Biology subjects

Warris, A.

Publications and source records attributed to Warris, A..

5 recordsLinked to original sources

bioRxiv2026

A murine model to study chronic airway fungal colonisation that recapitulates human disease

Aspergillus fumigatus is a ubiquitous environmental mould and a leading cause of chronic fungal-associated respiratory disease, yet the mechanisms by which persistent airway colonisation drives immune adaptation and lung pathology remain poorly understood. Progress in this area has been limited by the lack of in vivo models that recapitulate stable, non-invasive fungal persistence without immunosuppression. Here, we developed and optimised a murine model of chronic airway colonisation using agar bead-embedded A. fumigatus conidia delivered intratracheally. Embedding did not impair fungal germination or hyphal growth, and the agar matrix was immunologically inert, supporting its use as a neutral scaffold. This approach established stable fungal persistence in the airways for at least three weeks in immunocompetent mice without inducing invasive disease or systemic morbidity. Colonisation elicited a transient, airway-restricted innate immune response characterised by early neutrophil and monocyte recruitment and increased CXCL1, MIP-1, MIP-1{beta}, and TNF production, which resolved over time. Histopathological analysis revealed a progressive sequence of disease-relevant features, including initial immune containment, followed by mucus hypersecretion, and airway remodelling. At the adaptive level, persistent colonisation induced a dynamic T cell response that transitioned from an early polyfunctional profile to a sustained Th17-dominant phenotype. Importantly, application of this model in CFTR-deficient mice uncovered enhanced collagen deposition and fibrotic remodelling without altered fungal burden, demonstrating its utility in modelling disease-relevant outcomes in susceptible hosts. Together, this study establishes a robust and physiologically relevant platform for investigating host-fungal interactions during chronic airway colonisation. This model provides new opportunities to dissect mechanisms of immune adaptation, fungal persistence, and tissue remodelling, and to identify therapeutic strategies targeting chronic Aspergillus-associated lung disease.

immunology↗

bioRxiv2025

Competition with Pseudomonas aeruginosa induces Staphylococcus aureus in an antibiotic-tolerant viable but non culturable state

Interactions between different species of pathogenic microbes often affect clinical outcome by altering the virulence or antibiotic resistance of individual microbes. By investigating the interactions between Staphylococcus aureus and Pseudomonas aeruginosa at the population, single-cell and molecular level we discovered that a sub-population of S. aureus enters in a viable non-culturable state that it is not detected via standard microbiology assays. In the presence of P. aeruginosa, S. aureus adopts a survival lifestyle similar to previously described intracellular S. aureus persisters, downregulating nitrogen metabolism and amino acid biosynthesis, while upregulating protein maturation processes. Entrance in a viable but non culturable state is the primary survival strategy of S. aureus in response to vancomycin treatment, whereas only a minority of the S. aureus population survive ciprofloxacin treatment while in a viable but non culturable state. These bacterial interactions may shape the evolution of resistance traits of co-infecting pathogens. Manipulating these interspecies adaptations could provide new opportunities for early therapeutic interventions.

microbiology↗

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↗

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↗

bioRxiv2018

Meropenem vs standard of care for treatment of neonatal late onset sepsis (NeoMero1): a randomised controlled trial

BackgroundThe early use of broad-spectrum antibiotics remains the cornerstone for the treatment of neonatal late onset sepsis (LOS). However, which antibiotics should be used is still debatable, as relevant studies were conducted more than 20 years ago, were single centre or country, insufficiently powered, evaluated antibiotics not in clinical use anymore and had variable inclusion/exclusion criteria and outcome measures. Moreover, antibiotic-resistant bacteria have become a major problem in many countries worldwide. We hypothesized that efficacy of meropenem as a broad spectrum antibiotic is superior to standard of care regimen (SOC) in empiric treatment of LOS and thus aimed to compare the efficacy and safety of meropenem to SOC in infants aged <90 days with LOS.\n\nMethods and findingsNeoMero-1 was a randomized, open-label, phase III superiority trial conducted in 18 neonatal units in 6 countries. Infants with post-menstrual age (PMA) of [≤]44 weeks with positive blood culture and one, or those with negative culture and at least with two predefined clinical and laboratory signs suggestive of LOS, or those with PMA >44 weeks meeting the Goldstein criteria of sepsis, were randomized in a 1:1 ratio to receive meropenem or SOC (ampicillin+gentamicin or cefotaxime+gentamicin) for 8-14 days. The primary outcome was treatment success (survival, no modification of allocated therapy, resolution/improvement of clinical and laboratory markers, no need of additional antibiotics and presumed/confirmed eradication of pathogens) at test-of-cure visit (TOC) in full analysis set. Stool samples were tested at baseline and day 28 for meropenem-resistant Gram-negative organisms (CRGNO).\n\nThe primary analysis was performed in all randomised patients (full analysis set) and in patients with culture confirmed LOS. Proportions of participants with successful outcome were compared by using a logistic regression model adjusted for the stratification factors.\n\nFrom September 3rd 2012 to November 30th 2014, in total 136 patients in each arm were randomized; 140 (52%) were culture positive. Success at TOC was achieved in 44/136 (32%) in the meropenem arm vs. 31/135 (23%) in the SOC arm (p=0.087); 17/63 (27%) vs. 10/77 (13%) in patients with positive cultures (p=0.022). The main reason of failure was modification of allocated therapy. Adverse events occurred in 72% and serious adverse events in 17% of patients, the mortality rate was 6% with no differences between study arms. Cumulative acquisition of CRGNO by day 28 occurred in 4% in the meropenem and 12% in the SOC arm (p=0.052).\n\nConclusionsMeropenem was not superior to SOC in terms of success at TOC, short term hearing disturbances, safety or mortality and did not outselect colonization with CRGNOs. Meropenem as broad-spectrum antibiotic should be reserved for neonates who are more likely to have Gram-negative LOS, especially in NICUs where microorganisms producing ESBL and AmpC beta-lactamases are circulating.

clinical trials↗