Search Results (117)

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of invasive disease, yet contemporary genomic data from Canada remain scarce. We investigated 56 cases of invasive SDSE infection identified between 2018 and 2022 in two major tertiary care teaching hospitals in Toronto, Ontario, and characterized 49 corresponding isolates by whole-genome sequencing. Nearly three-quarters of infections were caused by the globally expanding ST20 emm type stG62647 lineage. Patients infected with this lineage were significantly older than those infected with non-ST20 lineages across both bloodstream and non-blood infections. Core-genome phylogenetic analysis revealed a highly clonal ST20 cluster, although two isolates had divergent emm types suggesting recombination at the emm locus. Non-ST20 lineages were numerically smaller and genetically more heterogeneous, including distinct sublineages within ST3 and ST34. All isolates were susceptible to β-lactams and vancomycin. Resistance to tetracycline, erythromycin, and clindamycin was detected in a subset of isolates and was associated with genes tetM, tetO, ermA, ermB, and msrD. Several antimicrobial resistance determinants were located on mobile genetic elements, including integrative and conjugative elements. Our findings provide a contemporary genomic view of invasive SDSE in Toronto, highlighting the dominance of the ST20 stG62647 lineage in agreement with recent global observations. Full article

The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025^T, isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025^T within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, “P. massiliensis”, P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5–89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C_15:0, iso-C_17:0 3-OH, and C_15:0. Conditioned medium from ASD2025^T antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025^T (=VKM B-3926^T = JCM 37967^T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed. Full article

Extraintestinal pathogenic Escherichia coli (ExPEC) poses escalating threats to human and veterinary health amid rising antimicrobial resistance. We isolated a highly virulent ExPEC strain RZ-13 (ST345, O134:H21) from diarrheic calves at a large beef cattle farm in Rizhao City, and conducted whole genome sequencing, conjugation experiments, and antimicrobial susceptibility testing to elucidate its genomic architecture and resistance mechanisms. The RZ-13 genome comprises one chromosome and four plasmids. The chromosome harbors virulence factors for adhesion, invasion, biofilm formation, and iron acquisition. Notably, plasmids pRZ13-1 (265,777 bp, IncHI2-IncHI2A) and pRZ13-3 (74,304 bp, IncFII) carry the majority of resistance genes. Plasmid pRZ13-1 carries 25 resistance genes, including bla_CTX-M-55, floR, qnrS1, sul3, and tet(A), as well as a complete tellurite resistance gene cluster, terABCDEFZY1. Its multidrug resistance (MDR) region features an IS26-mediated tandem amplification and an approximately 29 kb inverted structure. Comparative analysis indicated that the MDR region carried by this plasmid is highly prevalent in both animal-derived and human-derived isolates. Plasmid pRZ13-3 harbors an IS91-mediated mobile region that integrates both antimicrobial resistance and stress adaptation genes, which have been repeatedly identified in plasmids from diverse sources, including animals and humans. Conjugation experiments confirmed both pRZ13-1 and pRZ13-3 plasmids are self-transmissible and confer multidrug-resistant phenotypes to recipient strains, with pRZ13-3 exhibiting an exceptionally high transfer frequency of 8.9 × 10⁻², substantially exceeding that of previously reported IncFII plasmids. These findings demonstrate that pRZ13-1 and pRZ13-3 serve as critical vehicles for resistance dissemination through complex mobile genetic element structures and efficient horizontal transfer, highlighting the urgent need for surveillance of livestock-reservoir ExPEC to mitigate public health risks. Full article

Endoplasmic reticulum-mediated protein quality control (ERQC) safeguards secretory pathway proteostasis by recognizing, retaining, repairing, and removing misfolded proteins, and is therefore essential for plant growth, development, and stress tolerance. This system relies on ER-associated degradation (ERAD), in which irreparably misfolded proteins are first recognized in the ER, then exported across the ER membrane to the cytosol, where they are ubiquitinated by ER membrane-anchored ubiquitin ligases, and subsequently degraded by the cytosolic proteasome. Studies in yeast and mammals have defined several conserved ERAD branches, including a multiprotein ERAD complex centered on the polytopic ER membrane E3 ligase HMG-CoA reductase degradation protein 1 (Hrd1), which integrates substrate recognition, membrane retrotranslocation, ubiquitin conjugation, and cytosolic extraction. Recent advances in Arabidopsis show that plants retain the core Hrd1 ERAD architecture while incorporating additional regulatory elements that adapt this machinery to plant-specific physiological demands. Genetic and biochemical analyses of misfolded receptor kinases and engineered substrates have uncovered conserved and plant-specific components of the plant Hrd1 complex, revealing how the plant ERAD pathway integrates ERQC with hormone signaling, stress adaptation, immune responses, and growth regulation. This review synthesizes recent advances in plant ERAD research and highlights key conceptual and mechanistic questions that remain to be resolved. Full article

The convergence of global plastic pollution and antimicrobial resistance crises has intensified concerns about the role of microplastics (MPs) in disseminating antibiotic resistance genes (ARGs) in marine environments. This review synthesizes the mechanistic pathways through which MPs act as vectors for ARG propagation, supported by a bibliometric analysis of 144 studies retrieved from Scopus. MPs possess distinct physicochemical properties such as nanoplastic formation, polymer-specific sorption, weathering-induced oxidation, and additive leachate release that facilitate microbial colonization and biofilm formation. These plastisphere biofilms, enriched with mobile genetic elements including integrons, transposons, and plasmids, promote ARG transfer via conjugation, transformation, and transduction. Environmental modulators like salinity, oxygen, nutrients, pH, UV exposure, and reactive oxygen species further accelerate horizontal gene transfer, while co-selection pressures from heavy metals and antibiotics amplify resistance dissemination. Bibliometric mapping reveals a sharp rise in publications since 2018, with China leading contributions and major research themes centered on horizontal gene transfer, metagenomics, nanoplastics, and biofilm-mediated resistome evolution. Overall, marine MPs substantially intensify ARG spread through complex microbe–plastic–pollutant interactions, posing significant ecological and public health risks. Addressing current gaps, such as limited field validation, underexplored nanoplastic mechanisms, geographic bias, and lack of standardized monitoring, requires harmonized surveillance, omics integration, pollutant mixture modeling, and One Health-based risk assessment to inform global policy interventions. Full article

Composite integrative and conjugative elements (ICEs) frequently mediate the co-transfer of multiple antibiotic resistance genes during horizontal gene transfer, but their formation mechanisms remain unclear. This study investigated the site-specific integration of Tn1806 into ICESa2603-family ICEs in Streptococcus agalactiae by conjugation experiments. PCR screening of 161 S. agalactiae clinical isolates identified potential Tn1806-like ICE carriers; whole-genome sequencing was performed to further characterize the macrolide-resistance isolates from this group. PCR detection resulted in 24 carrying Tn1806-like ICEs being found, five of which were macrolide-resistant. Genomic analysis for these five revealed distinct Tn1806-like ICEs (ICESag16, ICESag57, ICESag139, ICESag167, and ICESag220), three of which were found nested within another ICE (ICESpy009, an ICESa2603-family ICE). Conjugation experiments confirmed ICESag167 could integrate into the snf2 (methyltransferase containing a SNF2 helicase domain) of ICESpy009 in recipient cells, generating a composite ICE. Re-conjugation verified the transferability of composite ICE at low frequencies (8.63 × 10⁻⁸), during which some nested ICESag167 were excised and transferred independently. This work provides first experimental evidence supporting Tn1806 nesting within another ICE as a mechanism for resistance accumulation and mobile element evolution in S. agalactiae. The spread of such composite ICEs may confer multiple forms of resistance to new hosts, challenging infection treatment and raising public health concerns. Full article

Thermodynamic entropy generation quantifies irreversibility in energy conversion processes, providing rigorous thermodynamic foundations for optimizing efficiency and sustainability in thermal and energy systems. This critical review synthesizes advances in computational entropy modeling across numerical methods, optimization strategies, and sustainable energy applications. Computational fluid dynamics, finite element methods, and lattice Boltzmann methods enable spatially resolved entropy analysis in convective, conjugate, and microscale systems, but exhibit varying maturity levels and accuracy–cost trade-offs. The minimization of entropy generation and the integration of artificial intelligence demonstrate quantifiable performance improvements in heat exchangers, renewable energy systems, and smart grids, with reported efficiency gains of 15 to 39% in specific applications under controlled conditions. While overall performance depends critically on system scale, operating regime, and baseline configuration, persistent limitations still constrain practical deployment. Systematic conflation between thermodynamic entropy (quantifying physical irreversibility) and information entropy (measuring statistical uncertainty) leads to inappropriate method selection; validation challenges arise from entropy’s status as a non-directly-measurable state function; high-order maximum entropy models achieve superior uncertainty quantification but require prohibitive computational resources; and standardized benchmarking protocols remain absent. Research fragmentation across thermodynamics, information theory, and machine learning communities limits integrated frameworks capable of addressing multi-scale, transient, multiphysics systems. This review provides structured, cross-method, application-aware synthesis identifying where computational entropy modeling achieves industrial readiness versus research-stage development, offering forward-looking insights on physics-informed machine learning, unified theoretical frameworks, and real-time entropy-aware control as critical directions for advancing sustainable energy system design. Full article

Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism. Full article

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia. Full article

In this work, a dual-band, dual-mode, circularly polarized fully woven textile antenna with capability for Simultaneous Wireless Information and Power Transfer (SWIPT) in wearable applications is presented. The power and the data transfer modes work at 2.4 and 5.4 GHz, respectively. The radiating element is based on a square patch with an asymmetrical U-shaped slot and a chamfered corner. A single-diode rectifier, required for the power transfer mode, is mounted on a carrier thread and then connected to the antenna through a T-match network located at one of the patch corners. This feeding technique simultaneously provides complex conjugate matching to the rectifier and circular polarization. On the other hand, a coaxial probe port is used for the data transfer mode. A prototype was implemented and experimentally characterized. Regarding the power transfer mode, the measured RF-DC conversion efficiency is about 50% when the available power at the rectifier input is −10 dBm, and the axial ratio is smaller than 3 dB. In the data transfer mode, the antenna gain and the axial ratio are 0 and 2 dB, respectively. The experimental results are in good agreement with simulations, validating the proposed structure and design methods, and they are comparable to the state of the art for textile antennas/rectennas. Furthermore, the combination of the fully woven technology and the proposed single-layer layout provides a large degree of integration and robustness, which are valuable characteristics for wearable devices. Full article

Accurate conjugate heat transfer (CHT) analysis is critical to the thermal management of hypersonic vehicles operating in rarefied environments, where non-equilibrium gas dynamics dominate. While numerous sophisticated CHT solvers exist for continuum flows, they are physically invalidated by rarefaction effects. This paper presents a novel partitioned coupling framework that bridges this methodological gap by utilizing the preCICE library to non-intrusively integrate the Direct Simulation Monte Carlo (DSMC) method, implemented in SPARTA, with the finite element method (FEM) via FEniCS for high-fidelity simulations of rarefied hypersonic CHT. The robustness and accuracy of this approach are validated through three test cases: a quasi-1D flat plate benchmark confirms the fundamental coupling mechanism against a reference finite difference solution; a 2D flat-nosed cylinder demonstrates the capability of the framework to handle highly non-uniform heat flux distributions and resolve the ensuing transient thermal response within the solid; finally, a standard cylinder case confirms the compatibility with curved geometries and its stability and accuracy in long-duration simulations. This work establishes a validated and accessible pathway for high-fidelity aerothermal analysis in rarefied gas dynamics, effectively decoupling the complexities of multi-physics implementation from the focus on fundamental physics. Full article

Selenium, a crucial trace element, has garnered significant attention in functional food development due to its effective conversion into organic forms. This study systematically investigated the selenium enrichment potential and metabolic regulation mechanisms of 50 lactic acid bacteria (LAB) strains from Xinjiang. Through sodium selenite tolerance tests, eight core strains with over 80% selenium enrichment were selected, with optimal enrichment conditions being a 37 °C temperature, 2% sodium chloride concentration, and pH of 6.0 in MRS medium. Functional tests demonstrated that selenium-enriched strains exhibited a significantly enhanced antioxidant capacity (demonstrated by DPPH and ABTS free radical scavenging activities) and improved gastrointestinal fluid tolerance, with strain No.41 showing the most outstanding performance. Scanning electron microscopy combined with energy-dispersive X-ray spectroscopy (SEM-EDX) revealed nanoscale selenium (1.34 keV) on cell surfaces. Further characterization showed that 68.94% of selenium was incorporated into selenoproteins, 7.61% into nucleic acids, and 7.02% into polysaccharides. Integrated metabolomic and proteomic studies have shown that selenium reduces the content of L-cysteine primarily by replacing sulfur and competing for key sites in cysteine-S-conjugate-β-lyase, S-adenosyl-L-cysteine hydrolase, and homocysteine synthase, ultimately leading to the synthesis of selenocysteine and selenomethionine. A correlation analysis between differential metabolites and proteins revealed selenium’s significant impacts on the metabolic networks of LAB, antioxidant mechanisms, energy metabolism, and membrane stability. This research provides new insights for developing selenium-enriched probiotics for functional dairy products and health supplements. Full article

Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. Methods: Minimum inhibitory concentrations (MICs) were determined by broth microdilution for SHZ29. Whole genomic sequencing and bioinformatic analysis were performed to depict the structure of the novel tet(X6)-carrying ICE. Inverse PCR and conjugation experiments were conducted to investigate the transfer ability of the ICE. Results: We depicted a novel tet(X6)-carrying ICE, named ICECleSHZ29, which is 74,906 bp in size and inserted into the 3′ end of tRNA-Met-CAT gene of the C. lecithinasegens strain SHZ29, with 17 bp direct repeats (5′-tcccgtcttcgctacaa-3′). This ICE possesses a 38 kb conserved backbone and four variable regions (VR1-4), with VR3 aggregating multiple resistance genes, including tet(X6), tet(X2), erm(F), ere(D), floR, catB, sul2, ant(6)-I and bla_OXA-1327. NCBI database searching identified 13 additional ICEs sharing a similar backbone to ICECleSHZ29. These ICECleSHZ29-like ICEs could be classified into two types based on their distinct insertion sites: Type I, inserted at the tRNA-Met-CAT gene; and Type II, inserted at the tRNA-Glu-TTC gene. Phylogenetic analysis indicated that differences in integrases may result in differences in the insertion site among these ICEs. A circular intermediate form of ICECleSHZ29 was detected by inverse PCR. However, the conjugation experiments using Escherichia coli EC600 as recipients failed. Conclusions: To our knowledge, this study provides the first report of tet(X6) in C. lecithinasegens and characterizes its carrier, a novel ICE: ICECleSHZ29. Full article

Rotating detonation engines (RDEs) are expected to have higher specific work and efficiency, but the high-temperature transonic flow delivered by the combustor poses relevant design and technological difficulties. This work proposes a 1D model for turbine internal cooling design which can be used to explore multiple design options during the preliminary design of the cooling system. Being based on an energy balance applied to an infinitesimal control volume, the model is general and can be adapted to other applications. The model is applied to design a cooling system for a pre-existing stator blade geometry. Both the inputs and the outputs of the 1D simulation are in good agreement with the values found in the literature. Subsequently, 1D results are compared to a full conjugate heat transfer (CHT) simulation. The agreement on the internal heat transfer coefficient is excellent and is entirely within the uncertainty of the correlation. Despite some criticality in finding agreement with the thermal power distribution, the Mach number, the total pressure drop, and the coolant temperature increase in the cooling channels are accurately predicted by the 1D code, thus confirming its value as a preliminary design tool. To guarantee the integrity of the blade at the extremities, a cooling solution with coolant injection at the leading and trailing edge is studied. A finite element analysis of the cooled blade ensures the structural feasibility of the cooling system. The computational economy of the 1D code is then exploited to perform a global sensitivity analysis using a polynomial chaos expansion (PCE) surrogate model to compute Sobol’ indices. Full article

In this paper, the use of nilpotent Lie algebras as the basis for homomorphic encryption based on additive operations is explored. The $g$-setting is set up over $g{l}_n\left({\mathbb{Z}}_q\right)$) and the group $G=exp\left(g\right)$, and it is noted that the exponential and logarithm series are truncated by nilpotency in a natural way. From this, an additive symmetric conjugation scheme is constructed: given a message element $M$ and a central randomizer $U\in z\left(g\right),$ we encrypt $=Kexp\left(M+U\right)K^{-1}$ and decrypt to $M=log\left(K^{-1}CK\right)-U$. The scheme is additive in nature, with the security defined in the IND-CPA model. Integrity is ensured using an encrypt-then-MAC construction. These properties together provide both confidentiality and robustness while preserving the homomorphic functionality. The scheme realizes additive homomorphism through a truncated BCH-sum, so it is suitable for ciphertext summations. We implemented a prototype and took reproducible measurements (Python 3.11/NumPy) of the series $\{{10,10}^2,{10}^3,{10}^4,{10}^5\}$ over 10 iterations, reporting the medians and 95% confidence intervals. The graphs exhibit that the latency per operation remains constant at fixed values, and the total time scales approximately linearly with the batch size; we also report the throughput, peak memory usage, $\mid C\mid /\mid M\mid$ expansion rate, and achievable aggregation depth. The applications are federated reporting, IoT telemetry, and privacy-preserving aggregations in DBMS; the limitations include its additive nature (lacking general multiplicative homomorphism), IND-CPA (but not CCA), and side-channel resistance requirements. We place our approach in contrast to the standard FHE building blocks BFV/BGV/CKKS nd the emerging NIST PQC standards (FIPS 203/204/205), as a well-established security model with future engineering optimizations. Full article