Matthew C. Fisher

A Direct DNA Extraction Workflow for Metabarcoding Fungal Bioaerosols from Adhesive Samplers

This paper presents an optimized DNA extraction protocol for adhesive samplers to enable culture-independent ITS2-based metabarcoding of fungal bioaerosols, revealing site-specific and seasonal fungal community dynamics.

The pangenome of Aspergillus fumigatus highlights the dynamics of gene gain-loss over evolutionary timescales in a human fungal pathogen

This paper quantifies gene gain and loss dynamics in Aspergillus fumigatus over a century using a global pangenome, revealing slow genome evolution and lineage-specific resistance mechanisms.

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.

Metabolic control of mitochondrial plasticity and extracellular vesicle biology drives Cryptococcus neoformans virulence

This study identifies metabolic stress integration as a central mechanism driving virulence in Cryptococcus neoformans by linking glucose limitation to mitochondrial plasticity and extracellular vesicle biology.

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus

This study describes six new Cryptococcus species using genomic and phenotypic data, revealing ecological associations, chromosomal variation, and metabolic differences across the genus.

Lineage-specific trait variation generates widespread, contemporaneous coexistence and competitive exclusion dynamics in an invasive, multihost wildlife parasite

The paper shows how lineage-specific trait variation in an amphibian parasite leads to different coexistence and competitive exclusion dynamics in Europe and Africa.

Genomic epidemiology of emerging terbinafine-resistant Trichophyton indotineae

The paper identifies terbinafine-resistant Trichophyton indotineae isolates globally, finds high genetic similarity and resistance linked to SQLE mutations, and suggests alternative resistance mechanisms.

Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom

This study uses genomic data to trace the introduction and transmission of Candida auris in the UK between 2014 and 2019, identifying at least three introductions and multiple transmission events.

Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

The paper identifies two-speed genome evolution in fungal pathogens, where virulence-related genes are enriched in repeat-rich regions while core genes are in repeat-poor regions.

HMMploidy: inference of ploidy levels from short-read sequencing data

HMMploidy infers ploidy levels from short-read sequencing data, outperforming existing methods at low-depth with large sample sizes and revealing aneuploidy in Cryptococcus neoformans.

Tracing patterns of evolution and acquisition of drug resistant Aspergillus fumigatus infection from the environment using population genomics

The paper uses population genomics to trace the evolution and environmental acquisition of drug-resistant Aspergillus fumigatus, finding evidence of resistant isolates transmitted from the environment to patients.

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.

Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians

The paper develops and evaluates non-lethal protocols for isolating chytrid fungi from amphibians, showing their global application and effectiveness in recovering fungal isolates.

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.

A population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent cryptococcal meningitis infection

The paper uses whole-genome sequencing to determine whether recurrent cryptococcal meningitis in HIV patients results from relapse or reinfection, finding clonal relationships in most cases and novel hypermutator mechanisms in others.