Search Results (3,667)

The emergence and global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) represent a major public health concern. However, the characterization and capacity for horizontal gene transfer (HGT) of ESBL-E. coli in captive black bears remain substantially understudied. In the present study, 19 ESBL-E. coli strains were successfully identified (13.38%, 19/142). A total of 11 sequence types (STs) were identified from 19 ESBL-E. coli strains using MLST. This included eight known types (ST10, ST2690, ST208, ST695, ST4160, ST540, ST3865 and ST2792) and three new STs. Antimicrobial susceptibility testing demonstrated that all 19 ESBL-E. coli exhibited high resistance to KZ (100.00%), CRO (78.95%), and CTX (73.68%). Polymerase chain reaction (PCR) screening for 14 β-lactam antibiotic resistance genes (ARGs) and their variants revealed that bla_CTX-M was the most prevalent, followed by bla_SHV, bla_TEM, and bla_DHA. Furthermore, eight β-lactamase variants were detected, including five bla_CTX-M variants (bla_CTX-M-15, bla_CTX-M-3, bla_CTX-M-14, bla_CTX-M-55, and bla_CTX-M-27) and one variant each of bla_SHV-1, bla_TEM-1, and bla_DHA-14. Conjugation assays revealed that eight ESBL-E. coli strains were capable of conjugative transfer. Five plasmid types (IncFII, IncW, IncFrepB, IncY, and IncHI1) and three mobile genetic elements (MGEs) (IS26, ISEcp1, and trbC) were identified as co-transferred with bla_CTX-M. ESBL-E. coli poses a potential threat to captive black bears and may lead to further transmission. Consequently, the implementation of continuous surveillance and targeted interventions is imperative to prevent the transmission of ESBL-E. coli. Full article

The genus Aeromonas is widely distributed in aquatic environments, where it is a frequent fish pathogen. It has also been described in association with human infections, with most cases caused by A. caviae, A. veronii biovar sobria, and A. hydrophila. More recently, A. dhakensis has emerged as an increasingly important human pathogen. Transmission occurs primarily through ingestion or contacts with aquatic sources, or by consuming contaminated food, particularly from aquatic origins. Growing resistance in Aeromonas has been reported for penicillins (including their combinations with classical β-lactamase inhibitors), cephalosporins, and carbapenems. Among the β-lactam antibiotics, only fourth-generation cephalosporins remain almost uniformly active. Furthermore, the co-occurrence of resistance genes for third-generation cephalosporins and carbapenems within the same isolates is increasing. Recently, the presence of mobile genes conferring colistin resistance has also been documented, with resistance rates sometimes exceeding 30%. This evolution of colistin resistance is likely linked to its use in aquaculture, and together with the rise in β-lactam resistance, may be transforming Aeromonas into a significant reservoir of resistance genes that could potentially be transferred to species more commonly associated with human infections, such as the Enterobacterales. Full article

To enhance the L-threonine synthesis level in Escherichia coli, this study constructed screening markers rich in L-threonine rare codons. By replacing all the threonine codons in the protein sequences with a high proportion of threonine with L-threonine rare codons and linking them to the fluorescent proteins with the same replacement, high-throughput screening of L-threonine production mutant strains was achieved. To address the metabolic imbalance caused by overexpression of a single enzyme, an artificial multi-enzyme complex system was constructed based on the principle of cellulosome self-assembly. By co-locating ThrC-DocA and ThrB-CohA, the substrate transfer path was shortened, achieving a 31.7% increase in L-threonine production. Furthermore, combined with multi-copy chromosomal integration technology via CRISPR-associated transposase (MUCICAT) technology, the thrC-docA-thrB-cohA gene cluster was integrated into the genome of the high-yield strains obtained through screening, eliminating the plasmid-dependent metabolic burden and significantly enhancing genetic stability. The modular assembly of metabolic pathways by using cellulosome elements provides a new paradigm for the optimization of complex pathways and lays a theoretical and technical foundation for the efficient production of L-threonine. Full article

Background/Objectives: Klebsiella pneumoniae ST258 and ST11 are global high-risk antimicrobial-resistant clones known for their virulence and resistance gene dissemination. This study aims to identify these clones in a Greek tertiary hospital and understand their resistance profiles and transmission dynamics. Methods: In January 2025, we isolated two distinct carbapenem-resistant K. pneumoniae in a Greek tertiary hospital: INT18S from an ICU patient’s bronchioalveolar lavage and INT20U from a urine sample in the emergency unit. Antimicrobial susceptibility testing (via Microscan system) and Whole-Genome Sequencing (WGS) were conducted on both isolates and their genomes were submitted to the NCBI. Results: The INT18S isolate carried the bla_KPC-2 gene and belonged to the ST258 clone. The INT20U isolate carried the bla_NDM-1 gene and belonged to the ST11 clone lineage. Both isolates contained at least one of the extended spectra β-lactamase genes tested (TEM, SHV, OXA-1 and CTX-M group). Conclusions: The co-existence of the high-risk K. pneumoniae clones ST258 and ST11 in different hospital departments increases the risk of resistance gene transfer and suggests potential intra-hospital transmission pathways. Understanding their resistance profiles is critical for guiding treatment strategies and preventing the spread of multidrug-resistant pathogens. Full article

Wheat blast, caused by Pyricularia oryzae Triticum lineage (PoTl), is one of the most destructive and significant fungal diseases affecting wheat crops. The stability of the G143A mutation in the cytB gene, which confers resistance to Quinone outside inhibitor fungicides (QoIs) in PoTl isolates, has not been extensively studied. This study was conducted to evaluate the stability of fungicide resistance, fitness, and competitive ability of the QoI-resistant (R) PoTl isolates group over nine and five consecutive transfer cycles in vitro and in vivo, respectively, without fungicide exposure. No changes in azoxystrobin sensitivity were observed in either the QoI-resistant or sensitive (S) PoTl isolate groups after the successive transfer cycles in vitro and in vivo. The mycelial growth of the QoI-R PoTl isolate group remained stable, while the conidial germination capacity increased over time. For the QoI-resistant isolates, leaf and head disease, conidial production, and the latent period on wheat leaves did not change between the first and fifth infection cycles. In each transfer cycle, the highest levels of leaf and head disease, as well as the largest quantities of conidia collected from wheat leaves, were observed in isolate mixtures. Also, the G143A mutation responsible for QoI resistance remained stable after five transfer cycles of the QoI-resistant (0S:100R) isolate on wheat leaves. Our findings indicate that the G143A mutation remains stable, and there are adaptive benefits in QoI-R PoTl isolates. We discuss the ecological implications of the wheat blast population’s adaptation and PoTl QoIs resistance stability in wheat-cropping areas in Brazil. Full article

Background/Objectives: Antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in K. pneumoniae pathogenicity. Methods: Prophages were extracted from 89 Kenyan K. pneumoniae genomes. The intact prophages were examined for virulence genes carriage, and their phylogenetic relationships were established. Results: Eighty-eight (~99%) of the genomes encode at least a single prophage, and there is an average of four prophages and 2.8% contributory genomes per bacterial strain. From the 364 prophages identified, 250 (68.7%) were intact, while 58 (15.9%) and 57 (15.7%) were questionable and incomplete, respectively. Approximately, 30% of the intact prophages encode 38 virulence genes that are linked to iron uptake (8), regulation (6), adherence (5), secretion system (4), antiphagocytosis (4), autotransporter (4), immune modulation (3), invasion (2), toxin (1) and cell surface/capsule (1). Phylogenetic analyses revealed three distinct clades of the intact prophages irrespective of their hosts, sources and locations, which support the plasticity of the genomes and potential to mediate horizontal gene transfer. Conclusions: This study provides first evidence showing the diverse prophages that are encoded in K. pneumoniae from SSA with particular focus on Kenyan strains. This also shows the potential roles these prophages play in the pathogenicity and success of K. pneumoniae and could improve knowledge and complement control strategies in the region and across the globe. Further work is needed to show the expression of these genes through lysogenisation. Full article

Background. Dystroglycanopathies (DGPs) constitute a set of recessive, neuromuscular congenital dystrophies that result from impaired glycosylation of dystroglycan (DG). These disorders typically course with CNS alterations, which, alongside gradual muscular dystrophy, may include brain malformations, intellectual disability and a panoply of ocular defects. In this process, the protein products of 22 genes, collectively dubbed DGP-associated genes, directly or indirectly participate sequentially along a complex, branched biosynthetic pathway. POMGNT2 and POMGNT1 are two enzymes whose catalytic activity consists of transferring the same substrate, a molecule of N-acetylglucosamine (GlcNAc) to a common substrate, the O-mannosylated α subunit of DG. Despite their presumptive role in retinal homeostasis, there are currently no reports describing their expression pattern or function in this tissue. Purpose. This work focuses on POMGNT2 and POMGNT1 expression in the mammalian retina, and on the characterization of their distribution across retinal layers, and in the 661W photoreceptor cell line. Methods. The expression of POMGNT2 protein in different mammalian species’ retinas, including those of mice, rats, cows and monkeys, was assessed by immunoblotting. Additionally, POMGNT2 and POMGNT1 distribution profiles were analyzed using immunofluorescence confocal microscopy in retinal sections of monkeys and mice, and in 661W cultured cells. Results. Expression of POMGNT2 was detected in the neural retina of all species studied, being present in both cytoplasmic and nuclear fractions of the monkey and mouse, and in 661W cells. In the cytoplasm, POMGNT2 was concentrated in the endoplasmic reticulum (ER) and/or Golgi complex, depending on the species and cell type, whereas POMGNT1 accumulated only in the Golgi complex in both monkey and mouse retinas. Additionally, both proteins were present in the nucleus of the 661W cells, concentrating in the euchromatin and heterochromatin, as well as in nuclear PML and Cajal bodies, and nuclear speckles. Conclusions. Our results are indicative that POMGNT2 and POMGNT1 participate in the synthesis of O-mannosyl glycans added to α-dystroglycan in the ER and/or Golgi complex in the cytoplasm of mammalian retinal cells. Also, they could play a role in the modulation of gene expression at the mRNA level, which remains to be established, in a number of nuclear compartments in transformed retinal neurons. Full article

Salt and low temperature are serious abiotic stresses and important constraints to agricultural productivity across the globe. These abiotic stresses negatively affect plant growth and physiological, biochemical, and molecular processes. Glycine betaine (GB) is an important osmoprotectant that enables plants to resist salinity, low temperature, and drought. GB can be synthesized in many organisms, including animals, plants, and bacteria. In higher plants, GB is synthesized through two-step oxidation of choline. However, rice, an important food crop, cannot synthesize GB. Thus, conferring the ability to synthesize GB to rice through genetic engineering is of great significance for enhancing its tolerance to abiotic stress. Recently, an enzyme, GSDMT (glycine, sarcosine, and dimethylglycine methyltransferase) was found in a diatom, Talassiosira pseudonana, and found able to catalyze the three successive methylation steps of glycine to form GB. This biosynthetic pathway for GB synthesis is also the simplest in living organisms. Here, the optimized codon of the TpGSDMT gene sequence was synthesized and cloned into an overexpression vector, pBWA(V)HS, which contains a CaMV 35S promoter, and then, the constructed vector was transferred into rice (Oryza sativa L. ssp. Japonica). The GB content in transgenic rice showing overexpression of TpGSDMT was significantly increased, and these transformants exhibited markedly enhanced tolerance to salt and low temperature. These results indicate that the TpGSDMT gene can be used for the genetic improvement in crop plants’ resistance to salinity and low temperature. Full article

Phage therapy has garnered significant attention due to the rise of life-threatening multidrug-resistant pathogenic bacteria and the growing awareness of the transfer of resistance genes between pathogens. Considering this, phage therapy applications are being extended to target plant pathogenic bacteria, such as Erwinia amylovora, which causes fire blight in apple and pear orchards. Understanding the mechanisms involved in phage resistance is crucial for enhancing the effectiveness of phage therapy. Despite the challenges of naturally developing a bacteriophage-insensitive mutant (BIM) of E. amylovora (without traditional mutagenesis methods), this study successfully created a BIM against the podovirus ϕEa46-1-A1. The parent strain, E. amylovora D7, and the BIM B6-2 were extensively compared at genomic, transcriptomic, and phenotypic levels. The phenotypic comparison included the metabolic behavior, biofilm formation, and in planta evaluations of pathogenicity. The results revealed a mutation in strain B6-2 in the rcsB gene, which encodes a second regulator in the Rcs two-component phosphorelay system (TCS). This mutation resulted in significant changes in the B6-2 BIM, including downregulation of amylovoran gene expression (e.g., an average log₂ fold change of −4.35 across amsA-L), visible alterations in biofilm formation, increased sensitivity to antibiotics (22.4% more sensitive to streptomycin), and a loss of pathogenicity as assessed in an apple seedling virulence model in comparison to the wildtype strain. The findings presented in this study highlight the critical role of the Rcs phosphorelay system in phage resistance in E. amylovora. Based on these findings, we have proposed a model that explains the effect of the B6-2 rcsB mutation on the Rcs phosphorelay system and its contribution to the development of phage resistance in E. amylovora. Full article

The widespread use of plastics has caused severe environmental pollution, driving interest in biodegradable alternatives like polylactic acid (PLA). However, incomplete degradation of biodegradable plastics under natural conditions may generate micro/nanoplastics that could exacerbate ecological risks. This study investigated the combined effects of UV-aged microplastics from biodegradable PLA and conventional PET, along with sulfamethoxazole (SMX), on the conjugative transfer of antibiotic resistance genes (ARGs) between bacteria. Using UV aging to simulate environmental weathering, the microplastic morphology, adsorption behavior, and interaction with SMX were characterized. The study further evaluated the bacterial viability, ROS level, membrane permeability, and the expression of conjugative transfer-related genes to elucidate the underlying mechanisms. Results showed that aged PLA released significantly more nanoplastics and exhibited higher adsorption affinity for SMX than PET. Combined exposure to aged PLA and SMX significantly enhanced ARG transfer frequency by approximately 14.5-fold compared to the control. Mechanistic studies revealed that this promotion was associated with increased intracellular ROS levels, elevated membrane permeability, and upregulation of conjugative related genes. These findings underscore that biodegradable plastics, after environmental aging, may pose greater ecological risks than conventional plastics, and highlight the importance of considering environmental aging in the risk assessment of plastics. Full article

Multidrug-resistant (MDR) Streptococcus suis (S. suis) is a zoonotic pathogen capable of infecting pigs across all age groups, leading to conditions such as meningitis, arthritis, and endocarditis. In humans, infections can result in septic arthritis, meningitis, necrotizing fasciitis, and septicemia, which may be fatal. The absence of a complete genome sequence hinders comprehensive bioinformatic studies of MDR S. suis derived from pigs. In this study, we present the whole-genome sequence of MDR S. suis serotype 2 ST01 isolated from joint fluid samples obtained from pigs. Whole-genome analysis revealed that the ST01 chromosome carries 19 antibiotic resistance genes that confer resistance to major classes of antibiotic including aminoglycosides, tetracyclines, fluoroquinolones, lincosamides, polypeptide, and nitrofurans. Additionally, it contains 15 virulence factors associated with immune modulation, bacterial adherence, and stress survival. Whole-genome analysis identified 84 horizontal gene transfer elements in ST01 (comprising 28 genomic islands, 52 transposons, and 4 prophages), alongside mutations resulting in reduced virulence (302 instances) and loss of pathogenicity (34 instances). Furthermore, 18 antibiotic targets along with 21 lethal mutations were identified as potential targets for preventing, controlling, and treating infection caused by MDR S. suis serotype 2 ST01. In vivo infection experiments demonstrated that intraperitoneal inoculation with ST01 resulted in mortality among Kunming mice, with a median lethal dose (LD₅₀) of 5.62 × 10⁹ CFU/mL. Histopathological analysis revealed varying degrees of lesions in the infected organs of the mice. This study thus provides valuable insights into strategies aimed at combating S. suis infections and their transmission within swine populations. Full article

The proliferation of antibiotic resistance genes (ARGs) in livestock manure has raised growing environmental and public health concerns. Composting is widely recognized as an effective method to mitigate ARG dissemination; however, recent studies have increasingly reported a rebound in ARG abundance during the curing stage of composting, undermining its long-term effectiveness. Here, “rebound” refers to a renewed increase in ARG abundance—either in absolute terms or relative to the 16S rRNA gene—following its decline to a minimum during the thermophilic phase. This review systematically summarizes the dynamic changes in ARGs throughout the composting process, with a particular focus on the mechanisms and drivers underlying ARG rebound. Vertical and horizontal gene transfer, along with microbial succession, are discussed as key contributors to this phenomenon. Current strategies to suppress ARG rebound, including microbial community manipulation, hyperthermophilic composting, and exogenous amendments, are evaluated. Furthermore, the roles of heavy metals and extracellular polymeric substances in promoting ARG persistence are examined, highlighting their potential involvement in ARG rebound. This review aims to provide a comprehensive understanding of ARG rebound in composting and to inform the development of more effective, integrated mitigation strategies. Full article

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant–microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed. Full article

Soil alkalinity severely restricts the cultivation of Lupinus angustifolius, a valuable legume. Wild soybean (Glycine soja) is a leguminous plant with extremely strong alkaline resistance (pH 8.5). Transferring the alkali-tolerant genes from wild soybeans into lupinus can effectively enhance the alkali tolerance. In this study, we combined transcriptome profiling and genetic transformation to elucidate the molecular basis of alkaline stress response in lupinus. RNA-seq analysis of root tips under acid (HCl, pH 4.0) and alkali (NaHCO₃, pH 8.5) stress revealed 104,353 annotated unigenes, with differential expression patterns highlighting enrichment in cellular component, binding, and catalytic activity categories. KEGG pathway analysis indicated that early responses involved ribosome-related pathways, while later stages activated plant hormone signaling and MAPK pathways. Notably, no homeodomain-leucine zipper (HD-Zip) family genes were identified in the lupinus genome. Therefore, we transferred GsHZ4, an alkali-resistant HD-Zip transcription factor from wild soybean into lupinus hairy roots via Agrobacterium rhizogenes-mediated transformation. Overexpression of GsHZ4 significantly enhanced antioxidant enzyme activities (CAT, POD, and SOD) and reduced malondialdehyde content under NaHCO₃ stress. Furthermore, the promoter of GsHZ4 expression was strongly induced by indole-3-acetic acid (IAA). Key alkali-responsive genes (LaKIN, LaMYB34, LaDnaJ1, LaDnaJ20, LaNAC22, and LaNAC35) were upregulated in transgenic lines, suggesting that GsHZ4 integrates into the endogenous stress-regulation network. Our findings demonstrate that heterologous expression of GsHZ4 can enhance alkaline tolerance of lupinus, providing a novel strategy for breeding stress-resistant varieties and expanding lupinus cultivation in saline–alkali soils. Full article

Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts’ genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics. Full article