Search Results (875)

Phytopathogenic viruses severely impact major crops, leading to significant social and economic losses. Among them, begomoviruses pose a serious threat to key cultivars in subtropical and tropical regions despite ongoing efforts to limit their spread. Early detection of these pathogens in field crops and associated weeds is essential for the timely implementation of management strategies to mitigate viral disease outbreaks. In this study, we applied a sensitive loop-mediated isothermal amplification (LAMP) assay for the detection of tomato yellow leaf curl virus (TYLCV), tomato latent virus (TLV), and tomato mottle Taino virus (ToMoTV) in agro-inoculated Nicotiana benthamiana and Solanum lycopersicum. Importantly, LAMP assays also enabled the identification of these viruses in both symptomatic and asymptomatic field-grown tomato plants, detecting a higher number of infected plants than dot blot hybridization and PCR. Field surveys further revealed mixed infections of TYLCV, TLV, and ToMoTV within individual tomato plants, uncovering a complex epidemiological scenario. Full article

Background: Erysipelothrix rhusiopathiae is an important zoonotic pathogen in poultry, yet little is known about its antimicrobial resistance (AMR) dynamics in avian hosts. With growing concerns about subtherapeutic antimicrobial use in animal agriculture, poultry-origin isolates represent a potential but under-characterized reservoir of resistance genes. Methods: We phenotypically tested 38 E. rhusiopathiae strains isolated from geese, ducks, and turkeys in Hungary (2024) using broth microdilution against 18 antimicrobial agents, following Clinical Laboratory Standards Institute (CLSI) guidelines. Nineteen phenotypically resistant strains were selected for whole-genome sequencing (Illumina platform), followed by de novo hybrid assembly, gene annotation (Prokka, CARD, VFDB), mobile element detection (Mobile Element Finder), and phylogenetic inference (autoMLST). Results: All isolates were susceptible to β-lactams, including penicillin, amoxicillin, and third-generation cephalosporins. Resistance to tetracyclines (up to 10.5%) and florfenicol (5.3%) was most frequently detected. Genomic analysis revealed the presence of tetM (9/19), tetT (2/19), and erm(47) (2/19) genes, all associated with chromosomally integrated mobile elements, ICE Tn6009 and IS ISErh6. Phylogenomic analysis demonstrated tight clustering into four clades, suggesting clonal expansion. Notably, one strain harbored a 64.8 kb genomic island carrying ermC, the first such finding in poultry-derived E. rhusiopathiae. Conclusions: Our data highlights the early emergence of mobile AMR determinants in E. rhusiopathiae from poultry and suggests that horizontal gene transfer may drive resistance even in chromosomally encoded contexts. The genomic stability and phylogenetic homogeneity of avian isolates underscore the need for targeted AMR surveillance in poultry sectors to mitigate potential zoonotic transmission risks. Full article

Streptococcus dysgalactiae subsp. equisimilis (SDSE) has historically been recognized as a human pathogen, yet β-hemolytic streptococci consistent with SDSE have been documented in pigs for nearly a century. To investigate the population structure of porcine SDSE and the phylogenetic relationships between swine and human strains, we characterized 41 isolates recovered from diseased pigs in Quebec, Canada (2019–2022). Infected animals spanned all major production stages and frequently presented with invasive disease, including arthritis, endocarditis, and sudden death. Core-genome phylogenetics resolved two heterogeneous porcine clades separated by long internal branches and clearly distinct from dominant human SDSE lineages. Most porcine isolates were emm-negative or contained structurally altered emm regions compared with human strains. Analysis of Lancefield antigen loci identified a predominant group C lineage and a minority group L lineage, recapitulating historical serogroup distributions described since the early-20th century. Phenotypic testing showed susceptibility to β-lactams and florfenicol but high levels of resistance to tetracycline, macrolides and lincosamides. Detected antimicrobial resistance (AMR) genes correlated well with phenotypes, and multidrug resistance was frequent. Hybrid genome assemblies revealed integrative and mobilizable elements carrying AMR determinants. Collectively, our data indicate that porcine SDSE represents a long-standing, genetically structured, host-adapted population with notable AMR potential, underscoring the need for continued swine SDSE genomic surveillance. Full article

A new iodine–dextrin–lithium complex (IDLC) was synthesized and structurally characterized as a hybrid supramolecular system combining antiseptic, stabilizing, and biocompatible components. The compound integrates iodine as the primary antimicrobial agent, lithium as a coordination and stabilization element, and dextrin as a biodegradable polysaccharide matrix enabling sustained release. Physicochemical analyses confirmed the formation of a uniform, thermally stable complex. Biological evaluation revealed strong bactericidal activity, with minimum bactericidal concentrations (MBCs) ranging from 1.95 to 15.63 µg mL⁻¹ against both Gram-positive and Gram-negative pathogens, including multidrug-resistant Staphylococcus aureus and Acinetobacter baumannii. Cytotoxicity studies revealed moderate, concentration-dependent effects on human peripheral blood mononuclear cells (CC₅₀ = 0.23–0.48 mg/mL; 11.7–24.4 μg I/mL) and low toxicity toward MDCK cells (CC₅₀ = 10–20 mg/mL; 507–1014 μg I/mL), confirming a favorable safety profile. IDLC exhibited cytotoxic effects on tumor cell lines (HepG2, HeLa, AGS, K562, and H9) as well as on the normal MeT-5A cell line; however, the CC₅₀ values are similar, and selectivity indices are close to 1, indicating no selective cytotoxicity toward tumor cells. Thus, IDLC demonstrates non-specific cytotoxicity at high concentrations, consistent with its iodine content. The research confirms that iodine can be effectively stabilized within a dextrin-lithium framework to yield a biologically active, thermally resistant complex, suitable for pharmaceutical use. Full article

Most land plants engage in a mutualistic interaction with arbuscular mycorrhizal fungi (AMF), for which Rhizophagus irregularis is a model species. Like plant pathogenic fungi, AMF genomes encode hundreds of putative effector proteins. However, for only a few, the molecular mechanisms by which they alter the host’s physiology are known. Here, we combined several reverse genetic approaches to unravel the role of the RIRG190 effector protein in arbuscular mycorrhiza (AM) symbiosis. Using multiple heterologous tools, evidence is provided that the RIRG190 effector is secreted and localizes to the plant nucleus. Moreover, by means of yeast two-hybrid (Y2H) and ratiometric bimolecular fluorescence complementation (rBIFC) assays, the data demonstrate that RIRG190 interacts with the protein Something About Silencing (SAS10), known to be involved in rRNA biogenesis in the nucleolus of cortical cells. Our findings suggest that rRNA biogenesis is a key process modulated by AMF, potentially to enhance plant metabolic activity, facilitating cell cycle progression, and to support the establishment of the symbiosis. Full article

Probe-based capture represents a highly sensitive and cost-effective approach for overcoming host background and enriching viruses in metagenomic NGS (mNGS) libraries. Using clinical specimens collected globally from patients with fever or respiratory illness, we generated mNGS libraries by random priming and Nextera XT tagmentation, followed by target enrichment (teNGS) with Comprehensive Viral Research Panel (CVRP) probes. Capture pool sizes and total reads were optimized, and libraries were initially sequenced separately. Using only 3–4% of reads required for standard mNGS, teNGS achieved increased sensitivity, 100–10,000× increases in depth, and >50% genome coverage for pathogens with titers ≥ 1000 cp/mL. Application to >2000 clinical specimens from various matrices and to contrived samples containing viruses absent from the CVRP probe set enabled detection of diverse viral families and established a minimum 65% nucleotide identity for hybridization, respectively. To save time and resources, teNGS and mNGS libraries were then combined into one sequencing run: teamNGS. In addition to streamlining the workflow, teamNGS also improved genome recovery. Coupling methods maintain the sensitivity and coverage for viruses achieved by enrichment alone while also ensuring comprehensive recovery of non-viral microbes. teamNGS has the potential to improve patient management and lower the rates of unnecessary testing and antibiotic use. Full article

Antimicrobial resistance (AMR) has become a major health crisis worldwide, and it is expected to surpass cancer as one of the leading causes of death by 2050. Conventional antibiotics are struggling to keep pace with the rapidly evolving resistance trends, underscoring the urgent need for novel antimicrobial therapeutic strategies. Antimicrobial peptides (AMPs) function through diverse, often membrane-disrupting mechanisms that can address the latest challenges to resistance. However, the identification, prediction, and optimization of novel AMPs can be impeded by several issues, including extensive sequence spaces, context-dependent activity, and the higher costs associated with wet laboratory screenings. Recent developments in artificial intelligence (AI) have enabled large-scale mining of genomes, metagenomes, and quantitative species-resolved activity prediction, i.e., MIC, and de novo AMPs designed with integrated stability and toxicity filters. The current review has synthesized and highlighted progress across different discriminative models, such as classical machine learning and deep learning models and transformer embeddings, alongside graphs and geometric encoders, structure-guided and multi-modal hybrid learning approaches, closed-loop generative methods, and large language models (LLMs) predicted frameworks. This review compares models’ benchmark performances, highlighting AI-predicted novel hybrid approaches for designing AMPs, validated by in vitro and in vivo methods against clinical and resistant pathogens to increase overall experimental hit rates. Based on observations, multimodal paradigm strategies are proposed, focusing on identification, prediction, and characterization, followed by design frameworks, linking active-learning lab cycles, mechanistic interpretability, curated data resources, and uncertainty estimation. Therefore, for reproducible benchmarks and interoperable data, collaborative computational and wet lab experimental validations must be required to accelerate AI-driven novel AMP discovery to combat multidrug-resistant Gram-negative pathogens. Full article

ESKAPE bacteria are a major global threat due to their rapid antibiotic resistance acquisition and severe healthcare-associated infections. Effective countermeasures require epidemiological surveillance and resistance transmission studies, particularly for antimicrobial-resistant (AMR) colonization in intensive care unit (ICU) patients. Whole-genome sequencing (WGS) provides critical information on resistance spread and mechanisms. In the provided protocol, rectal and oropharyngeal swabs, or endotracheal aspirate/bronchoalveolar lavage for intubated patients, are collected at ICU admission and twice weekly. Patient interviews and medical records identify risk factors for resistant microflora. Samples undergo cultivation, species identification, antibiotic susceptibility testing, and DNA extraction. Sequencing is performed using second- and third-generation platforms, with selected isolates subject to hybrid genome assembly. Resistance genes, virulence factors, and typing profiles (MLST, cgMLST) are determined. This protocol characterizes the ICU patient colonization by AMR pathogens, including species distribution, phenotypic and genotypic resistance profiles, clonal structure, and temporal changes. It estimates detection frequency and colonization patterns at each locus, identifies key risk factors, including prior community or inter-facility exposure, and analyzes associations between risk factors and admission colonization. The study aims to estimate AMR infection risk and severity in ICU patients through the comprehensive analysis of colonization dynamics, resistance patterns, and clonal characteristics using WGS data on pathogen composition and AMR trends. Full article

Grape (Vitis vinifera spp.) accessions exhibit rich diversity, and understanding their genetic variation and evolutionary relationships is crucial for cultivar selection and utilization. A highly representative SNP marker set was developed in this study based on re-sequencing data analysis, to clarify the phylogenetic relationships among 96 grape accessions and to evaluate the genetic resolution of core markers. Using PN40024 as the reference genome, high-quality SNP loci were screened from resequencing data of the 96 accessions. A phylogenetic tree was constructed, and genetic diversity was analyzed using PCA and population structure analysis. The results showed that the 96 accessions were mainly divided into four groups: European (‘Merlot’, ‘Chardonnay’), American (‘Beta’, ‘Concord’), Euro-American hybrids (‘Vidal’, ‘Miguang’), and wild populations along with their hybrid progeny (‘Zuoyouhong’, ‘Huajia 8’). PCA and ADMIXTURE validated population differentiation, revealing clear separation between wild and cultivated accessions. Through screening of core SNP markers, 384,304 candidate SNPs suitable for probe design were identified. Further refinement yielded 2000 and 10,000 SNP markers. Detailed analysis of core marker characteristics showed that their minor allele frequency (MAF) was predominantly between 0.1 and 0.3, with the majority distributed in CDS (38.65%), intronic (30.2%), and intergenic regions. The most common mutation types were [A/G] (35%) and [C/T] (34%) transitions. The 2000 core SNPs were associated with 1220 functional genes and were significantly enriched in pathways such as protein binding, RNA transport, and plant–pathogen interaction. These findings provide an efficient tool for grape genetic diversity analysis, cultivar identification, and molecular breeding, laying the groundwork for the precise utilization of grape germplasm resources. Full article

Rare-earth oxide (REO) nanoparticles (NPs)—such as cerium (CeO₂), samarium (Sm₂O₃), neodymium (Nd₂O₃), terbium (Tb₄O₇), and praseodymium (Pr₂O₃)—have demonstrated strong antimicrobial activity against multidrug-resistant bacteria. Their effectiveness is attributed to unique physicochemical properties, including oxygen vacancies and redox cycling, which facilitate the generation of reactive oxygen species (ROS) that damage microbial membranes and biomolecules. Additionally, electrostatic interactions with microbial surfaces and sustained ion release contribute to membrane disruption and long-term antimicrobial effects. REOs also inhibit bacterial enzymes, DNA, and protein synthesis, providing broad-spectrum activity against Gram-positive, Gram-negative, and fungal pathogens. However, dose-dependent cytotoxicity to mammalian cells—primarily due to excessive ROS generation—and nanoparticle aggregation in biological media remain challenges. Surface functionalization with polymers, peptides, or metal dopants (e.g., Ag, Zn, and Cu) can mitigate cytotoxicity and enhance selectivity. Scalable and sustainable synthesis remains a challenge due to high synthesis costs and scalability issues in industrial production. Green and biogenic routes using plant or microbial extracts can produce REOs at lower cost and with improved safety. Advanced continuous flow and microwave-assisted synthesis offer improved particle uniformity and production yields. Biomedical applications include antimicrobial coatings, wound dressings, and hybrid nanozyme systems for oxidative disinfection. However, comprehensive and intensive toxicological evaluations, along with regulatory frameworks, are required before clinical deployment. Full article

Enterococcus alishanensis JNUCC 77 (=BLH10) was isolated from the flowers of Zinnia elegans collected at Ilchul Land, Jeju Island, Republic of Korea. Whole-genome sequencing was conducted to clarify its taxonomic position, genomic composition, and adaptive metabolic potential. The assembled genome comprised five contigs totaling 3.86 Mb, with a G + C content of 35.6% and 100% completeness. Genome-based phylogenomic analyses using the Type Strain Genome Server (TYGS) and digital DNA–DNA hybridization (dDDH) confirmed that strain JNUCC 77 belongs to E. alishanensis. Functional annotation revealed enrichment of genes related to transcriptional regulation, carbohydrate metabolism, replication, and DNA repair, suggesting a lifestyle adapted to oxidative and UV-exposed floral habitats rather than pathogenic competitiveness. Genome mining with antiSMASH identified two putative biosynthetic regions associated with terpenoid and isoprenoid metabolism, which are commonly linked to redox regulation and cellular protection. These genomic features indicate that E. alishanensis JNUCC 77 has evolved a metal-assisted, redox-regulated survival strategy suitable for floral microenvironments. Given its origin from vibrant flowers and its genomic potential for redox-protective metabolism, this strain represents an attractive microbial resource for future development of nature-inspired postbiotic and cosmeceutical ingredients that align with the clean and eco-friendly image of flower-derived biotechnologies. Full article

The agro-industrial sector in Indonesia produces significant amounts of nutrient-rich waste and wastewater, which pose environmental risks but also present opportunities for valorization within a circular bioeconomy. Microalgae provide a promising solution for transforming these wastewaters into valuable products such as biomass for bioenergy, biofertilizers, or pigments, all while helping to remediate pollutants. This review synthesizes current knowledge on the use of major Indonesian agro-industrial effluents, specifically palm oil mill effluent (POME), byproducts from cassava and sugarcane, and soybean residues, as substrates for microalgal biomass production and cultivation. Furthermore, various cultivation strategies are summarized, including autotrophic, heterotrophic, and mixotrophic methods, as well as the use of open ponds, photobioreactors, and hybrid systems. These cultivation processes influence biomass yield, metabolite production, and nutrient removal. Reported studies indicate high removal efficiencies for organic loads, nitrogen, and phosphorus, along with considerable production of lipids, proteins, pigments, and biofuels. Yet, effluent pretreatment, concerns about heavy metal and pathogen contamination, high downstream processing costs, and biosafety issues remains as challenges. Nonetheless, the application of microalgal cultivation into Indonesia’s agro-industrial wastes treatment can provide the dual benefits of waste mitigation and resource recovery, helping to advance climate goals and promote rural development. Full article

Foot rot, a disease caused by the fungal plant pathogen Diaporthe destruens, has been a major problem throughout East Asia. In major sweet-potato-producing regions, developing sweet potato cultivars that are resistant to foot rot has become an urgent priority. The possibility of selecting resistant cultivars by using polyphenols in the stems as markers was recently suggested, but this selection method has not been tested in the crossbreeding of sweet potato cultivars. In this study, we crossed the sweet potato cultivars ‘Konaishin’ and ‘Tamaakane’ (each of which is resistant to foot rot), analyzed the polyphenols in the stems of the resulting hybrid lines, and evaluated the possibility of selecting resistant lines. As a result, KT No. 7 and KT No. 8 showed similar or lower total polyphenol contents (145.9 and 112.9 mg GAE 100 g⁻¹ FW, respectively) compared to ‘Tamaakane’ (142.2 mg GAE 100 g⁻¹ FW). The selected line, KT No. 7, exhibited the highest resistance among the hybrids when it was directly inoculated with the foot rot pathogen using stems as test material, showing a disease severity value of 1.8, which was substantially lower than that of ‘Tamaakane’ (50.0). These results suggest that stem polyphenol content has potential as a marker for identifying promising candidates with foot rot resistance, although its predictive value may vary depending on genetic and environmental factors. This approach may help improve the efficiency of foot rot resistance screening in sweet potato breeding programs. Full article

Background: Multidrug-resistant (MDR) pulmonary infections represent a critical global health challenge, necessitating innovative therapeutic approaches. Green synthesis methodologies offer sustainable alternatives for nanoparticle fabrication while addressing antimicrobial resistance. Methods: Stimuli-responsive chitosan–silver hybrid nanoparticles (CS–Ag HNPs) were biosynthesized using Pseudomonas fluorescens bacterial extracts and loaded with ciprofloxacin for targeted pulmonary delivery. Comprehensive characterization included dynamic light scattering, transmission electron microscopy, UV–visible spectroscopy, and aerodynamic assessment via next-generation impactor. Antimicrobial efficacy was evaluated against MDR Pseudomonas aeruginosa and Klebsiella pneumoniae, including biofilm disruption studies, and biocompatibility was assessed. Molecular docking analysis elucidated binding mechanisms. Cytotoxicity and epithelial barrier integrity were evaluated using Calu-3 cell models. Results: The biosynthesized NPs exhibited optimal physicochemical properties (180 ± 20 nm, PDI 0.21 ± 0.04, ζ-potential + 32.4 ± 3.1 mV) with high encapsulation efficiency (68.2 ± 4.0%). Aerodynamic analysis revealed excellent inhalation characteristics (MMAD 2.6 μm, FPF 65 ± 5%). The hybrid system demonstrated 4-fold enhanced antimicrobial activity against MDR pathogens and significant biofilm disruption (70% for P. aeruginosa, 65% for K. pneumoniae) compared to free ciprofloxacin. Cell viability remained ≥85% at therapeutic concentrations. Molecular docking revealed enhanced drug-target binding affinity (−11.2 vs. −9.3 kcal/mol) and multi-residue interactions. Conclusions: Green-synthesized CS–Ag HNPs represent a promising sustainable platform for combating pulmonary MDR infections through enhanced antimicrobial efficacy and optimal aerodynamic properties. Full article

The use of clinically important antibiotics in U.S. poultry production has decreased drastically over the past decade. They can only be used to treat diseases under the supervision of a veterinarian. Reducing antibiotic use, even for disease treatment, can improve the long-term sustainability of the industry. In the current study, we examined the effect of supplementation of a low dose of trans-cinnamaldehyde (TC; 0.03%), a GRAS-status plant-derived compound, with or without oxytetracycline (OTC; 16 μg/mL), an anti-30S ribosomal subunit targeting antibiotic, on the multidrug-resistant (MDR) S. Heidelberg (SH) in turkey poults. Two independent experiments were conducted (N = 96). In each experiment, 48, straight-run, day-old, commercial Hybrid Converter turkey poults were randomly assigned to 6 treatments of 8 birds each: Negative Control [NC; −SH, −TC, −OTC, −0.06% Miglyol (MIG, emulsifier for TC in water)], Positive Control (PC; +SH, −TC, −OTC, −MIG), MIG Control (MIG; +SH, −TC, −OTC, +MIG), TC Group (TC; +SH, +TC, −OTC, +MIG), OTC group (OTC; +SH, −TC, +OTC, −MIG), and TC+OTC group (TC+OTC; +SH, +TC, +OTC, +MIG). OTC was supplemented from day 1 through drinking water throughout the experiment. The birds in the TC and TC+OTC groups were supplemented with TC in their drinking water for 7 days post-challenge. All birds were challenged on day 7 with 6 log₁₀ CFU of SH/bird via crop gavage. On day 14, all birds were euthanized to collect the cecum, liver, and spleen for pathogen recovery. TC at 0.03% emulsified in MIG was highly effective in reducing MDR SH colonization in turkey poults (p < 0.05) compared to the SH control (>4.5 log₁₀ CFU/g reduction) on day 14. The OTC group reduced the pathogen load by 2.5 log₁₀ CFU/g by day 14. TC enhanced the effect of OTC, reducing pathogen load by ~3.9 log₁₀ CFU/g compared to the SH control after 7 days. TC significantly reduced SH invasion into the liver and spleen compared with the SH control on day 14. The results of the study indicate that TC at 0.03% can augment OTC at 16 μg/mL for the treatment of MDR SH infection in poults and could be an industry-sustainable strategy. Full article