Biology subjects

Armstrong-James, D.

Publications and source records attributed to Armstrong-James, D..

10 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↗

bioRxiv2025

Mgl2+ cDC2 triggering of fungal allergic inflammation depends on a spore induced glycolytic shift fuelled by local availability of glucose

Fungal spores are a major cause of severe asthmatic disease. However, the precise events that cause individuals to become sensitised to spores are poorly understood. Mgl2+ type 2 conventional dendritic cells (Mgl2+ cDC2s) are critical in coordinating allergic airway inflammation in mice following repeated exposure to inhaled spores. Yet, whether these DCs are directly acquiring spores from the airway, and the downstream mechanism(s) upon fungal uptake causing DCs to trigger allergic inflammation are unknown. Here we find that spores are acquired by lung DCs after inhalation although these events are rare ([~] 0.5% of the cDC2 population). Transcriptomics on isolated spore+ Mgl2+ cDC2s, compared to spore- Mgl2+ cDC2s from the same environment, revealed that a major consequence of fungal uptake was a boost in metabolic activity. Single-cell metabolic profiling revealed this increase in Mgl2+ cDC2 metabolism upon spore acquisition was fuelled by a glycolytic shift. To pinpoint if nutrient availability and acquisition is an important determinant of this response, mass spectrometry-based metabolomics revealed that, during fungal allergic inflammation, the local airway nutrient environment is altered. To ascertain which of these could be fuelling DC responses, we identified which substrates that feed into glycolysis were crucial. Of these, we found that glucose availability acts as a key rheostat in shaping cDC2 responses to spores. These data highlight a crucial role for glycolytic metabolism in driving cDC2 responses to spores, which is governed by glucose availability, defining novel targets for future therapeutic development of fungal allergic inflammation.

immunology↗

bioRxiv2025

Selective targeting of IL-1RAP-dependent eosinophilic inflammation in allergic fungal airway disease

It is estimated that in excess of 10 million people around the globe are affected by severe asthma and fungal sensitisation (SAFS) or allergic bronchopulmonary aspergillosis (ABPA), severe asthma endotypes driven by hypersensitivity to environmentally ubiquitous fungal pathogens, primarily Aspergillus fumigatus. Here, we sought to define the immunological pathways underlying these allergic fungal airway diseases. To do so, we exploit the chronic exposure repeat challenge model using live A. fumigatus conidia to systematically define the key immunological pathways driving airway inflammation in allergic fungal airway disease. In response to daily intranasal challenge, we observed increased absolute numbers of neutrophils and eosinophils in bronchoalveolar lavage fluid (BALF), characteristic of human allergic fungal airway disease, with significant depletion of the alveolar macrophage population. Transcriptomic analysis of BALF cells identified increased expression of IL-1 family cytokines and receptors including IL-1{beta}, IL-1RL1, IL-1R2 and the IL-18 binding protein. Complementary proteomic analysis of BALF revealed increased levels of cell death related proteins calprotectin and IL-1 Receptor Accessory Protein (IL-1RAP). Targeting IL-1RAP, using knockout mice, led to selective reduction in eosinophilia, IL-5 and IL-13 in the airways without impairment of fungal killing. This study identifies a role for IL-1RAP in the generation of eosinophilia independent of neutrophil influx and highlights its potential as a novel immunotherapeutic target for the treatment of allergic fungal airway disease. Author SummaryAllergic bronchopulmonary aspergillosis (ABPA) is a form of lung disease primarily affecting those with asthma or cystic fibrosis induced by the ubiquitous pathogen Aspergillus fumigatus. Understanding the immunological mechanisms contributing to this airway disease is important for the development of novel treatments to improve quality of life and preserve lung function. In this study, we show that an Aspergillus fumigatus repeat challenge model phenocopies immunological features of allergic fungal airway disease and is hallmarked by increased IL-1 family signalling. We identify the IL-1RAP as a contributor to eosinophilia and the release of Type 2 cytokines during allergic fungal airway disease. This work represents major step in describing the molecular mechanisms of airway eosinophilia in response to fungal exposure and lays the groundwork for further dissection of inflammatory pathways to target with immunotherapeutic approaches.

immunology↗

bioRxiv2024

Increased NFAT and NFκB signalling contribute to the hyperinflammatory phenotype in response to Aspergillus fumigatus in cystic fibrosis

Aspergillus fumigatus (Af) is a major mould pathogen found ubiquitously in the air. It commonly infects the airways of people with cystic fibrosis (CF) leading to Aspergillus bronchitis or allergic bronchopulmonary aspergillosis. Resident alveolar macrophages and recruited neutrophils are important first lines of defence for clearance of Af in the lung. However, their contribution to the inflammatory phenotype in CF during Af infection is not well understood. Here, utilising CFTR deficient mice we describe a hyperinflammatory phenotype in both acute and allergic murine models of pulmonary aspergillosis. We show that during aspergillosis, CFTR deficiency leads to increased alveolar macrophage death and persistent inflammation of the airways in CF, accompanied by impaired fungal control. Utilising CFTR deficient murine cells and primary human CF cells we show that at a cellular level there is increased activation of NF{kappa}B and NFAT in response to Af which, as in in vivo models, is associated with increased cell death and reduced fungal control. Taken together, these studies indicate that CFTR deficiency promotes increased activation of inflammatory pathways, the induction of macrophage cell death and reduced fungal control contributing to the hyper-inflammatory of pulmonary aspergillosis phenotypes in CF. Author SummaryThe airways of people with cystic fibrosis (pwCF) are commonly colonised with Aspergillus fumigatus (Af) resulting in a persistent hyperinflammatory state and the development of allergy. Understanding how first line defence innate cells, such as alveolar macrophages and neutrophils, contribute to this hyperinflammatory phenotype is important in developing novel treatments to preserve lung function in pwCF. In this study, we report that CFTR deficiency leads to increased alveolar macrophage death and persistent inflammation of the airways in pwCF, which is associated with impaired control of infection. We identify the increased activation of the transcription factors NF{kappa}B and NFAT as the mechanism of increased inflammatory cytokine production in CFTR deficient cells. This work is the first step in describing molecular mechanisms of hyperinflammation in CF in response to fungal infection and lays the groundwork for further dissection of inflammatory pathways to target with immunotherapeutic approaches.

immunology↗

bioRxiv2024

Mycobacterial lipoarabinomannan negatively interferes with macrophage responses to Aspergillus fumigatus in-vitro

IntroductionOver 1 million people have chronic pulmonary aspergillosis (CPA) secondary to pulmonary tuberculosis. Additionally, Aspergillus fumigatus (Af) has been reported as one of the most common pathogens associated with mycobacteria in patients with cystic fibrosis. Mycobacterial virulence factors, like lipoarabinomannan, have been shown to interfere with hosts intracellular pathways required for an effective immune response, however, the immunological basis for mycobacterial-fungal coinfection is still unknown. We therefore investigated the effect of lipoarabinomannan on macrophage responses against Af. MethodsBone marrow-derived macrophages (BMDMs) were stimulated with non-mannose-capped lipoarabinomannan (LAM) from Mycobacterium smegmatis or mannose-capped lipoarabinomannan (ManLAM) from Mycobacterium tuberculosis for 2 hours and then infected with swollen Af conidia. Cell death was assessed by lactate dehydrogenase release. Cytokine release was measured in supernatant using Enzyme Linked Immuno-Sorbent Assay (ELISA). Colony forming units counting and time-lapse fluorescence microscopy was performed for studying conidia killing by macrophages. ResultsBMDMs stimulated with LAM showed increased cell death and inflammatory cytokine release in a dose-dependent manner, characterised by a significant increase of IL-1{beta} release. Time-lapse fluorescence microscopy and CFUs revealed that both LAM and ManLAM significantly decrease the capacity of macrophages to kill Af conidia within the first 6 hours of infection. ConclusionsThe mycobacterial virulence factor, lipoarabinomannan, disrupts macrophage capacity to efficiently clear Af at early stages of infection in-vitro.

immunology↗

bioRxiv2024

Precision-cut lung slices in air-liquid interface (PCLS-ALI): A novel ex-vivo model for the study of Pulmonary Aspergillosis

Pulmonary Aspergillosis is a respiratory infection with a high mortality rate, which affects patients with immunosuppression or structural lung defects. Antifungal treatment options are few and many have narrow therapeutic margins and potentially serious side effects. In recent years, there are growing numbers of reports of antifungal resistance. Thus, there is an urgent need for effective models to study fungal pathogenesis and test antifungal therapies in the respiratory system. Here, we present a novel ex-vivo model using precision-cut lung slices in an air-liquid interface platform to evaluate lung tissue responses to fungal infection and antifungal treatment. Readouts assessed were lactate dehydrogenase for tissue damage, release of inflammatory cytokines (TNF-, IL-1{beta}, CXCL1), and histology for confirmation of hyphal invasion. Overall, the PCLS-ALI model is a promising approach for understanding lung tissue responses to fungal infections, which fulfils the reduction and refinement components of the 3Rs guiding principles for ethical use of experimental animals.

immunology↗

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↗

bioRxiv2021

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

Infections caused by opportunistic fungal pathogens are increasingly resistant to first-line azole antifungal drugs. However, despite its clinical importance, little is known about the extent to which susceptible patients acquire infection from drug resistant genotypes in the environment. Here, we present a population genomic analysis of the mould Aspergillus fumigatus from across the United Kingdom and Republic of Ireland. First, we show occurrences where azole resistant isolates of near identical genotypes were obtained from both environmental and clinical sources, indicating with high confidence the infection of patients with resistant isolates transmitted from the environment. Second, we find that the fungus is structured into two clades ( A and B) with little interclade recombination and the majority of environmental azole resistance genetically clustered inside Clade A. Genome-scans show the impact of selective sweeps across multiple regions of the genome. These signatures of positive selection are seen in regions containing canonical genes encoding fungicide resistance in the ergosterol biosynthetic pathway, whilst other regions under selection have no defined function. Phenotyping identified genes in these regions that could act as modifiers of resistance showing the utility of reverse genetic approaches to dissect the complex genomic architecture of fungal drug resistance. Understanding the environmental drivers and genetic basis of evolving fungal drug resistance needs urgent attention, especially in light of increasing numbers of patients with severe viral respiratory tract infections who are susceptible to opportunistic fungal superinfections.

genomics↗

bioRxiv2019

Comparative Evaluation of Micronaut-AM and CLSI broth micro-dilution method for antifungal susceptibility testing of Aspergillus species against four commonly used antifungals

The aim of this study was to evaluate a colorimetric method, Micronaut-AM, for determining susceptibility testing of anidulafungin, amphotericin, voriconazole and itraconazole by comparing the Minimum Inhibitory (Effective) Concentrations (MICs/MECs) obtained by this method to those generated by the reference Clinical Laboratory Standard Investigation (CLSI) method. 78 clinical isolates of Aspergillus species, nine of them azole-resistant, were tested against above antifungals. A fumigatus ATCC 204305 was used as a reference strain and test was performed in accordance with slightly modified yeast susceptibility testing instruction of the manufacture; conidia suspension inoculum and alamarBlue concentration were optimised. These same isolates were referred to Bristol Mycology reference laboratory and tested by CLSI method. The MICs and MECs generated by the two methods were compared using concordance analysis.\n\nMicronaut-AM (MN) showed significant concordance (P< 0.0001) with CLSI method and overall agreement was high ([≥] 90%). In addition, Micronaut-AM produced echinocandin MECs results within 18-24h incubation time and reliably detected azole resistant isolates. Essential agreement (within 2 log2 dilution of median) between MN and CLSI reference laboratory method was 99 % for anidulafungin, 100 % for amphotericin; 90% for voriconazole and 87 % for itraconazole. Categorical agreement for anidulafungin, amphotericin B, voriconazole and itraconazole were 100%, 96%, 97% and 99% respectively.\n\nMicronaut-AM showed very good agreement with the reference broth micro-dilution method results for all antifungal agents tested and was able to detect azole resistance. This colorimetric method is very promising and appears to be a suitable alternative susceptibility testing method to labour intensive broth microdilution method for Aspergillus species.

microbiology↗

bioRxiv2017

Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris

BackgroundCandida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients.\n\nMethodsTo understand the epidemiology of C. auris infection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context.\n\nFindingsPhylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations are novel for this pathogen.\n\nInterpretationMultiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.\n\nFundingAntimicrobial Research Collaborative, Imperial College London

epidemiology↗