Search Results (1,183)

Ascosphaera apis is a fungal pathogen of honeybee larvae and the primary cause of chalkbrood disease, which weakens bee colonies, impairing their ability to function effectively and making them more susceptible to other pathogens and environmental stressors. This study aimed to develop and validate an in-house matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral library for A. apis. A new MALDI-TOF MS library was constructed using reference Ascosphaera species and validated through whole-genome-based confirmation of 31 clinical isolates of A. apis. Three different protein extraction methods were tested and compared: liquid cultivation, formic acid–ethanol extraction and extended direct transfer. Our findings demonstrate that MALDI-TOF MS is a rapid and reliable tool for identifying A. apis under the tested laboratory conditions and within the analyzed strain set, with no misidentifications observed for the liquid cultivation and formic acid–ethanol extraction methods. The extended direct mycelium transfer method was slightly less effective but still showed a high sensitivity of 83.9%. This study provides a foundation for improving diagnostic approaches in the management of honeybee fungal diseases. Full article

The Xi’an Beilin Museum preserves a large collection of archeological photographic negatives and films dating from the 1950s to the early 1980s. These images document significant archeological discoveries, including Tang dynasty imperial tomb murals, the excavation of the terracotta warriors, and various historical grottoes and stone carvings. As unique visual records of cultural heritage, these materials provide valuable references for studying environmental deterioration processes and for guiding conservation and restoration practices. However, long-term storage under uncontrolled environmental conditions has resulted in severe degradation of the negatives, including mold contamination, emulsion layer powdering, deformation, and partial detachment. Among these deterioration phenomena, microbial growth is particularly destructive because fungal hyphae cause light scattering and image obscuration, preventing scanning and digital archiving. In this study, mold species present on the negatives were isolated and identified using morphological observation and ITS rDNA sequence analysis. Based on the characteristics of the microbial contamination, targeted removal and restoration treatments were applied to recover the original image information. Furthermore, preventive protection strategies were implemented through the development of antifungal storage materials and protective containers. The results establish an integrated conservation approach combining microbial identification, restoration treatment, risk elimination, and preventive protection, providing a scientific basis for the long-term preservation of historical photographic archives. Full article

This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris. Full article

Mating-type identification is fundamental to studies of genetic diversity and genetic breeding in fungi, especially for tetrapolar basidiomycetes, whose mating types are determined by two multiallelic loci, A and B. Traditional mating-type identification of monokaryons relies on manual inference based on hybridization experiments; however, this process is highly complex, time-consuming, and error-prone when applied to large-scale studies. In this study, we isolated 30 monokaryons from protoplasts derived from 15 dikaryons of Flammulina velutipes and developed a software tool, Mating-Type Imputation (MTI), to automatically, rapidly, and accurately infer monokaryon mating types in tetrapolar fungi using a combinatorial pruning traversal algorithm. Using a compatibility matrix derived from 435 hybridization experiments involving these 30 monokaryons, MTI required only a few minutes to accurately infer the mating types of all monokaryons-a task that typically takes several days for manual inference by experienced investigators. Furthermore, MTI enabled us to investigate how false-positive and false-negative interactions influence mating-type inference results. Using a simulated compatibility matrix, we found that MTI could accurately detect potential false negatives in compatibility and successfully infer the true mating-type combinations even in the presence of limited false negatives; conversely, the tool was easily misled by any false positives, resulting in incorrect mating-type combinations. This indicates that false-positive records in hybridization experiments must be strictly eliminated during mating-type inference. In summary, MTI provides an efficient tool for inferring the mating types of tetrapolar fungi, offering technical support for mating-type studies of edible and medicinal fungi, and holds significant theoretical value and broad application potential in the fields of fungal genetic diversity and breeding research. Full article

Alternaria brown spot, caused by the tangerine pathotype of Alternaria alternata, is a destructive fungal disease affecting citrus production worldwide. Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes constitute a major class of plant immune receptors; however, their genome-wide characteristics and potential association with Alternaria brown spot resistance loci in citrus remain poorly understood. In this study, we performed a comprehensive genome-wide identification and comparative analysis of NBS-LRR genes across representative citrus species. A total of 417 and 326 NBS-LRR genes were identified in Citrus reticulata and Citrus clementina, respectively, and were classified into NL, CNL, TNL, and RNL subfamilies based on domain architecture. Phylogenetic reconstruction, gene structure analysis, conserved motif composition, chromosomal distribution, synteny relationships, and promoter cis-element profiling collectively revealed considerable structural variation and lineage-specific expansion of the NBS-LRR gene family in citrus genomes. By integrating previously reported quantitative trait locus (QTL) data for Alternaria brown spot, we identified several NBS-LRR genes located within a resistance-associated genomic interval on chromosome 3. Among these, a candidate gene, designated LRR2, exhibited differential transcriptional responses upon pathogen inoculation and displayed distinct sequence variations between citrus genotypes. Structural modeling and molecular docking analyses suggested potential binding interfaces between LRR2 and multiple host-selective toxins, although the biological relevance of these interactions requires further experimental validation. Subcellular localization assays in Nicotiana benthamiana showed that LRR2 is distributed in both the nucleus and cytoplasm. Notably, transient overexpression of LRR2 triggered hypersensitive response-like cell death and H₂O₂ accumulation. Collectively, this study provides a comprehensive overview of the citrus NBS-LRR gene family and presents a multifaceted characterization of a QTL-anchored candidate gene. These findings establish a genomic and molecular framework for further functional investigations of citrus–Alternaria interactions. Full article

Basidiomycetes can colonize sweet chestnut (Castanea sativa Mill) xylem, causing white or brown rot and losses in wood quality. The aim of this study was to assess the degradative potential of five Basidiomycota strains (Armillaria mellea (Vahl) P. Kumm. (Am), Fistulina hepatica (Shaeff.) With. (Fh), and Laetiporus sulphureus (Bull.) Murrill (Ls), and two strains of Ganoderma resinaceum Boud.) on three chestnut woods differing in chemistry. The woods differed in nitrogen content (0.3%–1.0%), carbon/nitrogen (C/N) ratio (43–150), and phenolic-related traits. In a 39-day laboratory assay, the five fungal strains were inoculated on three chestnut woods and compared for colonization time, extracellular enzymatic activity, and C mineralization. Fungal colonization strongly depended on fungus × wood interaction: L. sulphureus colonized all woods within 6 days, whereas the two G. resinaceum strains required 9–33 days depending on wood type; A. mellea and F. hepatica colonized only selected woods (up to 39 days). Enzymatic screening indicated laccase activity mainly in G. resinaceum (and to a lesser extent A. mellea), while L. sulphureus expressed cellulolytic activity but no laccase. Over 39 days, total C mineralization peaked under G. resinaceum on the two Sicilian woods (up to 270–300 mg CO₂–C g⁻¹ dry wood), whereas the Tuscan wood (highest C/N and phenolic content) markedly inhibited most strains; only L. sulphureus increased mineralization in this wood (85 mg CO₂–C g⁻¹ dry wood). These findings indicate that wood chemistry, especially C/N ratio and phenolic traits, strongly modulates strain-specific decay patterns. Overall, these results highlight the need for an integrated biological–biochemical approach to evaluate fungal decay potential and to inform both the selection of more durable chestnut woods for wood products and the identification of efficient strains to accelerate lignocellulosic biomass composting. Full article

Background/Objectives: Urine samples are the most frequently analyzed specimens in clinical microbiology laboratories. Although urine culture remains the gold standard for diagnosing urinary tract infections, it is time-consuming and resource-intensive. Therefore, reliable screening methods capable of predicting urine culture positivity are needed to optimize laboratory workflow. Automated urine analysis based on flow cytometry enables efficient screening and identification of samples with a low probability of bacterial infection, thereby rationalizing microbiological testing. This study evaluated the usefulness of a multivariable approach to support interpretation of flow cytometry results following the implementation of the Sysmex UF-4000 urine flow cytometer. Methods: Routinely collected urine samples from outpatients and hospitalized patients were analyzed using the UF-4000 flow cytometer, with a positivity threshold of ≥100 leukocytes/µL. Urinary parameters were compared between samples with positive and negative cultures. Multivariable logistic regression was applied to identify independent predictors of a positive urine culture. Urinary sediment parameters, including leukocyte, bacterial, fungal, and squamous epithelial cell counts, were assessed as covariates. Results: Urine samples with positive cultures showed significantly higher leukocyte counts (median 355.0, IQR 146.5–1429.4) and bacterial counts (median 9805.2, IQR 1134.3–45,011.5). Fungal and squamous epithelial cell counts differed only slightly between groups, although the differences were statistically significant (p < 0.001). Leukocyte counts were higher in urine samples from which Gram-negative bacteria were isolated compared with samples containing Gram-positive bacterial isolates (p < 0.001). The multivariable model demonstrated the most favorable overall performance, combining high sensitivity with improved specificity and the highest negative predictive value (AUC = 0.927). Optimal cut-off values were 70 leukocytes/µL and 105 bacteria/µL. Conclusions: Leukocyte and bacterial counts were the strongest predictors of positive urine culture results. A multivariable model including only these two parameters demonstrated high diagnostic accuracy and may serve as a practical screening tool to identify urine samples with a low probability of bacterial infection. The implementation of this approach could support more efficient use of urine cultures and help optimize laboratory workflow. Full article

Invasive candidiasis (IC) remains a significant cause of morbidity and mortality among critically ill, hematologic, and neonatal patients worldwide. Rapid and accurate diagnosis is essential to guide timely antifungal therapy and improve outcomes. Among available diagnostic tools, 1,3-β-D-glucan (BDG), a polysaccharide component of the fungal cell wall, has emerged as a key biomarker. BDG assays allow for early detection of probable IC, often preceding positive blood cultures, and offer prognostic information based on serial measurements. Species-specific differences in Candida cell wall composition influence BDG release and diagnostic sensitivity. Candida albicans generally correlates with high BDG levels, whereas Nakaseomyces glabrata, Candida parapsilosis, and Candida auris exhibit variable or lower glucan exposure, limiting assay sensitivity. BDG performance is affected by patient-specific factors, such as prior surgery, transfusions, or coexisting bacterial infections, which may lead to false-positive results. Molecular techniques, including PCR-based assays, provide complementary diagnostic accuracy and species identification, and their combination with BDG testing enhances sensitivity up to 90%. Serial BDG monitoring supports risk stratification and treatment response assessment, with persistent elevations predicting worse outcomes. In neonatal and pediatric populations, optimal cut-off values remain under investigation, highlighting the need for integration with clinical and microbiological data. Overall, BDG represents a valuable adjunct in a multimodal diagnostic workflow, providing both diagnostic and prognostic insights in invasive candidiasis management. Full article

Background/Objectives: Antimicrobial resistance (AMR) in companion animals is an emerging public health threat due to zoonotic potential and limited therapeutic options. Dogs with otitis externa may harbor multidrug-resistant (MDR) bacteria, including Escherichia coli (E. coli), Proteus mirabilis (P. mirabilis), and Enterobacter cloacae complex (E. cloacae complex), some producing extended-spectrum beta-lactamase (ESBL) or AmpC β-lactamases. This study aimed to assess the prevalence, AMR patterns, MDR occurrence, β-lactamase production, and co-infection profiles of these pathogens in canine otitis externa. Methods: Ear canal samples were collected from 592 dogs presenting clinical signs of otitis externa, with one sample per dog included in the analysis. Samples were collected from veterinary clinics in Timiș County, Romania, from 2022 to 2025. Samples were cultured on blood agar and MacConkey agar, followed by biochemical testing and MALDI-TOF mass spectrometry for bacterial identification. Antimicrobial susceptibility testing against 15 agents across six classes was performed using the VITEK^® 2 system. MDR and β-lactamase production (ESBL, AmpC) were determined according to CLSI 2018 veterinary guidelines. Co-isolation with bacterial and fungal species were recorded. Results: E. coli, P. mirabilis, and E. cloacae complex were isolated in 9.12%, 6.25%, and 1.2% of cases, respectively. E. coli exhibited the highest resistance to aminoglycosides (tobramycin 72.2%, gentamicin 61.1%) and full susceptibility to carbapenems. P. mirabilis showed the highest resistance to ampicillin (54%) and trimethoprim + sulfamethoxazole (46%), with complete susceptibility to carbapenems and fluoroquinolones. E. cloacae complex displayed universal resistance to cephalosporins but remained susceptible to non-cephalosporin β-lactams (piperacillin–tazobactam), carbapenems and aminoglycosides. MDR prevalence was 35.2% for E. coli, 18.9% for P. mirabilis, and 14.3% for the E. cloacae complex. ESBL production was detected in 13% of E. coli and 8.1% of P. mirabilis isolates, while all E. cloacae complex isolates were AmpC-positive. Co-isolations were common, primarily involving Staphylococcus pseudintermedius (S. pseudintermedius) and Malassezia pachydermatis (M. pachydermatis). Conclusions: MDR and β-lactamase-producing bacteria were identified in dogs with otitis externa, emphasizing the importance of routine antimicrobial susceptibility testing, targeted therapy based on local resistance profiles, and continuous AMR surveillance to prevent treatment failure and mitigate zoonotic risk. Full article

Canker and dieback diseases caused by fungal pathogens represent an increasing threat to woody plants in both urban and forest environments, where sustainable management options are urgently needed. In this study, the biocontrol potential of Bacillus strain N1 was investigated against Neofusicoccum parvum and Gnomoniopsis smithogilvyi, causal agents of canker diseases on Eucalyptus globulus and Castanea sativa, respectively. The whole-genome sequence confirmed the taxonomic identification of strain N1 as B. velezensis, showing high average nucleotide identity and digital DNA–DNA hybridization values with reference strains. AntiSMASH analysis revealed the presence of multiple biosynthetic gene clusters associated with the production of antimicrobial secondary metabolites, including polyketides, non-ribosomal peptides, and lipopeptides, reflecting strain N1’s genomic potential to produce compounds that may contribute to its antifungal activity. Moreover, B. velezensis strain N1 significantly inhibited the growth of N. parvum and G. smithogilvyi and showed a biocontrol efficacy on detached eucalyptus and chestnut shoots. In both preventive and curative treatments and pathosystems, the application of B. velezensis N1 resulted in a significant reduction in the length of necrotic lesions, compared to pathogen-only controls, while no phytotoxic effects were observed on treated shoots. Overall, this study supported B. velezensis N1 as a promising candidate for the sustainable control of canker-associated pathogens in woody plants. Full article

Healthy and asymptomatic cats may serve as reservoirs of fungal pathogens, facilitating transmission through direct contact or environmental contamination, and they may represent an underrecognized source of subclinical fungal infection in humans, particularly among cat owners and veterinarians. We evaluated the prevalence of fungal species in healthy cats and their owners, assessed potential cat–human transmission, identified feline lifestyle factors associated with Microsporum canis carriage, and evaluated antifungal susceptibility of the most prevalent isolated fungi. We collected 59 cat facial hair and 59 owner nail samples for fungal isolation and identification. Five fungal species were identified, M. canis, Aspergillus flavus, A. niger, A. fumigatus, and A. terreus, which were found in both cats and humans. Aspergillus spp. were the most frequently detected fungi in both groups. Significant associations between cats and owners were observed for M. canis (p = 0.010) and A. niger (p = 0.050). Long-haired cats showed a significantly higher prevalence of carrying M. canis (p = 0.024), while other lifestyle factors were not associated with fungal carriage. The antifungal susceptibility profiles of the tested fungi were broadly similar between feline and human isolates; however, resistance to itraconazole and amphotericin B was detected among Aspergillus spp. Healthy cats and their owners frequently share fungal species, especially M. canis, which suggests possible household zoonotic transmission. Long-haired cats are at higher risk of M. canis carriage. Full article

Iron Age settlements in the Salento peninsula (Southern Italy, 8th–6th century BC) underwent fundamental transformations in social organization, marked by the emergence of local elites through trade development and intense contacts with the Greek world. This study examines organic residue assemblages from 99 ceramic sherds from one key Iron Age site to clarify the role of locally produced ceramics—both coarse ware containers and Japigian matt-painted vessels—in commensal and beverage production practices. Chromatographic analyses identified a wide variety of animal and plant by-products, including fats, oils, waxes, and resin compounds. Integrated phytolith and starch analysis revealed evidence consistent with fermentation processes, particularly through the identification of fungal remains and damaged starch granules suggesting brewing activities in a subset of vessels. Matt-painted pottery forms—characterized by conical rims, funnel-shaped necks, bowls, and jugs—show distinctive use-alteration patterns and residue profiles associated with fermented beverage consumption and preparation in approximately 26% of the analyzed assemblage. Integrating organic residue analysis, experimental archaeology, and microfossil investigation suggests the central role of locally produced pottery in Iron Age commensal activities and status display, though alternative interpretations for some biomarker profiles cannot be excluded. This multiproxy approach demonstrates functional differentiation and consumption practices, refining interpretations of vessel use and providing new insights into food economies and social life during the Iron Age in southern Italy. Full article

Early-stage fungal contamination in maize kernels is difficult to identify visually and it can cause severe quality and safety risks during storage and transportation. Short-wave infrared (SWIR) hyperspectral imaging offers a rapid, non-destructive approach by capturing chemical information related to water, proteins, and lipids. This study investigates the early detection and classification of Gibberella zeae contamination in maize kernels using SWIR hyperspectral imaging combined with machine learning. Two maize varieties were artificially inoculated and cultured under controlled conditions, followed by hyperspectral data collection over six contamination stages. Various preprocessing techniques including standard normal variate (SNV), second derivative (SD), multiplicative scatter correction (MSC), and derivatives were evaluated to enhance data quality. Feature wavelength selection was performed using successive projections algorithm (SPA), competitive adaptive reweighted sampling (CARS), and uninformative variable elimination (UVE), significantly reducing redundancy and improving classification performance. Multiple models, including linear discriminant analysis (LDA), multilayer perceptron (MLP), support vector machine (SVM), a convolutional neural network (CNN), long short-term memory (LSTM) network, and a hybrid architecture Transformer that integrated a CNN, a LSTM network, and a Transformer (abbreviated as CLT), were constructed for both binary (healthy vs. contaminated) and multiclass classification tasks. Specifically, the multiclass task consisted of six contamination stages corresponding to contamination time from Day 0 to Day 5. The best binary classification task accuracy of 100% was achieved using SNV-preprocessed data with the MLP model. For multiclass classification task, the SD-preprocessed LDA model reached a test accuracy of 92.56%. Combined with appropriate preprocessing, feature selection and modeling, these results demonstrate that hyperspectral imaging is a powerful tool for the non-destructive, early-stage identification of fungal contamination in maize kernels, offering strong support for food safety and quality monitoring. Full article

The genera Pestalotiopsis, Neopestalotiopsis, and Pseudopestalotiopsis share highly similar morphological characteristics. Although species within these genera are recognized as plant pathogens, their pathogenicity can differ even on the same host plant, highlighting the importance of accurate genus-level identification for effective disease management. However, reliable discrimination among these genera based solely on morphology or internal transcribed spacer (ITS) amplicon length is difficult. Therefore, molecular approaches based on ITS sequence data are required for practical and reliable genus-level identification. This study aimed to develop genus-specific PCR primers through comparative genome analysis using genus-specific gene regions identified from available genomic data. The performance of these primers was evaluated using 49 isolates obtained from banana, Japanese andromeda, loquat, rubber, and tea. The primer sets achieved an overall identification accuracy of 97%. One strain could not be assigned to Pestalotiopsis, which exhibited morphological characteristics inconsistent with the genus and was positioned outside the main Pestalotiopsis clade in phylogenetic analyses, supporting the taxonomic validity of the primer-based identification. These results demonstrate that the developed primers provide a reliable and practical tool for genus-level identification and taxonomic assignment of these morphologically similar fungal pathogens, including direct detection from infected plant tissues. Full article

Well established long ago for bacterial and fungal detection, Matrix-Assisted Laser Desorption/Ionization–Time of Flight (MALDI-TOF) technique is not so well established in the virology field, and taking care of its advantages (speed, precision and low cost), this can be a powerful method for viral identification. To explore the feasibility and potential of MALDI-TOF for viral detection, this study shows the development of an in-house spectral library including several uninfected cell cultures and cultures infected with different clinically relevant viruses, such as SARS-CoV-2. This library was applied to the identification of viral infections directly on cell cultures, assessing the ability of the technique to discriminate between infected and non-infected profiles. Additionally, bioinformatic analyses were conducted to evaluate the structure, specificity, and reproducibility of the in-house library, and to understand its strengths and limitations. Sensitivity and specificity of the method were estimated by testing multiple culture batches from selected viruses included in the library. Together, these results provide a deeper understanding of the performance and applicability of MALDI-TOF in the virological context, highlighting its potential as a valuable research platform and a prospective tool for clinical viral detection. Full article