Journal of Fungi最新文献

There was an error in the original publication [...].

The early diagnosis of invasive candidiasis remains challenging in immunocompromised and other high-risk patients, prompting interest in artificial intelligence models for assisting clinical decision-making. We conducted a PROSPERO-registered systematic review and meta-analysis of artificial intelligence-based predictive models for the early identification of invasive Candida infections. We searched multiple databases for studies reporting model performance in hospitalized immuno-compromised patients. Data on study characteristics, model details, validation strategy, and diagnostic accuracy were extracted. A bivariate random-effects meta-analysis was performed for candidemia prediction models with compatible data. Eight studies met inclusion criteria. Models were typically developed using retrospective hospital data with heterogeneous populations and predictors. Five candidemia studies provided threshold-based performance data for meta-analysis. Pooled sensitivity and specificity for candidemia prediction were 81.3% (95% confidence interval (CI) 72.9-87.6%) and 81.6% (95% CI 68.4-90.1%), respectively. Most models achieved high negative predictive values, whereas positive predictive values were modest, reflecting low event prevalence. The risk of bias was generally moderate to high (PROBAST), and the certainty of evidence was low (GRADE) due to study limitations and indirectness. AI models show promise for early candidemia identification with moderate diagnostic accuracy. They may be useful as decision-support tools, but further multicenter prospective validation is needed before routine clinical adoption.

Molecular mechanisms determining pathogenicity of the Dutch elm disease fungus Ophiostoma novo-ulmi are poorly understood. Prior identification of the pathogenicity locus pat1 prompted a chromosome walking approach to elucidate gene function in this region. Among 17 identified genes, ONUg0282 (amtA) was predicted to encode a high-affinity ammonium transporter. In silico analyses confirmed the presence of four additional amt genes (amtB, amtC, amtD, and amtE) in both O. novo-ulmi and the less aggressive O. ulmi and that amtA and amtB belong to the Saccharomyces cerevisiae mep2 clade. The predicted amtA gene product showed features of Mep2-type transceptors, including amino acid residues corresponding to His-168 and His-318 in Escherichia coli AmtB protein, 11 transmembrane helices, and a conserved 22 amino acid motif immediately downstream of the last transmembrane helix. A knockdown amtA mutant with 25% residual expression was significantly less aggressive than wild-type O. novo-ulmi strain H327 when infecting Ulmus americana × U. parvifolia saplings. Predicted AmtA transporters from two CRISPR-Cas9 knockout mutants contained only five intact transmembrane helices. The ΔamtA mutants retained several wild-type phenotypic traits, including yeast-mycelium dimorphism, but were significantly less aggressive than H327 towards U. americana saplings. We concluded that ONUg0282 is an important determinant of aggressiveness in O. novo-ulmi.

Elsinoe fawcettii is a devastating citrus pathogen worldwide, yet high-quality genomic resources are lacking, limiting insights into its adaptive mechanisms. Seventeen strains collected from 13 host species across 5 Chinese provinces were confirmed as E. fawcettii by multi-loci (ITS, rpb2, tef1-α) phylogenetic and morphological analyses. A near-telomere-to-telomere (near-T2T) genome for representative strain FJ-Y-3 was constructed using integrated PacBio and Hi-C sequencing. The 24.40 Mb assembly was organized into 11 chromosomes with exceptional completeness (BUSCO: 97.1%) and continuity (scaffold N50: 2.18 Mb). Pan-genome analysis revealed a closed structure, with core genes representing 77.19% of the total, suggesting evolutionary adaptation through fine-regulation of conserved elements rather than extensive gene content variation. Accessory genes were significantly enriched in terpenoid/polyketide metabolism, cell surface remodeling, and xenobiotic degradation, underscoring metabolic plasticity. Whole-genome resequencing showed single-nucleotide polymorphisms as the dominant variant, with ~60% residing in regulatory regions, implicating cis-regulation as a key adaptive mechanism. This work provides a high-quality genome and multi-omics framework for E. fawcettii, establishing a crucial molecular foundation for understanding pathogen adaptation and developing sustainable disease management strategies.

Sclerotium formation represents a critical transition phase in the life cycle of morel, shifting from vegetative growth to dormant structures. The capacity for sclerotium formation directly influences the yield and stability of artificial cultivation. To elucidate the molecular regulatory mechanisms underlying this process, a combined transcriptomics and metabolomics approach was employed to analyze gene expression and metabolite dynamics during sclerotium development of Morchella eximia. A total of 2567 differentially expressed metabolites (DEMs) and 2314 differentially expressed genes (DEGs) were detected, primarily enriched in amino acid metabolism, lipid synthesis, and energy metabolism pathways. Amino acid metabolism facilitates protein synthesis and supplies carbon skeletons, while lipid metabolic networks, particularly de novo fatty acid synthesis from acetyl-CoA precursors, glycerophospholipid metabolism, sphingolipid metabolism, and unsaturated fatty acid biosynthesis, play a central role in sclerotium formation. A regulatory model was constructed, focusing on signal response, transcriptional regulation, nutrient transport and metabolism, morphology transition, lipid accumulation, and membrane system remodeling, demonstrating that lipids not only provide energy storage and membrane structural components for sclerotia but also mediate developmental transitions and environmental adaptation through signaling molecules and regulation of membrane properties. These findings systematically reveal the regulatory network governing morel sclerotium formation at the multi-omics level, with particular emphasis on the central role of lipid metabolism and membrane remodeling. The results offer a theoretical foundation for improving morel cultivation yield and stability through targeted metabolic regulation strategies.

Ophiocordyceps xuefengensis is an important medicinal fungus with considerable pharmaceutical and economic value. However, its industrial and scientific utilization has been severely limited by the lack of an efficient genetic transformation system, largely due to limited genomic information and wild growth. In this study, we established an efficient and stable plasmid transformation system within O. xuefengensis protoplasts mediated by PEG. To overcome low protoplast yield and transformation efficiency, key factors influencing protoplast preparation including enzyme composition and concentration, fungal age, and digestion conditions were systematically optimized. The optimal protocol involved digesting 4-day-old mycelia with a mixture of 1.5% lywallzyme 1 and 1.5% snailase at 34 °C and 130 rpm for 3.5 h, yielding at least 9.42 × 10⁷ CFU/mL protoplasts. Protoplast regeneration was significantly enhanced in PY medium supplemented with 0.6 M mannitol. Under these optimized conditions, a transformation efficiency of 45.5% was achieved, with stable plasmid integration confirmed over four successive generations. Furthermore, the transformation system was successfully applied to functional gene characterization by driving exogenous gene expression using the endogenous gpd1 promoter. This study provides a foundational platform for functional gene analysis and paves the way for further elucidation of growth and development mechanisms and metabolic engineering in O. xuefengensis.

Exogenous genes are generally expressed by integration into the chromosomes of Pichia pastoris. However, systematic studies on the chromosomal position effect are lacking, and locations that are conducive to the high expression of foreign genes are rarely reported. In this study, a genomic random insertion mutagenesis library for P. pastoris was successfully constructed using the piggyBac (PB) transposon system. Through sequencing, the sequence TTAA was identified as the major recognition site of the PB transposon, which exhibited relatively high coverage on P. pastoris chromosomes, making it a valuable tool for studying position effect variegation in P. pastoris. Using the enhanced green fluorescent protein gene (eGFP) as a reporter, two libraries including low-expression positions and high-expression positions were obtained by flow cytometry. The low-expression sites were mainly located upstream of ORFs around the promoter region and downstream near the terminator region, while the high-expression sites were predominantly located at the gene interior. KEGG and GO analyses showed that genes in high-expression positions were significantly enriched in the ATP-dependent chromatin remodeling and histone binding pathways, and genes in low-expression positions were significantly enriched in the MAPK signaling pathway, autophagy, mitochondrial autophagy, ABC transporters, and the arginine synthesis pathway. This study has clarified the genome-wide landscape of position effect variegation in P. pastoris. Additionally, it has provided novel insights into high-throughput screening strategies for strains with high exogenous gene expression.

The IMMY cryptococcal antigen (CrAg) lateral flow assay (LFA) is a reliable diagnostic tool for Cryptococcus detection, but false-positive results may arise from procedural or reagent-related errors, underscoring careful operation of the assay to ensure diagnostic accuracy and prevent unnecessary treatment. Two patients who were initially reported as CrAg-positive by a peripheral laboratory were referred to Kiruddu Hospital in Kampala, Uganda, for clinical assessment and confirmatory testing. Repeat tests were conducted using specimen diluent following the manufacturer's protocol, resulting in negative results. Semi-quantitative CrAg LFA testing and a series of control assays were performed to identify the source of error. We were able to consistently reproduce positive results when the titration diluent was inappropriately used instead of the specimen diluent. Serial dilutions confirmed persistent false positivity up to 1:80 when inappropriately using the titration diluent, while all dilutions that appropriately started with the specimen diluent remained negative. We hypothesize that the incorrect use of titration diluent instead of specimen diluent led to false-positive CrAg LFA results due to the absence of the blocking agent that neutralizes heterophilic antibodies. Procedural errors can lead to diagnostic misinterpretation and serious consequences in clinical management, emphasizing the importance of adherence to manufacturer's instructions.

Invasive fungal infections are frequent complications in patients with hematologic malignancies due to immunosuppression and intensive treatments. In Colombia, limited diagnostic availability, heterogeneous prescribing practices, and emerging antifungal resistance highlight the need for optimized use. We evaluated an interdisciplinary antifungal stewardship intervention in the hematology unit of a tertiary-care hospital. A quasi-experimental before-and-after study included 353 hospitalized patients receiving systemic antifungals between 1 January 2023 and 31 December 2024 (1154 prescriptions). Following the intervention, antifungal prescribing shifted toward increased prophylaxis and reduced therapeutic use, with substantial reduction in prophylactic Amphotericin B dosing, stable treatment dosing, and selective changes in agent choice, including decreased voriconazole and discontinuation of some broad-spectrum drugs. Microbiological sampling decreased, reflecting a more targeted diagnostic approach rather than improved documentation. Antifungal consumption patterns showed redistribution among agents rather than uniform reduction. Prophylaxis-related costs increased, while treatment-related costs decreased without statistical significance. ICU admissions and in-hospital mortality remained unchanged. These results demonstrate that structured antifungal stewardship programs are feasible and safe in hematology units in middle-income settings, supporting more rational antifungal use without compromising patient outcomes.

Candidozyma auris is an emerging multidrug-resistant yeast that readily contaminates healthcare environments, persisting on dry surfaces and enabling transmission and difficult-to-control outbreaks. A systematic review of environmental hygiene interventions targeting C. auris was conducted, focusing on efficacy against planktonic cells and surface-associated biofilms (including dry-surface biofilms, DSB where available). PubMed and Scopus were searched for English-language records published from 1 January 2017 to 30 September 2025, and study selection followed PRISMA 2020. Thirty-six studies from nine countries met the inclusion criteria. These were predominantly laboratory efficacy evaluations using carrier/suspension or quantitative surface methods reporting log₁₀ Colony Forming Unit (CFU) reductions; only seven studies assessed biofilm-associated C. auris. Across clades I-IV, chlorine-based disinfectants and oxidizing chemistries (hydrogen peroxide/peracetic acid formulations) most consistently achieved high-level reductions (often ≥ 5 log₁₀ CFU) under label-relevant conditions. In contrast, products containing only quaternary ammonium compounds (QACs) frequently underperformed and demonstrated greater variability. No-touch methods, particularly 254 nm ultraviolet-C light (UV-C), provided meaningful adjunctive reductions, but were highly dependent on dose delivery and geometry, and evidence for ozone-based approaches was mixed. Limited data on C. auris DSBs suggest planktonic testing may overestimate real-world conditions and underscore the importance of endpoints, such as transfer prevention and regrowth suppression.