repressible promoters. Here I present an ongoing study that uses these tools to investigate the morphological and cellular organisation of Z. tritici. I show evidence that Z. tritici is not growing like a yeast (=uni-cellular fungus), but rather forms multi-cellular, no-directed hyphae that consist of numerous mono-nucleated cells. These compartments are following their own cell-cycle and proliferate by lateral budding. Each cell within this "reproductive hypha" has the ability to switch to a hypha, which growth more directed. Interestingly, even when Woronin bodies are absent, most septal pores within the ‘reproductive hyphae’ remain sealed and the hypha is relatively insensitive against mechanical damage.  In contrast, conditional mutants defective in septa formation are vulnerable, but also show significantly reduced lateral budding. These results suggest that sealing compartments in the macropygnidiospores allows massive reproduction by budding. Moreover, it arms the fungus against mechanical stress, occurring when the macropygnidiospores are distributed in the field by rain splash. Our studies provide the first indication for a Z. tritici cellular adaptation, required for early stages of infection of wheat.

In sexual lineages recombination generates diversity thus enabling adaptation. How then do predominantly clonal diploid lineages cope? When stressed, Candida albicans induces loss-of-heterozygozity (LoH) at numerous genomic locations. Cellular stress response pathways are regulated by the environmentally response chaperone Hsp90. Does Hsp90 stress affect genome integrity and LoH thereby providing an alternative lineage diversifying mechanism, which enables adaptation?

LoH within a mitotic diploid lineage will generate individuals that are homozygous (AA or aa) at previously heterozygous (Aa) sites. The resulting exposure of homozygous recessives will lead to intra-lineage phenotypic diversification that could potentially enable adaption, thereby compensating for the lack meiotic recombination. Might this sort of intra-lineage diversification be similar to meiotic recombination in generating diversity and enabling adaptation? Using an established LoH system in Candida, we experimentally tested this hypothesis by scoring LoH rates across the genome in cells experiencing different types of Hsp90 stress. Global mapping of LoH events using ddRAD sequencing revealed that LoH events are chromosome-specific and dependent on the type of Hsp90 stress cells were exposed to. To determine adaptive consequence, we are currently measuring drug resistance and asses morphogenetic changes in cells having undergone LoH in response to Hsp90 stress.

Filamentous and some dimorphic fungi are renowned for the production of a diverse array of secondary metabolites (SMs). On one hand, these natural products are valued for their bioactive properties stemming from their functions in fungal biology, key among those being protection from abiotic and biotic stress and establishment of a secure niche, yet on the other hand these very same properties can result in harm to hosts of pathogenic fungi. Here I highlight several SMs involved in the virulence of diverse pathogenic fungi and offer a prospective on how to identify potential SM virulence factors through identification of endogenous protective mechanisms embedded in the genome of the producing fungus.

Oomycetes are fungal-like organisms that are classified as Chromalveolates and phylogenetically grouped with diatoms and brown algae. They are among the most important groups of disease-causing organisms in both agriculture and aquaculture and thus represent a huge threat for global food security. Some aquatic species can cause serious environmental disasters, wiping out our native aquatic animals, for example European crayfish and also several amphibians have been severely affected or have become extinct. One particular pathogen, Aphanomyces invadans, is now approaching European waters and represents a devastating pathogen that kills some fish species in a matter of days. It is a tremendous problem in countries where it has already arrived (e.g. Bangladesh, India and parts of Africa). There are also other aquatic oomycete pathogens known including Haliphthoros, Halioticida, Lagenidium, Atkinsiella spp. that infect marine and brackish animals including lobsters, langoustines, abalone and prawns. Saprolegnia parasitica is one of the most destructive fish pathogens and is found in most fresh water environments around the world. Remarkably, very little is actually known about the biology of these aquatic pathogens. However, what we do know is that they are: 1) potential invaders of marine & fresh water habitats, 2) they can cause serious economic or environmental damage and most importantly, 3) they are all uncontrollable at present. An overview of these various animal pathogenic oomycetes is presented. Furthermore our current knowledge about the cellular and molecular infection strategies of S. parasitica is being discussed.

The inability of innate immunity to build an immunological memory, considered one of the main characteristics differentiating it from adaptive immunity, has been recently challenged by studies in plants, invertebrates, and mammals. Long-term reprogramming of innate immunity, that induces adaptive traits and has been termed trained immunity characterises prototypical innate immune cells such as natural killer cells and monocytes, and provides protection against reinfection in a T/B-cell-independent manner. In contrast, trained immunity has been shown to be able to induce protection against reinfection in a monocyte-independent manner. Non-specific protective effects dependent on trained immunity have also been shown to be induced after BCG vaccination in humans. Specific signaling mechanisms including the dectin-1/Raf1 and NOD2-mediated pathways induce trained immunity, through induction of histone methylation and epigenetic reprogramming of monocyte function. Complex immunological and metabolic circuits link cell stimulation to a long-term epigenetic reprogramming of its function. The concept of trained immunity represents a paradigm change in immunity and its putative role in infection and inflammation may represent the next step in the design of future vaccines and immunotherapeutic approaches.

Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases affecting rice production. Blast disease, however, also affects more than 50 grass species, including other important crops such as pearl millet, finger millet, oats and barley. Recently, blast disease has spread to wheat in South America and there have been important outbreaks of wheat blast disease in Brazil, Bolivia, and Paraguay. Combatting blast disease of rice and the other cereals it infects is therefore vital to ensuring global food security. In my research group we are investigating the biology of plant infection by M. oryzae and trying to use this information to devise new control strategies for the disease. During plant infection, M. oryzae forms a specialised infection structure called an appressorium. The infection cell generates enormous turgor, which is focused as mechanical force to breach the rice cuticle. We are particularly interested in re-polarisation of the appressorium and how this is controlled by means of a turgor-sensing mechanism that re-organises the actin cytoskeleton at the base of the appressorium to bring about cuticle penetration. Once rice tissue is invaded, the fungus secretes a large repertoire of effector proteins into plant cells.  We are trying to understand how M. oryzae effectors facilitate invasion of plant tissue and modulate plant immunity.  We are seeking to apply the knowledge gained to develop both short term means of controlling rice blast disease, using existing resistance genes more efficiently, and in the longer term by devising more durable solution to the disease.

Exposure to fungal spores is an unavoidable, and sometimes fatal, consequence of human respiration. Amongst the plethora of species which populate the airborne microflora a single agent, Aspergillus fumigatus, accounts for ~90% of mould-related lung disease in humans. The molecular basis of disease pathology is poorly characterised, and the predominance of a single pathogenic species unexplained. Our recent studies revealed genetic regulation of A. fumigatus traits directing pulmonary tissue invasion and suggest that host damage results from the collateral activity of multiple gene products. We have used transcriptional profiling to gather a panoramic view of fungal gene expression during mould infection of the mammalian lung and used it as a tool with which to dissect avirulent phenotypes. Addressing the behaviour of a non-invasive mutant lacking the pH-responsive transcription factor PacC we discovered a combinatorial mode of tissue entry dependent upon sequential, and mechanistically distinct, perturbations of the pulmonary epithelium. Thus, analysis of the host-infecting transcriptome reveals stage-specific expression of physiologically relevant and co-ordinately regulated pathogen genes including a cohort of species-specific and/or host mimicking traits capable of promoting tissue damage. The implications of these findings with respect to the origin of pathogenicity within the Aspergillus genus will be discussed.

It has been almost 20 years since the fungal pathogen Batrachochytrium dendrobatidis was first described as a cause of amphibian mass mortality in captivity and the wild. Since then, it has been implicated in amphibian population declines on five continents, along with its congener (Batrachochytrium salamandrivorans), currently affecting wild caudate amphibians on the European continent. Despite this, there has been an almost complete lack of efforts to mitigate these fungal pathogens in nature, and existing strategies are arguably best suited to managing disease in the captive setting. Several approaches are being investigated, and generally fall into five categories: i) host species-specific manipulations of host and extended immunity; ii) ‘immunisation’ using avirulent forms of the pathogen; iii) antifungal applications; iv) environmental disinfection or reduction of pathogen density, and v) manipulation of host community composition through removal of targeted host species. To date, the only published example of pathogen elimination required combining chemical environmental disinfection (iv) with antifungal treatment (iii), a transferrable but controversial method requiring further investigation of potential environmental impacts. Although research suggests manipulation of immunity (i) may hold some promise, the lack of transferability and high levels of pathogen diversity suggest that these approaches will be difficult, if not impossible, to roll out across amphibian communities in a timely fashion. Attempts at immunising (ii) with killed fungus have failed, and early results investigating competitive interactions amongst pathogen genotypes indicate that avirulent forms are simply outcompeted by more virulent genotypes. Antifungal treatment (iii) alone offers only transient benefits and do not impair reinvasion by amphibian-associated chytrids. Environmental reduction of pathogen density (iv) has been shown to allow coexistence between lethal forms of the chytrids and highly susceptible hosts, and theoretical research suggests that elimination of key host species (v) may reduce pathogen burdens to less virulent levels. These categories are value driven with the primary goal of conserving amphibians and will inevitably involve ethical disputes. It is therefore important that scientific objectivity underpins decision to apply any mitigation action.

Cryptococcus species are a leading fungal cause of human disease and death worldwide. In Sub-Saharan Africa, HIV-related cryptococcal meningitis, caused by C. neoformans, is associated with a 70% 3-month mortality and around 200,000 deaths per year. Importantly, despite increased availability of antiretroviral drugs, cases have not decreased. Additionally, the emergence of a hypervirulent lineage of C. gattii in British Columbia has demonstrated the threat posed by Cryptococcus sp. in regions outside their usual range and to immunocompetent hosts.

A new point-of-care immunodiagnostic test is now being used to facilitate screening and pre-emptive antifungal treatment as a cost-effective prevention strategy in patients with late-stage HIV infection; as well as enabling earlier, primary care-based, diagnosis for all symptomatic cases. Drug discovery aimed specifically at Cryptococcus species is limited, but one promising new agent, Viamet-1129, is now entering clinical evaluation. Meanwhile, expanding access to current antifungal drugs, and optimising their use in regimens that are sustainable in resource-limited settings, together with earlier diagnosis, and therapeutic lumbar punctures to manage the common complication of raised cerebrospinal fluid pressure, have the potential to significantly reduce the global disease burden.

Numerous studies of various strategies for vaccination against Candida spp by multiple groups distributed internationally have been performed. Additionally, there has been an extensive effort to develop cryptococcal active and passive vaccines. Antigens used for Candida include heat killed whole organisms, attenuated live organisms, Candida enolase, the Candida cell surface iC3b receptors, mannans, beta-glucan, heat shock protein hsp90, hyphally-regulated protein (Hyr1), proteins from the Sap family (secreted aspartic proteins), and recombinant proteins from the ALS (agglutinin like sequence) gene family. Additionally, several glycoconjugate strategies have been tested experimentally.  Differing adjuvant strategies have been explored also. For Cryptococcus, in addition to a variety of antigens, various immunostimulatory strategies, to be used in combination with antigens, have been explored.  In nearly all preclinical studies, significant and encouraging efficacy has been found.

Coincident with the ever increasing prevalence of Candida spp in hospitalised patients and the high prevalence rates of cryptococcal infection in patients with HIV, has been a substantive increasing societal/medical interest in the development of vaccines for both of these yeasts. The high costs of human trials have been a considerable road block for robust development of fungal vaccines in general. Several million dollars are needed for a single Phase 1 trial in humans. The Swiss company Pevion completed a Phase 1 clinical trial of vaccination with a recombinant Sap2 protein for patients with recurrent vulvovaginal candidiasis (RVVC). NovaDigm Therapeutics, with a future focus on disseminated candidiasis, has completed two Phase 1 trials, and is conducting a Phase 1b/2a trial in patients with RVVC. The vaccine NDV-3 in these studies contains the recombinant antigen Als3. The results of the first six months of this NovaDigm 1b/2a trial are currently under statistical analysis. In all three of these trials, NDV-3 has elicited robust antibody responses (IgG and IgA) as well as evidence of Th1 and Th17 T-cell activation. The safety profile of NDV-3 has been comparable to similar recombinant vaccines with local site reactions but there have been no serious adverse events due to the vaccine. NovaDigm intends to assess the Hyr1 and Sap2 antigens in a combined vaccine with Als3. To our knowledge, no clinical trials have been conducted with active vaccination strategies for Cryptococcus to date.

Of additional interest is the discovery of a very high level of 3D, structural homology between the rAls3p-N, the antigen used in the NovaDigm trials, and surface adhesins of Staphylococcus aureus. In preclinical murine studies, vaccination with the Candida antigen protects against challenge with Staphylococcus aureus in septicaemic and skin infections. Subjects vaccinated with rAls3p-N in the Phase 1 and 1b/2a trials clinical trials have produced antibodies that are opsonophagocytic for Staphylococcus.  

The increasing need for prevention of Candida spp infections, intensive antigen and adjuvant searches, the possible of immuno-enhancement strategies, especially for Cryptococcus, coupled with the development of newer adjuvants, and the growing interest in both governmental and private funding sources, provide considerable optimism for vaccines being successfully developed for these yeasts.