Biology subjects

Traven, A.

Publications and source records attributed to Traven, A..

5 recordsLinked to original sources

bioRxiv2026

Short chain fatty acids potentiate azoles by reprogramming fungal acetyl-CoA metabolism

Pathogens colonise metabolically diverse host environments. How metabolites found in host environments regulate antimicrobial drug susceptibility remains to be fully understood. Here we report on the roles of gut metabolites, short chain fatty acids (SCFAs), in antifungal drug susceptibility of the gut commensal and fungal pathogen Candida albicans. A genetic screen revealed that C. albicans mutants in peroxisome biogenesis display increased tolerance to the antifungal drug fluconazole. Peroxisomes are important for the metabolism of SCFAs by {beta}-oxidation, and exposure to the SCFAs butyrate and crotonate increased susceptibility and reduced tolerance to fluconazole. To understand if SCFAs inhibit fluconazole tolerance through their ability to inhibit histone deacetylases (HDACs), we compared them with the HDAC inhibitor trichostatin A. These experiments did not reveal an obvious connection between the degree of HDAC inhibition and the degree of fluconazole tolerance reduction. Exposure of C. albicans to crotonate and butyrate revealed transcriptional reprogramming involving remodelling of acetyl-CoA metabolism by upregulation of genes for {beta}-oxidation, peroxisome biogenesis and intracellular transport of acetyl-CoA, while the expression of ergosterol biosynthesis genes was reduced. Since ergosterol gene expression is required to overcome fluconazole stress, these results explain how SCFAs reduce fluconazole tolerance. Taken together, our results implicate peroxisome biogenesis and metabolism in fluconazole susceptibility. We posit that balanced acetyl-CoA metabolism promotes sufficient ergosterol biosynthesis to overcome fluconazole stress and drive tolerant growth. These pathways are perturbed by metabolic changes induced by SCFAs. These findings add to our understanding of the importance of metabolic regulation in antimicrobial drug responses. SIGNIFICANCEMetabolites produced by microbiota or host cells regulate microbial metabolism, physiology and drug responses. In the gut, the human commensal and pathogen Candida albicans is exposed to short-chain fatty acids made by bacteria. C. albicans metabolises short-chain fatty acids via peroxisomal {beta}-oxidation. Additionally, short-chain fatty acids change gene expression by inhibiting histone deacetylases. We found that short-chain fatty acids increase the susceptibility of C. albicans to the antifungal drug fluconazole and reduce fluconazole tolerance. Our mechanistic studies indicate that metabolic utilisation of short-chain fatty acids by C. albicans reduces fluconazole tolerance by changing acetyl-CoA metabolism and causing lower expression of ergosterol biosynthesis genes. Thus, short-chain fatty acids increase fluconazole susceptibility by changing fungal metabolism, while inhibition of histone deacetylases may play a more minor role. These findings shed light on the roles of metabolism and abundant gut metabolites in tolerance to a front-line antifungal drug.

microbiology↗

bioRxiv2026

Antifungal resistance mechanisms and nosocomial transmission of Nakaseomyces glabratus: genomic investigation and observational study in Melbourne, Australia

Nakaseomyces glabratus (Candida glabrata) is a WHO high-priority fungal pathogen associated with fungal antimicrobial resistance (fAMR). Given nosocomial transmission occurs sporadically, resistant strains could be transmitted, a concern for critically ill patients. We conducted a genomic investigation and retrospective observational study of N. glabratus to identify any nosocomial transmission of fAMR and understand resistance mechanisms and clinical and demiological factors among patients at a quaternary hospital in Melbourne, Australia. We selected stored N. glabratus with and without fAMR associated with similar patient clinical characteristics and performed whole genome sequencing. Clinical and epidemiological data were extracted from medical records. Phylogenetic, mutational, copy-number variation (CNV) and mitochondrial genomic analyses were performed, with a focus on the fAMR gene PDR1. Of 54 isolates collected over seven years, 20 (37%) were fluconazole-resistant and four (7%) had elevated flucytosine minimum inhibitory concentrations (MICs) (range 2-32 g/ml). There were no significant clinical differences between patients with and without fluconazole resistance. Most (55%) fluconazole-resistant isolates carried PDR1 mutations. Resistance was distributed throughout the phylogeny suggesting predominantly independent acquisition. However, a cluster of four resistant isolates with the same PDR1 mutation suggested nosocomial transmission. One probable ERG11 gene duplication, and two petite variants with apparent mitochondrial genomic deletions, were seen in association with fluconazole resistance. In this study, we identified a small probable nosocomial fAMR transmission cluster, and novel variants in PDR1, ERG11 and FCY2 associated with fAMR phenotypes. Future study should confirm functional impacts and systematically investigate for nosocomial transmission of resistance, including colonisation states.

microbiology↗

bioRxiv2025

Regulation of airway fumarate by host and pathogen promotes S. aureus pneumonia

Staphylococcus aureus is a leading cause of healthcare-associated pneumonia, contributing significantly to morbidity and mortality worldwide. As a ubiquitous colonizer of the upper respiratory tract, S. aureus must undergo substantial metabolic adaptation to achieve persistent infection in the distinctive microenvironment of the lung. We observed that fumC, which encodes the enzyme that converts fumarate to malate, is highly conserved with low mutation rates in S. aureus isolates from chronic lung infections. Fumarate, a pro-inflammatory metabolite produced by macrophages during infection, is regulated by the host fumarate hydratase (FH) to limit inflammation. Here, we demonstrate that fumarate, which accumulates in the chronically infected lung, is detrimental to S. aureus, blocking primary metabolic pathways such as glycolysis and oxidative phosphorylation (OXPHOS). This creates a metabolic bottleneck that drives staphylococcal FH (FumC) activity for airway adaptation. FumC not only degrades fumarate but also directs its utilization into critical pathways including the tricarboxylic acid (TCA) cycle, gluconeogenesis and hexosamine synthesis to maintain metabolic fitness and form a protective biofilm. Itaconate, another abundant immunometabolite in the infected airway enhances FumC activity, in synergy with fumarate. In a mouse model of pneumonia, a {Delta}fumC mutant displays significant attenuation compared to its parent and complemented strains, particularly in fumarate- and itaconate-replete conditions. Our findings underscore the pivotal role of immunometabolites in promoting S. aureus pulmonary adaptation.

microbiology↗

bioRxiv2024

A new model of endotracheal tube biofilm identifies combinations of matrix-degrading enzymes and antimicrobials able to eradicate biofilms of pathogens that cause ventilator-associated pneumonia

Defined as a pneumonia occurring after more than 48 hours of mechanical ventilation via an endotracheal tube, ventilator-associated pneumonia results from biofilm formation on the indwelling tube, seeding the patients lower airways with pathogenic microbes such as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Candida albicans. Currently there is a lack of accurate in vitro models of ventilator-associated pneumonia development. This greatly limits our understanding of how the in-host environment alters pathogen physiology and the efficacy of ventilator-associated pneumonia prevention or treatment strategies. Here, we showcase a reproducible model that simulates biofilm formation of these pathogens in a host-mimicking environment, and demonstrate that the biofilm matrix produced differs from that observed in standard laboratory growth medium. In our model, pathogens are grown on endotracheal tube segments in the presence of a novel synthetic ventilator airway mucus (SVAM) medium that simulates the in-host environment. Matrix-degrading enzymes and cryo-SEM were employed to characterise the system in terms of biofilm matrix composition and structure, as compared to standard laboratory growth medium. As seen in patients, the biofilms of ventilator-associated pneumonia pathogens in our model either required very high concentrations of antimicrobials for eradication, or could not be eradicated. However, combining matrix-degrading enzymes with antimicrobials greatly improved biofilm eradication of all pathogens. Our in vitro endotracheal tube (IVETT) model informs on fundamental microbiology in the ventilator-associated pneumonia context, and has broad applicability as a screening platform for antibiofilm measures including the use of matrix-degrading enzymes as antimicrobial adjuvants. ImportanceThe incidence of ventilator-associated pneumonia in mechanically ventilated patients is between 5-40%, increasing to 50-80% in patients suffering from coronavirus disease 2019 (COVID-19). The mortality rate of ventilator-associated pneumonia patients can reach 45%. Treatment of the endotracheal tube biofilms that cause ventilator-associated pneumonia is extremely challenging, with causative organisms able to persist in endotracheal tube biofilm despite appropriate antimicrobial treatment in 56% of ventilator-associated pneumonia patients. Flawed antimicrobial susceptibility testing often means that ventilator-associated pneumonia pathogens are insufficiently treated, resulting in patients experiencing ventilator-associated pneumonia recurrence. Here we present an in vitro endotracheal tube biofilm model that recapitulates key aspects of endotracheal tube biofilms, including dense biofilm growth and elevated antimicrobial tolerance. Thus our biofilm model can be used as a ventilated airway simulating environment, aiding the development of anti-ventilator-associated pneumonia therapies and antimicrobial endotracheal tubes that can one day improve the clinical outcomes of mechanically ventilated patients.

microbiology↗

bioRxiv2023

Candida auris evades innate immunity by using metabolic strategies to escape and kill macrophages while avoiding antimicrobial inflammation

Candida auris causes life-threatening, drug-resistant infections. In addition to drug resistance, therapeutic innovation is hindered by our limited knowledge of the mechanisms used by C. auris to evade immunity and establish infection. Here we show that C. auris escapes phagocytic containment and kills macrophages, and demonstrate that the mechanisms rely on metabolic regulation. We found that C. auris-infected macrophages undergo immunometabolic reprogramming and increase glycolysis but this does not lead to the expected antimicrobial responses, as macrophages fail to activate IL-1{beta} cytokine and curb C. auris growth. Further analysis showed that C. auris relies on its own metabolic capacity to egress from macrophages, cause macrophage metabolic stress and cell death, and establish infection in vivo. We identified a transcriptional regulator of C. auris metabolism and macrophage evasion, and further show that, contrary to several other pathogens, C. auris-induced macrophage metabolic dysfunction and death fail to activate the NLRP3 inflammasome. Consequently, inflammasome-dependent antimicrobial responses remain inhibited throughout infection. Our findings establish a pivotal role for metabolic regulation in enabling C. auris to eliminate macrophages while remaining immunologically silent to ensure its own survival.

microbiology↗