R01AI169066

Mapping the Genomic and Molecular Mechanisms of Antifungal Resistance in the Emerging Fungal Pathogen Candida auris - Project Summary/Abstract

Candida auris is an emerging multidrug-resistant fungal pathogen of great clinical concern that is associated with outbreaks on six continents. A critical barrier to overcoming the high antifungal resistance in C. auris is the significant lack of understanding of its genetic, genomic, and molecular basis. The long-term goal of this project is to advance the treatment of C. auris.

The overall objective of this proposal is to fully understand the molecular and genetic basis of antifungal resistance in clinical isolates of this fungal pathogen. The central hypothesis behind this proposal is that antifungal resistance is mediated both by mechanisms analogous to those previously identified in other species of Candida, as well as novel mechanisms unique to this organism.

Aim 1 is to identify and delineate the genetic determinants of triazole resistance in clinical isolates of C. auris. Preliminary studies identified mutations in genes encoding the triazole target sterol demethylase (ERG11) and the novel transcription factor (TF) TAC1B as contributing to resistance in some but not all isolates. Genome-wide association studies (GWAS) and transcriptional profiling of a growing collection of clinical and experimentally evolved isolates will be used to identify novel genes and mutations linked to triazole resistance, which will be tested using CRISPR-Cas9 gene editing. The contribution of activating mutations in TF genes such as TAC1B and MRR1A will be determined using RNA-Seq and ChIP-Seq.

Aim 2 is to identify and delineate the genetic determinants of echinocandin resistance in clinical isolates of C. auris. Mutations in the gene encoding glucan synthase (FKS1) have been identified among isolates resistant to echinocandins. However, preliminary data indicate that some resistant isolates lack FKS1 mutations, and others exhibit high-level resistance that cannot be explained by such mutations alone. CRISPR-Cas9 gene editing will be used to assess mutations in FKS1 for their individual contribution to resistance. Novel candidate resistance genes and mutations will be identified using GWAS and transcriptional profiling of clinical and experimentally evolved isolates, and these genes will be tested by CRISPR-Cas9 gene editing.

Aim 3 is to identify and delineate the genetic determinants of amphotericin B resistance in clinical isolates of C. auris. In preliminary studies, mutations in the gene encoding sterol methyltransferase (ERG6) were identified as a cause of resistance to amphotericin B. Novel resistance genes and mutations will be identified using comprehensive sterol profiling, GWAS, and transcriptional profiling of clinical and experimentally evolved isolates, and mutations will be tested by CRISPR-Cas9 gene editing. The relationship between resistance and fitness will also be determined.

Understanding the basis of antifungal resistance is essential for the development of tools to better predict response to therapy, to aid rational drug design and development, and to assist in epidemiologic tracking of the spread of resistance. The proposed project will, for the first time, undertake a comprehensive examination of the genomic, genetic, and molecular basis of antifungal resistance in the emerging multidrug-resistant fungal pathogen C. auris.

St. Jude Children's Research Hospital

TO ASSIST PUBLIC AND PRIVATE NONPROFIT INSTITUTIONS AND INDIVIDUALS TO ESTABLISH, EXPAND AND IMPROVE BIOMEDICAL RESEARCH AND RESEARCH TRAINING IN INFECTIOUS DISEASES AND RELATED AREAS, TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS. TO ASSIST PUBLIC, PRIVATE AND COMMERCIAL INSTITUTIONS TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS, TO PROVIDE RESEARCH SERVICES AS REQUIRED BY THE AGENCY FOR PROGRAMS IN INFECTIOUS DISEASES, AND CONTROLLING DISEASE CAUSED BY INFECTIOUS OR PARASITIC AGENTS, ALLERGIC AND IMMUNOLOGIC DISEASES AND RELATED AREAS. PROJECTS RANGE FROM STUDIES OF MICROBIAL PHYSIOLOGY AND ANTIGENIC STRUCTURE TO COLLABORATIVE TRIALS OF EXPERIMENTAL DRUGS AND VACCINES, MECHANISMS OF RESISTANCE TO ANTIBIOTICS AS WELL AS RESEARCH DEALING WITH EPIDEMIOLOGICAL OBSERVATIONS IN HOSPITALIZED PATIENTS OR COMMUNITY POPULATIONS AND PROGRESS IN ALLERGIC AND IMMUNOLOGIC DISEASES. BECAUSE OF THIS DUAL FOCUS, THE PROGRAM ENCOMPASSES BOTH BASIC RESEARCH AND CLINICAL RESEARCH. SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM EXPANDS AND IMPROVES PRIVATE SECTOR PARTICIPATION IN BIOMEDICAL RESEARCH. THE SBIR PROGRAM INTENDS TO INCREASE AND FACILITATE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM STIMULATES AND FOSTERS SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. RESEARCH CAREER DEVELOPMENT AWARDS SUPPORT THE DEVELOPMENT OF SCIENTISTS DURING THE FORMATIVE STAGES OF THEIR CAREERS. INDIVIDUAL NATIONAL RESEARCH SERVICE AWARDS (NRSAS) ARE MADE DIRECTLY TO APPROVE APPLICANTS FOR RESEARCH TRAINING IN SPECIFIED BIOMEDICAL SHORTAGE AREAS. IN ADDITION, INSTITUTIONAL NATIONAL RESEARCH SERVICE AWARDS ARE MADE TO ENABLE INSTITUTIONS TO SELECT AND MAKE AWARDS TO INDIVIDUALS TO RECEIVE TRAINING UNDER THE AEGIS OF THEIR INSTITUTIONAL PROGRAM.

93.855 - Allergy and Infectious Diseases Research

National Institute of Allergy and Infectious Diseases (NIAID) [HHS - NIH]

Memphis, Tennessee 38105 United States

Single Zip Code

NIH Research Project Grant (Parent R01 Clinical Trial Not Allowed) (PA-20-185)

Amendment Since initial award the total obligations have increased 47% from $2,495,758 to $3,661,637.