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Investigating how the host immunity shapes the evolution of antifungal resistance

Principal Supervisor: Dr Hung-Ji TsaiLink opens in a new window

Co-supervisor: Rebecca Drummond

PhD project title: Investigating how the host immunity shapes the evolution of antifungal resistance.

University of Registration: University of Birmingham

Project outline:


Fungal infections affect billions of people, including >1.5 million global deaths each year. Our failure to achieve cure against fungal infections results from the high levels of tolerance and resistance to antifungal drugs in clinical fungal isolates. While there are only three antifungals in the clinics, the rapid emergence of multi-drug resistant fungal pathogens is devastating. In 2019, CDC, for the first time, listed two fungal pathogens (Candida albicans and Candida auris) as serious/urgent threats in antimicrobial resistance. Despite the clinical importance, our understanding of underlying mechanisms in the development of antifungal resistance remains little, and to date, there is no direct clinical strategy to combat drug resistance.

One common challenge targeting antifungal resistance is the causal relationship between large-scale genome instability (e.g., aneuploidy) and the evolution of drug resistance. While “aneuploidy” is a collective term of thousands of random chromosome stoichiometries, the indefinite genome types confer a wide range of phenotype variation and have prevented the development of strategies against aneuploid diseases [1]. However, whether and how these genome aneuploidization events occur remains elusive, especially at the host-pathogen axis. This project aims to investigate the evolution of antifungal resistance and to identify novel host and fungal factors contributing to this adaptive process.

Objective and Methods:

Objective 1: Determine the large-scale genomic alterations triggered by the host stress

As fungi possess a high level of genome plasticity, we will identify the types of genomic alterations (mutations/CNV/ploidy variations) when fungal pathogens encounter the host stress in a temporal manner. In parallel, how these genomic changes contribute to the evolution of antifungal resistance will be studied in both cell line and animal models, using cell-biological and multi-omics approaches.

The research outcome of this objective will reveal the mechanistic insights into how fungal pathogens tolerate antiproliferative stress and thrive from the host.

Objective 2: Investigate the underlying mechanisms of antifungal tolerance.

While aneuploid fungi share a unique biophysical signature, hypo-osmotic stress state, their cytoplasmic environment is altered, likely diluted [2]. This motivates us to reconsider the fungal-drug interactions, such as precision targeting and uptake/efflux. We aim to use high-throughput, genome-wide screens using both chemical and microscopy tools to identify both genetic and non-genetic factors conferring antifungal tolerance in aneuploidy. The research outcome of this objective will not only elucidate the host-fungal-drug interaction in the context of antifungal resistance but also provide a new paradigm for the design of antifungal compounds.

Together, this project will leverage both genomics, proteomics, biochemistry and cell biological approaches, combined with animal models of infections to understand the host-pathogen interactions during the evolution of antifungal resistance.


  1. Tsai, H.-J.; Nelliat, A. A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation. Genes 2019, 10, 787.
  2. Tsai, H.-J.; Nelliat, A.R.; Choudhury, M.I.; Kucharavy, A.; Bradford, W.D.; Cook, M.E.; Kim, J.; Mair, D.B.; Sun, S.X.; Schatz, M.C.; et al. Hypo-osmotic-like stress underlies general cellular defects of aneuploidy. Nature 2019, 570, 117–121.

BBSRC Strategic Research Priority: Understanding the rules of life Microbiology, System Biology, and


Techniques that will be undertaken during the project:

Molecular technologies: both basic and high-throughput lab techniques, including genome-wide cloning and strain manipulations in automation systems.

Biochemistry: protein purifications, western blotting and immunoprecipitation assays.

Cell biological methods: advanced quantitative microscopy, phagocytosis assays and related host-pathogen interactions assays.

Basic animal model of infections.

Genomics: genome-sequencing, barcode-sequencing.

Proteomics: LC/MS-based quantitative proteomics.


Contact: Dr Hung-Ji TsaiLink opens in a new window