{"id":{"repo_id":"exeter","oai_identifier":"oai:figshare.com:article/29844422"},"canonical_url":"https://search.dev.ndltd.org/etd/exeter/oai:figshare.com:article/29844422","repository":{"repo_id":"exeter","name":"University of Exeter","base_url":"https://api.figshare.com/v2/oai"},"display":{"title":"The evolution of virulence in Candida auris determined through experimental, ecological and epidemiological approaches","abstract":"Candida auris is an emerging human fungal pathogen that has rapidly transitioned from its first description in a case of ear infection in Japan in 2008 to a global public health threat featuring the spread of six clades across six continents. Major problems concerning its management include: (i) propensity to cause invasive human infec- tion, especially in critically unwell patients, with an associated mor- tality of 45%, (ii) near-universal antifungal drug resistance and rising pan-antifungal drug resistance, and (iii) protracted nosocomial out- breaks affecting hundreds of healthcare institutions and vulnerable patients. In this thesis, I begin by reviewing what is known concern- ing genomic innovation strategies and the evolution of pathogenicity in C. auris (Chapter 1). I developed a thermotolerant fish embryo model (Aphanius dispar) to interrogate host-pathogen gene expres- sion programmes across five clades (Chapter 2), and discovered the significant up-regulation of xenosiderophore transporters across the species during infection (Chapter 3). I expanded origin searches us- ing a metabarcoding approach with collaborators across several ma- rine niches, identifying multiple emerging human fungal pathogens in cetacean animals, scombriform fish, and Great Pacific Garbage Patch ocean plastic waste, including C. auris in Atlantic bluefin tuna (Chapter 4). I then examined the genotype of echinocandin refrac- tory clinical isolates, identifying features of heteroresistance and tol- erance associated with polyploidy (Chapter 5). Finally, I update the global genomic epidemiology of the ongoing C. auris outbreak across six continents using 12,644 strains, including seven clinical strains from the first single hospital four clade outbreak in Algeria, and demonstrate evidence of polyploid homothallism in C. auris for the first time (Chapter 6). I then summarise the insights of this thesis of genomic innovation in C. auris and discuss proposals for further research with the goal of understanding emerging fungal infections for global health benefit (Chapter 7).<p></p>","abstract_html":"Candida auris is an emerging human fungal pathogen that has rapidly transitioned from its first description in a case of ear infection in Japan in 2008 to a global public health threat featuring the spread of six clades across six continents. Major problems concerning its management include: (i) propensity to cause invasive human infec- tion, especially in critically unwell patients, with an associated mor- tality of 45%, (ii) near-universal antifungal drug resistance and rising pan-antifungal drug resistance, and (iii) protracted nosocomial out- breaks affecting hundreds of healthcare institutions and vulnerable patients. In this thesis, I begin by reviewing what is known concern- ing genomic innovation strategies and the evolution of pathogenicity in C. auris (Chapter 1). I developed a thermotolerant fish embryo model (Aphanius dispar) to interrogate host-pathogen gene expres- sion programmes across five clades (Chapter 2), and discovered the significant up-regulation of xenosiderophore transporters across the species during infection (Chapter 3). I expanded origin searches us- ing a metabarcoding approach with collaborators across several ma- rine niches, identifying multiple emerging human fungal pathogens in cetacean animals, scombriform fish, and Great Pacific Garbage Patch ocean plastic waste, including C. auris in Atlantic bluefin tuna (Chapter 4). I then examined the genotype of echinocandin refrac- tory clinical isolates, identifying features of heteroresistance and tol- erance associated with polyploidy (Chapter 5). Finally, I update the global genomic epidemiology of the ongoing C. auris outbreak across six continents using 12,644 strains, including seven clinical strains from the first single hospital four clade outbreak in Algeria, and demonstrate evidence of polyploid homothallism in C. auris for the first time (Chapter 6). I then summarise the insights of this thesis of genomic innovation in C. auris and discuss proposals for further research with the goal of understanding emerging fungal infections for global health benefit (Chapter 7).&lt;p&gt;&lt;/p&gt;","abstract_has_math":false,"creators":["H Gifford (20283939)"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-06-09T00:00:00Z","date_published":"2025-06-09T00:00:00Z","updated_at":"2026-07-27T19:32:39Z","subjects":["Candida","Transcriptomics","Genomics","Bioinformatics","Emerging Infectious Disease","Epidemiology","Ecology","Metabarcoding","Fungal Pathobiology","Fungal Immunology"],"languages":[],"rights":["All rights reserved","Open Access after 2027-06-09"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["10871/141085"],"render_values":[{"text":"10871/141085","href":null,"code":true}]}]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["H Gifford (20283939)"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-06-09T00:00:00Z"]},{"key":"dc:relation","label":"Dc Relation","values":["https://figshare.com/articles/thesis/The_evolution_of_virulence_in_Candida_auris_determined_through_experimental_ecological_and_epidemiological_approaches/29844422"]},{"key":"dc:type","label":"Dc Type","values":["Text","Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Candida","Transcriptomics","Genomics","Bioinformatics","Emerging Infectious Disease","Epidemiology","Ecology","Metabarcoding","Fungal Pathobiology","Fungal Immunology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["All rights reserved","Open Access after 2027-06-09"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["10871/141085"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Candida auris is an emerging human fungal pathogen that has rapidly transitioned from its first description in a case of ear infection in Japan in 2008 to a global public health threat featuring the spread of six clades across six continents. Major problems concerning its management include: (i) propensity to cause invasive human infec- tion, especially in critically unwell patients, with an associated mor- tality of 45%, (ii) near-universal antifungal drug resistance and rising pan-antifungal drug resistance, and (iii) protracted nosocomial out- breaks affecting hundreds of healthcare institutions and vulnerable patients. In this thesis, I begin by reviewing what is known concern- ing genomic innovation strategies and the evolution of pathogenicity in C. auris (Chapter 1). I developed a thermotolerant fish embryo model (Aphanius dispar) to interrogate host-pathogen gene expres- sion programmes across five clades (Chapter 2), and discovered the significant up-regulation of xenosiderophore transporters across the species during infection (Chapter 3). I expanded origin searches us- ing a metabarcoding approach with collaborators across several ma- rine niches, identifying multiple emerging human fungal pathogens in cetacean animals, scombriform fish, and Great Pacific Garbage Patch ocean plastic waste, including C. auris in Atlantic bluefin tuna (Chapter 4). I then examined the genotype of echinocandin refrac- tory clinical isolates, identifying features of heteroresistance and tol- erance associated with polyploidy (Chapter 5). Finally, I update the global genomic epidemiology of the ongoing C. auris outbreak across six continents using 12,644 strains, including seven clinical strains from the first single hospital four clade outbreak in Algeria, and demonstrate evidence of polyploid homothallism in C. auris for the first time (Chapter 6). I then summarise the insights of this thesis of genomic innovation in C. auris and discuss proposals for further research with the goal of understanding emerging fungal infections for global health benefit (Chapter 7).<p></p>"]},{"key":"dc:title","label":"Title","values":["The evolution of virulence in Candida auris determined through experimental, ecological and epidemiological approaches"]}]}],"canonical_facts":{"dc:creator":["H Gifford (20283939)"],"dc:date":["2025-06-09T00:00:00Z"],"dc:description":["Candida auris is an emerging human fungal pathogen that has rapidly transitioned from its first description in a case of ear infection in Japan in 2008 to a global public health threat featuring the spread of six clades across six continents. Major problems concerning its management include: (i) propensity to cause invasive human infec- tion, especially in critically unwell patients, with an associated mor- tality of 45%, (ii) near-universal antifungal drug resistance and rising pan-antifungal drug resistance, and (iii) protracted nosocomial out- breaks affecting hundreds of healthcare institutions and vulnerable patients. In this thesis, I begin by reviewing what is known concern- ing genomic innovation strategies and the evolution of pathogenicity in C. auris (Chapter 1). I developed a thermotolerant fish embryo model (Aphanius dispar) to interrogate host-pathogen gene expres- sion programmes across five clades (Chapter 2), and discovered the significant up-regulation of xenosiderophore transporters across the species during infection (Chapter 3). I expanded origin searches us- ing a metabarcoding approach with collaborators across several ma- rine niches, identifying multiple emerging human fungal pathogens in cetacean animals, scombriform fish, and Great Pacific Garbage Patch ocean plastic waste, including C. auris in Atlantic bluefin tuna (Chapter 4). I then examined the genotype of echinocandin refrac- tory clinical isolates, identifying features of heteroresistance and tol- erance associated with polyploidy (Chapter 5). Finally, I update the global genomic epidemiology of the ongoing C. auris outbreak across six continents using 12,644 strains, including seven clinical strains from the first single hospital four clade outbreak in Algeria, and demonstrate evidence of polyploid homothallism in C. auris for the first time (Chapter 6). I then summarise the insights of this thesis of genomic innovation in C. auris and discuss proposals for further research with the goal of understanding emerging fungal infections for global health benefit (Chapter 7).<p></p>"],"dc:identifier":["10871/141085"],"dc:relation":["https://figshare.com/articles/thesis/The_evolution_of_virulence_in_Candida_auris_determined_through_experimental_ecological_and_epidemiological_approaches/29844422"],"dc:rights":["All rights reserved","Open Access after 2027-06-09"],"dc:subject":["Candida","Transcriptomics","Genomics","Bioinformatics","Emerging Infectious Disease","Epidemiology","Ecology","Metabarcoding","Fungal Pathobiology","Fungal Immunology"],"dc:title":["The evolution of virulence in Candida auris determined through experimental, ecological and epidemiological approaches"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T19:32:39Z"}