Biology subjects

Gifford, H.

Publications and source records attributed to Gifford, H..

8 recordsLinked to original sources

bioRxiv2026

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

Candida (Candidozyma) auris is a critical priority fungal pathogen that emerged two decades ago near simultaneously on multiple continents. Since emergence, C. auris resistance to all four classes of antifungal drugs has been described, including pan-drug resistant isolates, sometimes evolving within patients. Here, we confirm the first isolation of C. auris from Antarctica and show cold-adapted phenotypes and an affinity for binding to nylon. We also provide evidence to suggest mutator phenotypes contribute to the rapid evolution of C. auris and are responsible for the emergence of multiple, distinct genetic clades worldwide. Isolates in clades I, III and IV with a mutator phenotype displayed elevated mutation rates compared to non-auris Candida species. This phenotype had a complex genetic basis and was associated with drug resistance mutations. We postulate that the mutator phenotype has a significant effect on evolutionary potential and is responsible for the emergence and rapid spread of drug-resistance C. auris and novel genetic clades.

microbiology↗

bioRxiv2026

Organization and evolution of sex-biased gene expression in Drosophila adult sexual circuits

Sexually dimorphic behaviors are widespread across animals. A key open question is how the underlying sexual circuits, which encode these behaviors, evolve to meet sex-specific fitness needs despite being built from largely shared developmental blueprints. Here, we use single-cell transcriptomics, leveraging the sex determination gene fruitless (fru) as a molecular handle, to examine the transcriptomic landscape and evolution of adult Drosophila sexual circuits at cellular resolution. We find that sex-biased gene expression is limited, highly cell-type-specific, and largely species-specific. Species divergence in gene expression is widespread and predominantly coupled between sexes, with sex-specific changes constrained by pleiotropic gene expression across cell types. Furthermore, a strong overlap of differentially expressed genes across sexes, species, and fru status points to a common set of genes, particularly neural signaling genes, whose expressions are highly labile across multiple contexts. Finally, transcriptomic divergence between sexes decreases from mid-pupae to adulthood, underscoring the developmentally dynamic nature of sex-biased gene expression. Our results provide fundamental insights into the organization and evolutionary mode of sex-biased gene expression, suggesting that sex-specific adaptation via selective gene programs at localized circuit nodes is a key mechanism that preserves circuit evolvability despite pervasive transcriptomic coupling between sexes.

evolutionary biology↗

bioRxiv2026

Global genomic epidemiology of Candida auris: analysis of 12,644 whole genome sequences from 1997-2024

Candida auris is a critical priority fungal pathogen (World Health Organization) that has emerged into human populations pre-1996 from an unknown environmental reservoir. Genomic sequencing data has been used extensively in the last decade, leading to a largely unharnessed dataset with potential to unlock understanding of emerging fungal pathogen evolution. Here, we compiled publicly available Illumina paired-end whole genome sequences (WGS) for variant calling, supplemented by isolates from the worlds first four-clade single-facility outbreak in Algeria (n = 7), totaling 12,644 WGS. We describe the geographic, clinical, and temporal epidemiology of the outbreak across the globe between 1997 and 2024, indicating a conserved six-clade structure. Despite the evidence of earlier species diversity in low- and lower-middle income countries (LLMIC), the majority of WGS derived from high-income (12,035, 93.2%) and upper-middle-income countries (719, 5.57%), where cases are believed to be imported from endemic regions, with few from lower-middle-income countries (165, 1.28%) and none from lower-income countries. Copy number variation was present, including azole drug target ERG11, with seven isolates displaying ten to fifteen copies. Alarmingly, the standing variation of C. auris reveals emerging variation in hot-spots of the echinocandin drug target FKS1, which encodes a {beta}-1,3-glucan synthase. Eighteen emerging FKS1 hot-spot variants have not been detected or described in databases, and mostly occured in Northern America (57/61, 93.4%), where echinocandin monotherapy is standard treatment. Well-studied FKS1 variants known to cause resistance are significantly more common in clade I isolates derived from urine compared to blood, consistent with a role for the urinary niche as a low echinocandin concentration safe-haven for the development of resistance. The insights from this global genomic epidemiology survey of C. auris highlight sequencing inequality and detect ongoing genomic innovation in clinical settings, raising predictable and urgent concerns around the ongoing use of echinocandin monotherapy and potential emerging antifungal drug resistance-related genotypes in high-income settings.

microbiology↗

bioRxiv2026

FKS1/2-variant independent mechanisms underlying the emergence of resistance in echinocandin-refractory Candida auris infections

The emerging fungus Candida auris is a drug resistant global public health threat and WHO critical priority pathogen. Recommended first-line invasive candidiasis treatment is echinocandin monotherapy, but C. auris can develop on-treatment resistance via FKS1/2 gene mutations and additional, previously unexplained mechanisms. To better understand echinocandin failure in C. auris, we sequenced the genomes of echinocandin refractory FKS1/2 wild-type C. auris serial isolates from two critically unwell patients in London, UK. Population analysis profiling revealed echinocandin heteroresistance, and in vitro culture of clinical isolates at supra-MIC concentrations of anidulafungin (8 g/ml) exhibited morphotypic heterogeneity. Small colony variants (SCVs) and large colony variants (LCVs) showed elevated MICs with polyploidy (to 4n and above) alongside adaptive changes in cell wall {beta}-1,3-glucan content. LCVs contained significantly more mutations in calcineurin-related stress tolerance pathway gene CRZ1 compared to clinical parents and SCVs, associated with further increases in MIC. These findings indicate progressive step-wise accrual of adaptation to echinocandins, including genomic instability, alterations in stress tolerance pathways, and cell wall remodeling, paving the way for resistance emergence. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/700071v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@14460b7org.highwire.dtl.DTLVardef@29a598org.highwire.dtl.DTLVardef@36d187org.highwire.dtl.DTLVardef@f62c8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

High-resolution comparative single-cell transcriptomics of doublesex-expressing neurons reveals evolutionary conservation and diversity of sexual circuits in Drosophila

Understanding how the cellular and molecular composition of neural circuits change during evolution is essential for deciphering how behavior evolves. Male sexual behaviors in Drosophila species are remarkably diverse, and the underlying sexual circuits are specified by sex determination genes. Here, we employed single-cell transcriptomics to systematically characterize and compare neuron cell types that express the sex determination gene doublesex in adult males across Drosophila species with divergent sexual behaviors. High-resolution profiling to delineate cellular diversity revealed a largely conserved set of cell types across four species, with minimal evolutionary gain or loss and potentially more prevalent changes in cell type abundance. In-depth comparisons between D. melanogaster and D. yakuba showed that transcriptomic conservation and differentially expressed genes between species are highly cell-type-specific, suggesting that cell types evolve as highly independent units. We identified widespread species differences in gene expression, particularly in the neuromodulatory signaling pathway, while preserving a conserved circuit layout in sexual identity and neurotransmitter properties. We further generated a female dataset in D. melanogaster to define sex differences in cell types and examine species divergence in relation to sex differences. Finally, we reported marker gene combinations that uniquely define each cell type, providing a foundational resource that enables the design of cell -type-specific genetic reagents. Overall, our study provides fundamental insights into the cellular diversity of sexual circuits and how evolution shapes cell types and gene expression in behavioral adaptations.

evolutionary biology↗

bioRxiv2024

Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish infection

Candida auris is a critical priority fungal pathogen (World Health Organization). Clinical management is challenging due to a high mortality rate, rapidly increasing antifungal resistance, and frequent nosocomial outbreaks. A critical bottleneck in understanding virulence is the lack of gene expression profiling models during infection. We developed a fish embryo yolk-sac microinjection model using Aphanius dispar (Arabian killifish; AK) at human body temperature. This enabled interrogation of infection dynamics via dual host-pathogen RNA-seq across five major clades of C. auris (I-V). Host responses included heat shock, complement activation, and nutritional immunity, notably haem oxygenase (HMOX) expression during clade IV infection. We identified a pathogen transcriptional signature across all five clades of C. auris strongly enriched for putative xenosiderophore transmembrane transporters. We describe this novel family and a sub-clade of five putative haem transport-related (HTR) genes. Only the basal clade V isolate formed filaments, associated with canonical and atypical regulators of morphogenesis. Clades I and IV demonstrated increased virulence, accompanied by up-regulation of three HTR genes in clade IV, and the non-mating mating-type locus (MTL) gene PIKA in both clades. Our study provides new insight into C. auris pathogenesis, highlighting species-wide in vivo up-regulation of XTC genes during host tissue infection. Significance statementCandida auris is an emerging human fungal pathogen and global public health threat, yet in vivo transcriptomic analysis of tissue infection has remained elusive. Using yolk-sac infection in Arabian killifish, we profiled gene expression across five major C. auris clades. We found that the basal clade V uniquely undergoes filamentation during infection, while all clades upregulate members of a large, expanded family of xenosiderophore transporter candidate genes. These findings highlight the important roles for iron acquisition and morphological switching in pathogenesis, revealing potential mechanisms of immune evasion and fungal persistence, and identifying candidate targets for antifungal therapy.

microbiology↗

bioRxiv2024

The thermotolerant Arabian killifish, Aphanius dispar, as a novel infection model for human fungal pathogens

Candida albicans: a fungal pathogen, can cause superficial and fatal infections in humans. An important virulence factor in C. albicans dissemination is the transformation from yeast to an invasive hyphal form, which is favoured at human body temperature. Zebrafish, a useful model for studying C. albicans infections, cannot survive at 37{degrees}C. Arabian killifish, Aphanius dispar, an emerging teleost model can tolerate temperatures up to 40 {degrees}C for up to 12 days (independent feeding time) allowing for longer analysis compared to zebrafish. This study introduces A. dispar as a thermo-relevant and a more accurate reporter of the virulence mechanisms relevant to C. albicans as a human pathogen. Using A. dispar, we tested virulence at human skin (30 {degrees}C), body temperature (37 {degrees}C) and a high fever condition (40{degrees}C). Infection by C. albicans at 37{degrees}C and 40{degrees}C significantly increased virulence, reduced survival of AKF embryos and formed invasive hyphal network compared to 30 {degrees}C. Two mutant strains of C. albicans. pmr1{Delta} (with aberrant cell surface glycans) exhibited reduced virulence at 37{degrees}C, whereas rsr1{Delta} (lacking a cell polarity marker) showed less virulence at 30 {degrees}C. Additionally, anti-fungal treatment rescued AKF survival in a dose-dependent manner, indicating AKFs potential for in vivo drug testing. Our data indicates the quantitative and qualitative importance of examining virulence traits at physiologically relevant temperatures and demonstrates an equivalence to findings for systemic infection derived in mouse models. The A. dispar embryo therefore provides an excellent in vivo model system for assessing virulence, drug-testing, and real-time imaging of host-pathogen interactions. Significance StatementThe virulence of many pathogens is dependent on host temperature. We demonstrate that the A. dispar embryo provides an excellent new thermo-relevant alternative to zebrafish and mouse models, which have limitations in terms of the range of temperatures that can be assessed in real-time. In this study, we have assessed C. albicans temperature-based virulence, focusing on human body and human skin temperatures (37, 40 and 30 {degrees}C, respectively) by examining different genetic backgrounds of C. albicans strains. The results indicate different C. albicans strains with genetic background show varied virulence depending on temperature indicating importance of examination of virulence mechanisms at physiological temperatures.

animal behavior and cognition↗

bioRxiv2024

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

BackgroundCandida auris is a globally emerging fungal pathogen that causes nosocomial invasive infections, particularly in intensive care units (ICU). Four prominent genetic clades originating from distinct geographic regions have been identified: South Asia (Clade I), East Asia (Clade II), Africa (Clade III) and South America (Clade IV) with each clade presenting differing antifungal resistance profiles. We aimed to elucidate the epidemiology of this infection in the United Kingdom (UK) 2014 - 2019 using genomic approaches. MethodsGenome sequences from 24 isolates from six patients in four London hospitals were combined with genome sequences from 183 additional outbreak isolates from nine UK hospitals. These data were used to assess the numbers and timings of C. auris lineage introductions into the UK and to infer subsequent patterns of inter- and intra-hospital transmission. FindingsWe found evidence for at least three introductions of C. auris into the UK, one from Clade I and one from Clade III. The evolutionary rate of C. auris Clade I and Clade III were estimated at 2.764 x 10-4 and 3.186 x 10-4 substitutions per polymorphic site per year, respectively, with entry into the UK as 2013 and 2016 for Clades I and III respectively. We observed temporal and geographical evidence for multiple transmission events between hospitals and identified local within-hospital patient-to-patient transmission events. InterpretationThese data confirm that C. auris is a newly emerged infection in the UK with at least three original introductions into this country. Our analysis shows that hospital outbreaks are linked and confirms that transmission amongst patients has occurred, explaining local hospital outbreaks. Our findings argue that enhanced surveillance of C. auris infection within the UK is necessary in order to protect healthcare and to curtail expansion of this emerging infection. FundingThis work was supported by a Wellcome Trust Institutional Strategic Support Fund Springboard Fellowship, and by the Medical Research Council (MR/R015600/1), the Natural Environment Research Council (NE/P001165/1) and the Wellcome Trust (219551/Z/19/Z). Research in contextSince its first description in 2009, Candida auris has spread across the globe. For this study, authors considered all publications describing whole genome sequences of isolates within the UK up until 2020 to assess the genomic epidemiology of this fungal pathogen. This study adds value to the current understanding of C. auris epidemiology by undertaking the first analysis to assess transmission between and within hospitals using genomic data. We also provide the first in-depth temporal analysis to estimate likely times of introduction into the UK. These results have clinical implications, encouraging hospitals to identify yeast upon admission and to assess multiple isolates from single patients, which may harbour much diversity in terms of genetics and drug resistance.

genomics↗