Fungal Genomics and Antagonistic Community Interactions
( FuGACI )

Environment

Interventions

Surveillance

Therapeutics

Transmission

Research Project: 2025-04-01 - 2028-03-31
Total sum awarded: €2 295 742

Emerging fungal pathogens within the Candida genus, including C. albicans, C. parapsilosis and C. auris, represent a growing public health concern on a global scale, and resistance to key antifungal drugs, particularly azoles and echinocandins, is on the rise. Epidemiological shifts, including range expansion and increased virulence or resistance, are being driven by climate change, global trade and human movement, and our ability to mitigate this increased risk to public health is limited by poor surveillance. The implementation and utility of genomics in Candida epidemiology significantly lags behind its use for bacterial pathogens, and there is little data on the transmission dynamics of these species between clinical and non-clinical (‘One-Health’) environments. Moreover, it is not known how competitive ecological interactions with co-colonising bacterial species impact on the survival and spread of fungi. This proposal brings together expertise in bacterial and fungal epidemiology, genomics, bioinformatics and microbiome ecology. We will combine existing global genomics datasets from clinical and wastewater settings, with novel genome and metagenome data from hospitals in Italy, Netherlands and Australia, and wastewater data from the UK. We will examine transmission dynamics and inter-species co-occurrence by implementing and optimising state-of-the-art bioinformatics analyses developed originally by project partners for bacterial pathogens. This will provide critical data on intra-species diversity and will help to identify potential intervention points.

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  • Edward Feil, University of Bath, United Kingdom (Coordinator)
  • Anita Schürch, University Medical Centre Utrecht, Netherlands (Partner)
  • Johanna Rhodes, Radboud University Medical Centre, Netherlands (Partner)
  • Jukka Corander, University of Oslo, Norway (Partner)
  • Hilary Browne, University College, Cork, Ireland (Partner)
  • Davide Sassera, IRCCS Fondazione Policlinico San Matteo, Italy (Partner)
  • Gerry Tonkin-Hill, University of Melbourne, Australia (Partner)

Advances in our ability to sequence the large numbers of genomes for key microbial pathogens have transformed our understanding of how dangerous strains emerge and spread. Genome data are also central to addressing basic evolutionary questions relating to antimicrobial resistance or enhanced virulence. However, when compared to viruses and bacteria, the potential of genomics is not being realised in fungal pathogens, due partly to the relative complexity of fungal genomes. There is an urgent need to address this; pathogenic fungi cause 13 million infections, and around 1 million deaths, globally per year1. Candida is an important fungal genus that contains numerous pathogenic species, such as C. albicans, C. auris and C. parapsilosis, and these are known to cause hospital outbreaks2. This project brings together experts in pathogen genomics to apply genome sequencing of Candida strains to address three distinct knowledge gaps. First, we will use genomics to understand how these species are transmitted in hospitals, and whether strains specifically adapted to health-care settings have emerged, as is the case with bacteria. Secondly, we will gauge the prevalence of Candida in different human communities by detecting the presence of the different species/ strains in wastewater, using technology informed by the genomics. Third genome data will be used to identify bacteria that can grow alongside Candida in the human gut, but inhibit the growth of the fungi. These bacteria will be characterised experimentally to assess their therapeutic potential.

Call

2024 - Interventions moving forward to promote action to counteract the emergence and spread of bacterial and fungal resistance and to improve treatments