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Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections
Pria N Ghosh1,2, Lola M Brookes1,3,4, Hannah M Edwards1
1Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary's Campus, Imperial College London, London W2 1PG, UK.
Abstract:
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
Insights
Emerging fungal pathogens threaten global food, ecosystems, and health. Genomics and other omics approaches offer powerful tools to understand and combat these threats, despite historical underinvestment and disciplinary separation.
Area of Science:
- Microbiology and Pathogen Research
- Genomics and Bioinformatics
- One Health Initiatives
Background:
- Emerging fungal pathogens present a significant and escalating global threat to agriculture, wildlife, and human health.
- Chronic underfunding has limited research into fungal pathogen epidemiology compared to bacterial and viral counterparts.
- Research on plant, human, and wildlife fungal diseases has historically been siloed, hindering interdisciplinary collaboration.
Purpose of the Study:
- To review advances in genomics and other omics approaches for studying fungal pathogens across different host systems.
- To identify barriers to the integration and underutilization of omics methodologies in mycology research.
- To recommend crucial omics methodologies for future capacity building in fungal pathogen research.
Main Methods:
- Review of current literature on genomics and multi-omics applications in plant, human, and wildlife mycoses.
- Analysis of common biological traits of emerging fungal pathogens across diverse hosts.
- Identification of interdisciplinary research gaps and underutilized omics techniques.
Main Results:
- Genomics and omics approaches are highly attractive for understanding fungal pathogen biology and epidemiology due to their untargeted nature.
- Despite disciplinary separation, many fungal pathogens share traits like genomic plasticity and wide host ranges, suggesting transferable omics insights.
- Significant barriers exist in linking different omics datasets and methodologies, leading to underutilization in various research fields.
Conclusions:
- Omics technologies are crucial for addressing the growing threat of emerging fungal pathogens.
- Enhanced interdisciplinary collaboration and capacity building in specific omics methodologies are essential for future progress.
- Integrating genomics with other omics data can illuminate the biology and epidemiology of fungal diseases across plant, human, and wildlife health.
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