Christina A. Cuomo

Parallel evolution under constraint shapes echinocandin resistance in Candida auris

Across 681 matched isolates and 22,388 genomes, high-level micafungin resistance in Candida auris arises through recurrent FKS1 hotspot mutations amid strong purifying selection, and FKS2 appears dispensable.

Antarctic marine microplastics reveals environmental persistence and rapid evolution of Candida auris

The paper isolates Candida auris from Antarctica, identifies cold-adapted traits, and links mutator phenotypes to rapid evolution and drug resistance in global C. auris clades.

Pooled CRISPRi screening reveals fungal-specific vulnerabilities across environments and genetic backgrounds

This study uses pooled CRISPRi screening in Candida albicans to identify dosage-sensitive genes across diverse environments and genetic backgrounds, highlighting potential antifungal targets.

Acquired Amphotericin B Resistance Attributed to a Mutated ERG3 in Candidozyma auris

This paper describes a clinical case of acquired amphotericin B resistance in Candidozyma auris due to a frameshift mutation in ERG3, showing a fitness cost associated with altered sterol production.

Ergosterol-depleted clinical isolates of Nakaseomyces glabratus can develop multi-drug resistance without apparent fitness and virulence defects

The paper identifies ergosterol depletion in Nakaseomyces glabratus as a mechanism for amphotericin B resistance without fitness or virulence defects.

Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9

This paper uses CRISPR-Cas9 to induce targeted loss of heterozygosity in Candida albicans and validates its role in antifungal resistance.

Mutations in transcription factors that confer fluconazole resistance also confer reduced susceptibility to manogepix in Candida auris, Candida albicans, Candida parapsilosis, and Candida glabrata (Nakaseomyces glabratus)

The paper identifies mutations in transcription factors that confer fluconazole resistance and also reduce susceptibility to manogepix in multiple Candida species.

Relative contributions of the ERG11VF125AL and MRR1AN647T mutations to fluconazole resistance in Clade III Candidozyma (Candida) auris clinical isolates

This study shows that the ERG11 mutation, not MRR1A, is primarily responsible for fluconazole resistance in Clade III C. auris isolates, while both mutations modestly affect voriconazole resistance but not other azoles.

Mutations in TAC1B drive CDR1 and MDR1 expression and azole resistance in C. auris

This study shows that TAC1B mutations in C. auris increase fluconazole and triazole resistance by upregulating CDR1 and MDR1, with CDR1 being the main driver.

Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion

The paper compares the genomes of pathogenic and non-pathogenic Cryptococcus species with related Kwoniella species, revealing gene gains/losses and chromosome fusion mechanisms linked to pathogenesis.

Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes

The paper identifies copy number variations in fluconazole resistance genes in Candida parapsilosis isolates using whole-genome sequencing and GWAS.

Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam

The paper uses population genomics and GWAS to analyze Talaromyces marneffei isolates from Vietnam, linking pathogen genetics to clinical phenotypes and identifying genomic regions under selection.

Genomic variation across a clinical Cryptococcus population linked to disease outcome

This study links genetic variation in Cryptococcus neoformans to clinical outcomes and virulence in animal models using GWAS and genomic data from 284 isolates.

Human and murine Cryptococcus neoformans infection selects for common genomic changes in an environmental isolate.

The paper shows that environmental Cryptococcus neoformans strains undergo genomic and phenotypic changes during mammalian infection, suggesting animal virulence drives genetic adaptation.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

The paper develops a method to trace horizontal gene transfer and persistence of carbapenem resistance genes across bacterial species using genomic data from clinical isolates.

Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations.

The paper analyzes whole-genome sequences of 121 Puccinia triticina isolates to study lineage evolution and mutation patterns in asexual lineages.

Chromosomal rearrangements and loss of subtelomeric adhesins linked to clade-specific phenotypes in Candida auris

The paper identifies chromosomal rearrangements and loss of subtelomeric adhesins in Clade II of Candida auris, linking these to reduced virulence and outbreak potential compared to other clades.

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses

This study traces the global emergence and evolutionary history of Candida auris using population genomic analyses of isolates from 19 countries, identifying clades, phylogeographic patterns, and antifungal resistance mechanisms.

Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase

The paper shows that DNA methylation persists in Cryptococcus neoformans despite the loss of a de novo methyltransferase, with methylation patterns maintained through replication and natural selection.

Cryptococcus neoformans recovered from olive trees (Olea europaea) in Turkey reveal allopatry with African and South American lineages

The paper isolates and genetically analyzes Cryptococcus neoformans from olive trees in Turkey, revealing a novel niche and geographic distribution patterns of fungal lineages.

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

The paper characterizes the diversity and evolution of the Msg gene superfamily across Pneumocystis species, revealing its functional roles in immune evasion and host adaptation.

Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single, Candida albicans infected macrophages

The paper studies transcriptional dynamics in macrophages and Candida albicans during infection, revealing coordinated gene expression changes and heterogeneity in infection outcomes.

Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans

This study identifies two C. elegans-specific genes, pals-22 and pals-25, which function as antagonistic regulators controlling the switch between growth and pathogen resistance.

Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging species

The paper analyzes genome assemblies and RNA-Seq data from Candida auris and related species to identify genomic features associated with drug resistance, mating potential, and virulence.

Transcriptional heterogeneity of Cryptococcus gattii VGII compared with non-VGII lineages underpins key pathogenicity pathways

This study compares the transcriptional responses of four C. gattii lineages to macrophages, identifying lineage-specific gene expression patterns and pathogenicity-related processes.

A Global Analysis of Mutations Accompanying Microevolution in the Heterozygous Diploid Pathogen Candida albicans

This study analyzes mutations in Candida albicans during microevolution, finding that de novo substitutions and LOH events drive short-term evolution, while purifying selection is strong during host infection.

Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum

The paper analyzes genome sequences of Trichophyton rubrum and Trichophyton interdigitale to show that T. rubrum is clonal with limited genetic variation and no evidence of sexual reproduction.

Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi

The paper analyzes genome data from dimorphic fungi to identify evolutionary mechanisms underlying their adaptation to human hosts.

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

This study analyzes the population genomics of Cryptococcus neoformans var. grubii, revealing hybridization, biogeographic relationships, and genetic structure across global isolates.

Population Genomics And The Evolution Of Virulence In The Fungal Pathogen Cryptococcus neoformans

This study uses population genomics to explore how environmental selective pressures shaped virulence traits in Cryptococcus neoformans, identifying genetic differences between clinical and environmental isolates.