Search Results (518)

Metastatic colorectal cancer (mCRC) accounts for 90% of CRC-related mortality. This review synthesizes insights from comparative genomics tracing evolutionary trajectories from primary tumor to disseminated disease. Multi-region sequencing reveals metastatic seeding often occurs early—before clinical detection—challenging linear progression models. The metastatic bottleneck reduces clonal diversity while enriching for dissemination-competent traits including SMAD4 loss, PTEN inactivation and metabolic reprogramming. Organ-specific adaptation yields distinct molecular signatures: liver metastases exhibit Wnt hyperactivation and TGF-β-driven immune suppression; peritoneal tumors display mucinous features; brain metastases show HER2 enrichment. The immune microenvironment evolves toward immunosuppressive configurations, with Microsatellite instability high (MSI-H) tumors acquiring B2M or JAK1/2 mutations. Circulating tumor DNA (ctDNA) enables real-time tracking of clonal dynamics, detecting molecular residual disease months before radiographic progression. Therapeutic resistance follows predictable evolutionary trajectories—from RAS/BRAF mutations to EGFR ectodomain alterations, HER2/MET amplifications and lineage plasticity—with metastasis-specific mechanisms including microenvironmental protection and cellular dormancy. The clinical future lies in interception: leveraging liquid biopsies for early detection, targeting both tumor-intrinsic vulnerabilities and permissive metastatic niches and adapting therapy dynamically to anticipate resistance. Understanding this genomic odyssey is essential for transforming mCRC into a controllable chronic condition. Full article

Background/Objectives: Carbapenem-resistant Acinetobacter baumannii poses a critical threat due to its ability to acquire multiple resistance mechanisms and persist under antibiotic pressure. This study aimed to elucidate the molecular basis of imipenem resistance in clinical A. baumannii isolates by integrating phenotypic, molecular, transcriptional, and clonal analyses. Methods: Eleven A. baumannii isolates identified by MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) were investigated. Antimicrobial susceptibility to imipenem and meropenem was assessed, followed by polymerase chain reaction (PCR) detection of Ade efflux pump, outer membrane porin, and OXA-type carbapenemase genes. Transcriptional responses to sub-inhibitory imipenem exposure were evaluated using quantitative real-time PCR, and clonal relatedness was assessed by arbitrarily primed PCR. Results: All isolates were carbapenem-resistant, with bla_OXA-23 detected in all isolates and bla_OXA-24 absent in one isolate. Transcriptional analysis revealed isolate-specific responses to imipenem exposure. Among Ade efflux pump components, only adeR exhibited expression changes, displaying either downregulation or upregulation depending on the isolate, whereas adeA, adeB, adeC, and adeS transcripts were not detected under the tested conditions. Outer membrane porin genes showed heterogeneous regulation, with ompA and carO downregulated, while some isolates showed increased expression. Expression of oprD varied among isolates, and omp33–36 transcripts were detected in a single isolate and were reduced after exposure. Clonal analysis identified nine distinct genotypes, indicating genetic diversity and the absence of clonal dominance. Conclusions: These findings highlight the multifactorial and heterogeneous nature of carbapenem resistance in A. baumannii, emphasizing the interplay between regulatory efflux mechanisms, porin modulation, and carbapenemase carriage. Full article

Intraspecific phenotypic diversity in clonally propagated crops is frequently constrained by narrow domestication histories and the widespread use of a limited number of elite cultivars. In Stevia rebaudiana, commercial production has largely centred on cv. ‘Morita II’, raising concerns about reduced diversity and adaptive potential. This study characterised and structured phenotypic diversity within a segregating population derived from ‘Morita II’ under tropical field conditions. Eighty-six progeny-derived genotypes (clonally propagated) plus the commercial control (87 genotypes total) were evaluated using 25 agromorphological descriptors (qualitative and quantitative). Quantitative traits showed broad variation, including plant height (28.26–119.50 cm) and dry yield rate (0.94–28.55 g plant⁻¹). Multivariate analyses of mixed descriptors (PCA and hierarchical clustering based on Gower distance) identified plant architecture, vegetative growth, and phenology as the main sources of differentiation. The first two principal components explained 19.65% and 12.58% of total phenotypic variance, respectively (32.23% cumulative). Hierarchical clustering (UPGMA; dissimilarity cut-off = 0.25) resolved four phenotypic groups (GI–GIV) with sizes n = 3, 1, 66, and 17, respectively, enabling the definition of contrasting ideotype candidates based on recurrent trait combinations. These results provide a quantitative baseline for phenotypic structuring, prioritization of materials for further evaluation, and management of clonal stevia collections in tropical production systems. These ideotype candidates should be considered preliminary until validated across environments and linked to chemical quality traits. Full article

Avian Infectious Bronchitis Virus (IBV) is a highly contagious Gammacoronavirus that poses a significant threat to the global poultry industry. Despite its worldwide prevalence, a critical knowledge gap exists regarding the genetic diversity of IBV in Central Asia, particularly in Uzbekistan. This study is the first comprehensive molecular characterization of IBV in Uzbekistan. This study also provides a unique and informative bioinformatic analysis of the detected strains. Three IBV strains were isolated and identified from chickens suspected of IBV infection. The isolates were identified and subjected to S1 gene sequencing, phylogenetic analysis, recombination screening, selective pressure mapping, and in silico structural and antigenic profiling. Phylogenetic inference revealed that the isolates clustered within the established genotypes GI-1, GI-13, and GI-23. Comparative alignments revealed distinct nucleotide and amino acid substitutions relative to global reference strains. The evolutionary patterns are consistent with a predominantly clonal mode of evolution. Structural modeling and B-cell epitope prediction revealed pronounced antigenic and topological divergence among the Uzbek isolates. Genotype-specific substitutions, particularly in solvent-exposed regions of the spike protein, were associated with altered epitope profiles, implying potential impacts on vaccine cross-protection. These findings contribute to current knowledge of IBV molecular characterization and provide the first reference framework for the Central Asian region. The study highlights the importance of continuous molecular surveillance, region-specific vaccination strategies, and integrated genomic monitoring for novel IBV variants. Full article

Background: Carbapenem-resistant Enterobacterales (CRE) are a global public health concern, with carbapenem-resistant Klebsiella pneumoniae (CR-Kp) recognised as the highest-priority pathogen. This study aimed to investigate the epidemiological features of CRE isolates throughout the COVID-19 pandemic in Buenos Aires, Argentina. Methods: A prospective study was conducted in two hospitals from 2019 to 2022, recovering all CRE from inpatients. Antimicrobial susceptibility was performed by automated and/or manual tests, according to CLSI. β-lactamases detection was performed using Multiplex PCR and MALDI-TOF MS. Kp typing was assessed by multiplex PCR and/or MLST based on WGS. Results: 22% (359/1594) were CRE, predominantly CR-Kp. Overall, high non-susceptibility (NS) rates were observed in both centres. NS remained largely stable in HA, except for a significant increase in colistin NS, whereas HB showed a rise in NS to multiple antimicrobials over time. A significant shift from multidrug-resistant to extensively drug-resistant and difficult-to-treat phenotypes was observed across the study periods. Out of 359 CRE, bla_KPC was confirmed in 141, bla_NDM in 170, and bla_KPC + bla_NDM in 20 isolates. Before the COVID-19 pandemic, KPC was the main carbapenemase in HB, while NDM was already the prevalent one in HA. In 2022, both enzymes showed similar prevalence. bla_KPC-2 and bla_NDM-5 were the prevalent alleles in K. pneumoniae. Before the COVID-19 pandemic, K. pneumoniae epidemiology varied by hospital, characterised by clonal diversity; however, in 2022, CG258-tonB79 drove the epidemiology in both hospitals. Conclusions: A more extensive resistance phenotype among CRE was evidenced throughout the COVID-19 pandemic, driven by carbapenemase-producing K. pneumoniae. NDM-5 and KPC-2 were the main carbapenemases identified. A temporal shift in carbapenemase prevalence was observed in each hospital, converging in similar frequencies of KPC and NDM by 2022 across both centres. This scenario was driven by the active dissemination of K. pneumoniae ST258. Full article

Background: Kawasaki disease (KD) is a systemic vasculitis of unknown origin, though recent evidence implicates viral pathogens in its pathogenesis. Given the central role of T cell receptors (TCRs) in antigen recognition and immune response, this study investigated the association between KD and viral infection through comparative analysis of TCR repertoires. Methods: TCR repertoires from KD patients, healthy children, and individuals with viral infections were comparatively analyzed. TCR diversity and V(D)J usage were assessed using Shannon’s entropy, the Mann–Whitney U test, and Fisher’s exact test. Positional motif enrichment analysis within CDR3 regions was performed based on paratope hotspot classification. Results: Relatively reduced TCR clonal abundance and diversity were observed in KD patients compared to healthy controls. While substantial overlap in VJ gene segment usage was detected between KD and cytomegalovirus (CMV) infection, limited overlap in clonal TCRαβ chains was found between KD and viral infection groups. A predominant TCR combination, TRAV14DV4-J13-TRBV20-1-J2-5, enriched with characteristic amino acid motifs (EET, YNE, LAG, GQG, and AYE), was frequently identified in KD. Conclusions: These observations suggest potential differences in TCR repertoire features between KD patients and both healthy and virus-infected groups. However, the relationship between KD pathogenesis and the viruses examined requires further investigation with larger cohorts. Full article

Non-coding RNAs (ncRNAs) are conserved in the genome of cells across the three domains of life. They comprise a diverse group that are particularly prominent in metazoans where they provide a crucial interface between genes and proteins, participating in key cellular processes at different levels: from control of DNA transcription to modulation of messenger RNA stability to modification of protein activity. The interactions of ncRNAs with one another as well as with other RNAs, DNA and proteins form the basis of a genome-wide regulatory network (GRN). Because of the mutual influence of its components on each other, the GRN is a dynamic system. Further, the GRN imposes constraints on which genes are expressed and when, leading to specific gene-expression patterns or transcriptomes. The configurations of the activities of all gene loci represent self-stabilizing cell states, referred to as “attractor” states, each of which corresponds to a distinct cell type. The cancer cell is also an attractor state that arises from a change in the topography of the epigenetic landscape caused by dysregulation of the GRN. It is proposed that the transition to a neoplastic attractor state is caused by ncRNA alterations, while subsequent somatic mutations of oncogenes and tumor suppressor genes drive cell proliferation and clonal expansion. Full article

Acute myeloid leukemia (AML) is a biologically heterogeneous hematologic malignancy arising from the oncogenic transformation of hematopoietic stem and progenitor cells, resulting in clonal expansion and progressive subclonal diversification. Although considerable advances have deepened our understanding of AML pathogenesis, major challenges persist, particularly regarding relapses and therapeutic resistance. In recent years, exosomes—extracellular vesicles of 30–150 nm in diameter of endosomal origin—have emerged as critical mediators of intercellular communication within the AML tumor microenvironment. These vesicles transport a diverse cargo of proteins, metabolites, and nucleic acids, including mRNA, non-coding RNA species, and DNA, which is selectively packaged during their biogenesis. Circulating exosomes have garnered attention as promising liquid biomarkers for diagnosis, prognosis, and monitoring minimal residual disease, while also representing potential therapeutic targets or delivery platforms. Nonetheless, significant knowledge gaps remain regarding the mechanisms governing exosome biogenesis, cargo selection, and the functional impact on leukemia progression and immune modulation. This review focuses on the role of exosomes in acute myeloid leukemia, with an emphasis on the molecular mechanisms underlying their involvement in pathogenesis, tumor communication, and resistance to therapies, as well as their potential as diagnostic biomarkers. Full article

Walnut (Juglans regia L.) performance and sustainability are closely linked to soil–plant–microbe interactions; nowadays, the combined influence of edaphic context, plantation development and rootstock genotype on walnut-associated microbiomes remains insufficiently resolved. Here, we integrated soil physicochemical characterization, community-level physiological profiling and 16S rRNA gene amplicon sequencing across walnut plantations in four Spanish regions. The design included 14-year clonal stands (Galicia, Gerona, Toledo), an age gradient in Galicia (4, 9 and 14 years), and four rootstocks (MJ209, Vlach, own-rooted ‘Chandler’ and J. regia seedling) in the Córdoba plantation. At the community-level, rhizospheres exhibited higher overall metabolic activity, displaying substrate-specific functional fingerprints across regions. Regarding stand ages, a functional peak was observed at middle age, with a decline in richness and diversity with age. Moreover, rootstock genotype further modulated rhizosphere metabolic function. Sequencing supported compositional differences among regions, ages and rootstocks, identifying a bacterial core of Juglans spp. rhizosphere and detecting 36 putative Plant Growth-Promoting Rhizobacteria (PGPR) genera, suggesting a potential reservoir and possible uses in plant biotechnology. Overall, walnut-associated microbiomes are jointly structured by soil gradients, plantation development and rootstock genotype, supporting site and genotype-tailored microbiome management. Full article

Enterobiasis, caused by the nematode Enterobius vermicularis, remains a widespread public health issue, yet data regarding its genetic structure in Southeast Europe are scarce. This study presents the first molecular and phylogenetic characterization of E. vermicularis isolates from Bulgaria. Between 2022 and 2025, perianal tape test samples were collected from 128 individuals (92.2% of whom were children) with enterobiasis from 17 regions of the country. Molecular identification was performed via nested PCR targeting a 324 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene, followed by Sanger sequencing. Phylogenetic relationships were analyzed using Maximum Likelihood (IQ-TREE), and population genetic indices were calculated using DnaSP v6. Phylogenetic analysis revealed that all 128 Bulgarian isolates belong to genotype B, clustering closely with sequences from other European and Asian countries. Genetic diversity analysis showed remarkably low variation, with a haplotype diversity (Hd) of 0.1507 ± 0.0416 and a nucleotide diversity (π) of 0.00082 ± 0.00015. Among the 11 identified haplotypes, a single dominant haplotype (Hap_1) accounted for 92.2% of all samples and was distributed across all sampled geographic regions. Tajima’s D was significantly negative (−2.314, < 0.05), suggesting a recent population expansion or purifying selection. The dominance of genotype B and the extremely low genetic diversity suggest a recent introduction or clonal expansion of E. vermicularis in Bulgaria. These findings provide essential baseline data for monitoring transmission dynamics and implementing effective control strategies in the Balkan region. Full article

This study examined clonal variation in Vitis vinifera L. cv. ‘Merzifon Karası’, a Turkish wine grape. Thirty-two clones were evaluated for key growth and enological characteristics, including cluster structure, berry attributes, yield components, millerandage index, and berry skin color. Considerable variability was observed in cluster weight (95.8–254.1 g), berry weight (0.64–3.06 g), and millerandage index (1.35–9.77), highlighting the importance of clonal selection for optimizing fruit set, cluster compactness, and overall vineyard performance. Promising clones, such as F13/29, K11/27, and H20/24, combined high yield, well-formed clusters, and low millerandage indices, whereas clone K13/10 exhibited exceptional uniformity in fruit set, achieving the lowest millerandage index. Incorporating berry skin color characteristics further identified K11/27, F13/29, and K13/10 as particularly favorable for both productivity and winemaking quality due to their dark berries, consistent fruit set, and well-formed clusters. These findings illustrate the potential of targeted clonal selection to enhance sustainable viticulture and improve fruit quality in ‘Merzifon Karası’. Full article

Background: Multiple myeloma (MM) is a hematologic malignancy characterized by clonal plasma cell expansion and diverse genomic rearrangements, including immunoglobulin heavy chain (IGH) translocations. Although RNA sequencing enables the comprehensive detection of IGH-associated fusions, routine molecular monitoring remains limited, particularly in non-secretory MM (NSMM), which lacks measurable serologic markers. Methods: Here, we contracted an integrated system combining RNA sequencing (RNA-seq) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) to identify and validate fusion gene-based molecular markers for minimal residual disease (MRD) monitoring. Results: The global fusion landscape was delineated by the sequencing analysis of bone marrow samples from 22 newly diagnosed patients with MM. A total of 362 fusion events were identified, of which 190 non-immunoglobulin fusions were selected for detailed characterization. Recurrent breakpoints were concentrated on chromosomes 1 and 19, and five recurrent fusions, DDX5::EEF1A1, OAZ1::KLF2, OAZ1::KLF16, PFKFB3::LINC02649, and PLXNB2::SCO2, were detected across nine patients. Functional enrichment analyses indicated the significant involvement of these genes in RNA splicing regulation, transcriptional misregulation in cancer-related pathways, and focal adhesion processes. Twenty-three fusion transcripts were validated using RT-PCR and Sanger sequencing, demonstrating high specificity for MM. Longitudinal monitoring revealed that the quantitative assessment of fusion transcript levels enabled earlier relapse detection than flow cytometry, including in NSMM, where conventional MRD tools are ineffective. Conclusions: These findings suggest that individualized fusion transcripts serve as robust molecular markers for MRD surveillance. The proposed RNA-seq–RT-qPCR pipeline offers a clinically practical strategy to enhance precision diagnosis and personalized treatment in MM. Full article

Background/Objectives: In food-producing animal (FPA) environments, healthy animals can act as reservoirs of potentially pathogenic Escherichia coli, which can be transmitted through the food chain to humans. This study aimed to evaluate cloacal E. coli in healthy Sicilian lambs subjected to an experimental feeding regimen by assessing bacterial levels, antimicrobial resistance, virulence traits, and the clonal relationships, as well as the impact of a pistachio skin as an agro-industrial by-product supplement during a 58-day feeding trial. Methods: A total of 295 E. coli isolates from the control (CTRL) and treatment (Treated) groups at initial time (T0) and final time (T1) were phenotypically and genotypically characterized using Kirby–Bauer antimicrobial testing, multiplex PCR for virulence genes, and PFGE for clonal analysis. Results: The feeding regimen did not significantly influence the prevalence, abundance, or virulence of the E. coli isolates. Shiga toxin-producing E. coli (STEC) were the most common pathotype, mainly carrying the stx1 gene, while the Enteroinvasive (EIEC) type was detected only sporadically. Enteropathogenic E. coli (EPEC) predominated at T0, while enteroaggregative E. coli (EAEC) at T1, and enterotoxigenic E. coli (ETEC), initially prevalent in Treated samples, disappeared by T1. Antimicrobial resistance profiles varied among isolates, with the highest resistance observed in the CTRL group. However, both groups exhibited high resistance to streptomycin, and 9% of CTRL isolates were multidrug resistant. A notable reduction in overall resistance rates, especially in the Treated group, was observed, indicating a dietary effect on the E. coli resistome. PFGE genotyping showed high genetic diversity, with resistance traits more frequently detected than virulence factors. Conclusions: This study highlights that healthy lambs serve as reservoirs for potentially human-pathogenic E. coli and suggests that dietary regimes could effectively reduce antibiotic resistance. Full article

Background: This study aimed to assess the presence of thermotolerant Campylobacter resistant to ciprofloxacin and erythromycin in poultry slaughterhouses and retail markets, as well as to characterize their multidrug resistance profiles, genetic determinants, and clonal relationships. Methods: Samples were collected at slaughterhouses from cecal content (n = 270), neck skin (n = 270), and wastewater (n = 9), and at retail markets from breast skin (n = 241). Isolates were obtained from mCCDA agar supplemented with ciprofloxacin (2 μg/mL) and identified as C. jejuni or C. coli by PCR. The agar microdilution test was used to determine the minimum inhibitory concentration for ciprofloxacin and erythromycin, and other critical antibiotics. Point mutations in gyrA (Thr86Ile) and 23S rRNA (A2075G), virulence genes (flaA, flhA, cadF, and cdt), and clonal relationships were assessed by PCR and PFGE. Results: At the slaughterhouses, thermotolerant Campylobacter spp. resistant to erythromycin and ciprofloxacin were detected in 48.55% (107/549) of the samples, whereas 4.56% (11/241) of retail samples were positive. The Thr86Ile substitution in gyrA and the A2075G mutation in the 23S rRNA gene were detected in 92.97% and 89.84% of the isolates, respectively. Most isolates (>80%) were multidrug resistant and harbored key virulence genes (flaA, flhA, and cadF). C. jejuni exhibited the highest prevalence of cdt genes (76.19%). There was substantial genotypic diversity among isolates, with broad distribution across the sampled matrices and sites. Conclusions: These findings highlight the circulation of multidrug-resistant and potentially virulent thermotolerant Campylobacter spp. in the later stages of the poultry meat supply chain. Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a major cause of bloodstream infections and poses serious challenges to clinical management because treatment options are limited. This study aimed to characterize antimicrobial resistance, virulence-associated features, and molecular epidemiology of CRKP bloodstream isolates using integrated phenotypic and genomic approaches. A total of 74 non-duplicate CRKP isolates were collected from bloodstream infections at three tertiary-care hospitals in Riyadh, Saudi Arabia, between 2022 and 2024. All isolates showed classical Klebsiella pneumoniae phenotypic characteristics, including intrinsic resistance to natural and aminopenicillins, and were classified as either multidrug-resistant (MDR) or extensively drug-resistant (XDR). Resistance to imipenem was universal, and resistance to other β-lactams and fluoroquinolones was high. Carbapenemase genes were detected in 96.0% of isolates using the GeneXpert^® Carba-R assay, with bla_OXA-48-like and bla_NDM being most common. Whole-genome sequencing demonstrated predominance of Ambler class D carbapenemases, particularly bla_OXA-232, with additional contributions from bla_NDM-1 and bla_NDM-5. Co-occurrence of carbapenemase genes was observed in a subset of isolates. Virulence analysis showed that 37.8% of isolates exhibited a hypermucoviscous phenotype, and more than half carried at least one virulence-associated determinant linked to capsule regulation or iron acquisition. In contrast, most isolates showed weak or no biofilm-forming capacity. Multilocus sequence typing revealed substantial genetic diversity but clear dominance of high-risk lineages, particularly ST147 and the emerging ST2096, both closely associated with bla_OXA-232 and bla_OXA-48-like genes. Capsular and O-antigen analysis showed a non-random distribution dominated by KL64 and O1/O2. Phylogenetic analysis was consistent with clonal expansion and suggested intra-hospital spread, with the intensive care unit serving as a key reservoir and dissemination to other wards. In conclusion, CRKP bloodstream infections in this setting are largely associated with a limited number of epidemic clones that combine extensive antimicrobial resistance with virulence-associated traits. These findings support the need for ongoing genome-based surveillance, strengthened infection control measures, and antimicrobial stewardship to limit the spread of high-risk K. pneumoniae lineages in healthcare settings. Full article