Search Results (1,368)

Antimicrobial resistance (AMR) emerges and circulates across interconnected human, animal, food, and environmental reservoirs; however, food fermentation systems remain underexplored as indicators of local AMR pressure, even though artisanal dairy fermentations may function as natural sentinels of AMR. In this study, we used an artisanal dairy fermentation chain as a One Health model to investigate whether environmentally exposed lactobacilli can reflect stage-associated shifts in resistance. A total of 1.085 isolates representing 16 Lactobacillus species were recovered from the same artisanal dairy matrix at two fermentation stages: day 5 (“Tyrovolia”; n = 518) and day 30 (“Kopanisti”; n = 567). Susceptibility to 14 antibiotics was evaluated by broth micro-dilution, and L. acidophilus was further screened for selected resistance genes. Overall resistance increased significantly from 69.88% (362/518) at day 5 to 77.25% (438/567) at day 30 (p = 0.0059), while multidrug resistance rose from 37.57% to 60.73% of resistant isolates (p < 0.001). Across the 224 species–antibiotic combinations examined, 129 (57.58%) showed an increased upper MIC limit at day 30, and resistance increased significantly for 9 of the 14 antibiotics tested, with the largest rises observed for metronidazole (RR = 7.67), chloramphenicol (RR = 5.74), quinupristin/dalfopristin (RR = 4.11), vancomycin (RR = 2.78), and trimethoprim (RR = 2.43). In contrast, erythromycin and oxytetracycline resistance declined significantly at the ripened stage. In L. acidophilus, 21 resistance genes were detected in 14/70 day-5 isolates and 19 genes in 13/71 day-30 isolates, but marked genotype–phenotype discordance was observed, including matrix-dependent expression patterns for tetM, ermB, and blaTEM. Collectively, these findings show that environmentally exposed artisanal dairy fermentations can enrich resistance phenotypes and may serve as sensitive sentinels of AMR dynamics at the human–animal–environment interface. Full article

The SERPINE1 gene encodes the serine protease inhibitor plasminogen activator inhibitor type-1 (PAI-1), a major negative regulator of the plasmin-dependent pericellular proteolytic cascade and a crucial determinant in the program of stromal remodeling. Recent omics approaches confirmed that high tumor SERPINE1 levels are prognostic for poor disease outcomes and shorter disease-free survival in various malignancies. Kinetic analysis of biomarkers of cell cycle transit in growth-synchronized p53 dual mutant human keratinocytes confirmed that PAI-1 transcription occurred early after growth activation of quiescent (G₀) cells and prior to G1 entry. Previous evidence has confirmed that differential residence of USF family members (USF1→USF2 switch) at the PE2 region hexanucleotide E box motif (CACGTG) in the SERPINE1 proximal promoter characterizes the G₀→G₁ transition period and the transcriptional status of the SERPINE1 gene. A consensus PE2 E box motif (5′-CACGTG-3′) at nucleotides −566 to −561 is required for USF occupancy of the PE2 E box and serum-stimulated SERPINE1 transcription. Interference with USF2 occupancy of the PE2 E Box site by a double-stranded PE2 “decoy”, or induced expression of a dominant-negative USF (A-USF) construct, attenuate serum- and TGF-β1-stimulated SERPINE1 synthesis. Tet-Off activation of an A-USF insert reduced both PAI-1 and PAI-2 transcripts while increasing the fraction of proliferating (Ki-67⁺ cells). Conversely, overexpression of USF2 or adenoviral delivery of a PAI-1 vector inhibited HaCaT colony expansion. These findings are discussed in this review and collectively suggest that the USF1→USF2 transition at the PE2 E box site and subsequent SERPINE1 transcription impact serum-stimulated keratinocyte growth and, likely, cell cycle progression. Full article

Clonal hematopoiesis (CH) is the expansion of clones from a single hematopoietic stem cell (HSC) in the bone marrow. Clonal hematopoiesis of indeterminate potential (CHIP) refers to CH defined by the presence of pre-leukemic driver mutations in at least 2% of alleles in sequenced peripheral blood. This phenomenon is, by definition, associated not only with the future development of acute myeloid leukemia but also with non-malignant conditions, including cardiovascular disease. However, the underlying molecular mechanisms for CH in non-malignant diseases, such as cardiovascular disease, are not fully explained. Certain subtypes of CHIP may give rise to proinflammatory immune cells, which, in turn, may promote atherosclerosis progression. Key subtypes of CHIP include mutations in genes encoding epigenetic regulators DNMT3A (DNA methyltransferase 3A), TET2 (ten-eleven translocation methylcytosine dioxygenase 2), and ASXL1 (associated sex combs-like 1), as well as mutations in the gene encoding hematopoietic cytokine signaling: JAK2 (Janus kinase 2). The aim of this review is to summarize the current knowledge of CHIP and its association with inflammation and cardiovascular risk factors. Full article

Background/Objectives: Atherosclerotic cardiovascular disease (ASCVD) remains the leading cause of death worldwide. The 2023 American Heart Association PREVENT equations represent a contemporary approach to cardiovascular risk estimation, yet they rely on resting clinical and biochemical parameters. This study aimed to evaluate the association between PREVENT-estimated 10-year cardiovascular risk and treadmill exercise testing (TET)-derived physiological variables. Methods: We conducted a single-center observational study of 391 participants (mean age 42.9 ± 9.0 years, 56.8% male) who underwent symptom-limited treadmill testing. Ten-year cardiovascular risk was estimated using PREVENT for total cardiovascular disease (CVD), ASCVD, and heart failure (HF). Hierarchical multivariable regression was performed using log-transformed PREVENT risk estimates to quantify the incremental association of exercise capacity (METs), hemodynamic markers (double product), autonomic recovery (heart rate recovery), and the ST/HR index beyond demographic (age, sex, BMI) and extended clinical base models incorporating available PREVENT input covariates. Results: Beyond the demographic base model, treadmill parameters were significantly associated with log-transformed PREVENT-CVD risk (ΔR² = 0.026, p < 0.001; Cohen’s f² = 0.154). Double product (standardized β = 0.116), HRR at 1 min (standardized β = −0.081), and maximum METs (standardized β = −0.079) were independently associated with risk estimates. However, when the full set of available PREVENT input covariates was included in the base model, the incremental association was negligible (ΔR² = 0.0004, p = 0.386), indicating substantial overlap between exercise-derived physiology and PREVENT-embedded clinical information. The incremental association was greatest in participants with intermediate (1–5%) and higher (≥5%) estimated risk (ΔR² = 0.052 and 0.246, respectively). Approximately 14% of participants shifted to a different quartile of estimated risk after inclusion of treadmill data. Conclusions: Treadmill-derived physiological parameters are significantly associated with PREVENT-estimated cardiovascular risk, but this association largely reflects shared pathophysiology with PREVENT input variables rather than statistically independent incremental information. Exercise testing may serve as a physiological complement to static risk estimation, particularly in intermediate-risk populations, by providing a dynamic physiological assessment that complements resting clinical measurements. Prospective studies with adjudicated cardiovascular outcomes are needed before clinical implementation. Full article

Pulmonary embolism (PE) is biologically heterogeneous. Despite guideline-directed anticoagulation, a subset of patients develops recurrent venous thromboembolism, persistent exertional limitation, residual perfusion defects, and progression to chronic thromboembolic pulmonary disease (CTEPD) or chronic thromboembolic pulmonary hypertension (CTEPH). Conventional risk factors explain much of the index event but incompletely account for thrombus non-resolution and chronic sequelae. Clonal hematopoiesis of indeterminate potential (CHIP)—the age-associated expansion of hematopoietic clones carrying somatic mutations—defines a measurable thrombo-inflammatory endophenotype that is strongly genotype- and clone-size (variant allele frequency; VAF)-dependent. Across human studies, JAK2-CHIP and TET2-CHIP show the most consistent associations with VTE/PE, whereas isolated DNMT3A-CHIP is frequently neutral, and larger clones tend to confer stronger effects. Mechanistically, CHIP can bias myeloid cells toward inflammasome/IL-1β signaling and endothelial activation, increase monocyte tissue factor activity, and promote immunothrombosis with neutrophil extracellular trap (NET) formation. NET-rich thrombi may adopt a dense fibrin–DNA–histone architecture that resists endogenous fibrinolysis, favoring organization and persistence. CTEPH offers a translational window to interrogate this model because thrombotic material and deep phenotyping are accessible. We synthesize genotype- and VAF-resolved clinical and mechanistic evidence using a structured strength-of-evidence framework and propose a pragmatic phenotyping roadmap with testable predictions for prospective post-PE validation. CHIP testing in PE/CTEPH remains investigational and should not currently change standard care. Full article

Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host–microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40–49 genes), including critical genes, such as tet(X), bla_OXA-427, and plasmidomes (16–22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance. Full article

Background: BRAF is a core component of the RAS–MAPK signaling pathway and an established oncogenic driver in several solid tumors and selected hematologic malignancies. In myeloid neoplasms, BRAF mutations are rare, and their prevalence, molecular context, and clinical significance remain incompletely defined. Available evidence is scattered across heterogeneous reports involving acute myeloid leukemia, myelodysplastic syndromes, myeloproliferative neoplasms, and overlap myelodysplastic/myeloproliferative neoplasms, with variable descriptions of mutation subtypes, co-mutational profiles, cytogenetic associations, therapeutic approaches, and clinical outcomes. To address these gaps, this review synthesizes data from the published literature up to 2025, summarizing the distribution, genetic landscape, and clinical impact of molecularly confirmed BRAF mutations across the spectrum of myeloid neoplasms. Results: Across published cohorts, BRAF mutations occurred in less than 1% of unselected myeloid neoplasms, with enrichment in chronic myelomonocytic leukemia and therapy-related or secondary acute myeloid leukemia. Both V600E and non-V600E variants were observed, typically within a complex genomic background involving ASXL1, TET2, DNMT3A, SRSF2, and RAS-pathway mutations. Acute myeloid leukemia cases showed poor prognosis, with median overall survival measured in months, whereas myelodysplastic syndromes and chronic myelomonocytic leukemia demonstrated relatively longer survival. Targeted MAPK inhibition produced hematologic responses in selected cases but rarely resulted in durable molecular clearance. Conclusions: BRAF mutations in myeloid neoplasms are rare, heterogeneous, and usually represent secondary events in clonal evolution. Although mutation clearance appears prognostically relevant, current targeted approaches provide limited durability, underscoring the need for prospective studies in this setting. Full article

Dogs, especially as pets but also an increasing number of stray dogs, share environments with humans, facilitating the transfer of antibiotic resistance genes (ARGs) between genetic compartments, with zoonotic and public health implications that must be addressed within One Health. In this cross-sectional comparative study, we explored the distribution of seven selected clinically relevant ARGs in both genomic DNA (gDNA) and plasmid DNA (pDNA), and the phenotypic resistance profile of the cultivable microbiota, between pet dogs (PeDs, n = 12) and free-roaming dogs (FRDs, n = 10) in Mexico. Tetracycline resistance genes (tetQ, tetW, and tetM) predominated in both compartments (40% to 100%), suggesting the presence of a core tetracycline-associated resistome. In contrast, plasmid-associated differences were group-specific: in pDNA cfxA was enriched in FRDs (90%) and tetK in PeDs (42%), whereas blaTEM-1 and ermC were absent in two dog populations. Cultivable bacteria from both groups exhibited phenotypic multidrug resistance, particularly by β-lactams, macrolides, lincosamides, and tetracyclines. FRDs also harbored pathogenic–zoonotic bacteria such as Yersinia enterocolitica, Campylobacter jejuni, and Enterococcus faecalis. Our findings indicated that FRDs and PeDs harbor substantial resistomes, with differences in plasmid-associated ARGs, revealing a transfer potential related to environmental exposure. Full article

Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics. Full article

Streptococcus suis is an emerging zoonotic pathogen that typically causes bacteremia or meningitis in humans, whereas vertebral osteomyelitis with epidural abscess is exceedingly rare and may be missed. We describe a 65-year-old farmer with fever and severe low back pain after long-term bare-handed handling of raw pig lungs. Pre-treatment blood cultures yielded S. suis identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After transient improvement on empirical therapy, fever recurred with worsening lumbar pain. Contrast-enhanced magnetic resonance imaging (MRI) demonstrated multilevel thoracolumbar pyogenic spondylitis with an epidural abscess and a sub-ligamentous abscess beneath the posterior longitudinal ligament (PLL) extending from L2 to L5. Computed tomography-guided lumbar biopsy followed by tissue metagenomic next-generation sequencing (mNGS) detected S. suis, providing concordant evidence supporting pathogen involvement at the vertebral focus. The bloodstream isolate (SS-JX2025-01) was serotype 2, sequence type 7 (ST7). It remained susceptible to β-lactams and glycopeptides but was resistant to macrolide–lincosamide and tetracycline classes, consistent with erm(B), tet(O), tet(40), and ant(6)-Ia detected by whole-genome sequencing (WGS). Virulence profiling revealed an epf⁺/sly⁺/mrp⁻ pattern with multiple adhesins and immune-evasion factors, whereas canonical 89K pathogenicity island markers were absent. Core-genome phylogeny placed SS-JX2025-01 within the Chinese ST7 lineage associated with previous outbreaks. This biopsy-supported case expands the clinical spectrum of invasive S. suis infection, highlights the value of tissue mNGS as an adjunct for supporting deep-seated foci in zoonotic infections, and underscores the importance of occupational prevention in small-scale farming households. Full article

DNA methylation is a fundamental epigenetic regulator in hepatocellular carcinoma (HCC). However, a key paradox remains: how do ubiquitously expressed enzymes like DNMTs and TETs achieve locus-specific regulation without intrinsic sequence specificity? This review aims to elucidate the “lncRNA–DNA methylation axis,” examining how long non-coding RNAs (lncRNAs) confer specificity and plasticity to methylation machinery. We synthesized current literature focusing on the structural mechanisms (e.g., R-loops, DNA:RNA triplexes) by which lncRNAs interact with DNMTs and TETs. We further analyzed the bidirectional regulation between lncRNAs and methylation enzymes and their impact on HCC phenotypes. lncRNAs function as modular scaffolds and guides, directing methylation machinery to specific genomic loci. Rather than binary switches, they act as an “epigenetic rheostat,” fine-tuning methylation intensity to balance stability with plasticity. Crucially, a reciprocal feedback loop exists: aberrant DNA methylation suppresses tumor-suppressive lncRNAs, which in turn unleashes DNMT activity, locking cells into a malignant state. This axis drives proliferation, metastasis, metabolic reprogramming, and therapeutic resistance. The lncRNA–DNA methylation axis is a central determinant of epigenetic heterogeneity in HCC. Moving beyond descriptive cataloging to a mechanistic understanding of this network offers new perspectives for developing targeted epigenetic therapies and biomarkers. Full article

Antimicrobial-resistant bacteria associated with poultry production pose an ongoing challenge for food safety and veterinary public health. The present study evaluated the prevalence, antimicrobial resistance phenotypes, and selected resistance genes of E. coli recovered from broiler chicken carcasses and cecal content in Romania. Over a 12-month period in 2024, a total of 444 samples were collected, including 300 carcasses obtained from slaughterhouses and retail outlets and 144 cecal samples collected at slaughterhouses. Isolates were recovered using standard microbiological procedures and confirmed through biochemical and automated identification systems. Antimicrobial susceptibility was assessed using a minimum inhibitory concentration–based automated platform, and extended-spectrum β-lactamase (ESBL) production was evaluated phenotypically. Target resistance genes were investigated by PCR. E. coli was identified in 36.0% of carcass samples and 64.6% of cecal samples. High resistance rates were observed for tetracycline (82.6%), ampicillin (68.3%), and trimethoprim–sulfamethoxazole (61.2%), while multidrug resistance occurred in 34.3% of isolates. ESBL production was detected in 11.1% of carcass isolates and 11.8% of cecal isolates and was associated with the presence of blaCTX-M. Additional resistance determinants, including blaTEM, tetA, tetB, sul1, dfrA1, and aadA1, were widely distributed among isolates from both sources. The results suggest that poultry carcasses may contribute to the dissemination of resistant and ESBL-producing E. coli, reflecting intestinal carriage and contamination during processing. Strengthened antimicrobial stewardship, systematic resistance monitoring, and improved hygiene practices throughout the poultry production chain are essential to reduce the public health impact of resistant bacteria. Full article

Accurately partitioning evapotranspiration (ET) into soil evaporation (E) and plant transpiration (T) is fundamental for improving water resource management, yet robust ET partitioning remains challenging. This study proposes a two-step ET partitioning strategy that first extracts pure E and T samples from long-term ET observations and then uses these samples to independently constrain E and T sub-models. The strategy was implemented in three classical two-source ET models: Shuttleworth–Wallace (SW), Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), and FAO-56 dual crop coefficient (FAO56-DK), and was compared against the conventional one-step calibration approach. Results show that the two-step strategy consistently improves the estimation of ET components and the transpiration fraction (T/ET). For the PT-JPL model, RMSEs of E, T, and ET decreased from 0.04, 0.06, and 0.078 to 0.03, 0.03, and 0.04 mm/30 min, respectively. In FAO56-DK, R² values increased from 0.08, 0.55, and 0.65 to 0.10, 0.65, and 0.75. The RMSE of T/ET declined from 0.21 to 0.18 in SW and from 0.47 to 0.34 in FAO56-DK. The effectiveness of pure samples depends on model structure, with E samples most beneficial for SW, T samples for FAO56-DK, and both for PT-JPL. Overall, these results demonstrate that pure-sample constraints substantially enhance ET partitioning accuracy. Full article

Background/Objectives: Acinetobacter baumannii is a leading cause of healthcare-associated infections and is frequently associated with multidrug resistance, severely limiting therapeutic options. The increasing prevalence of carbapenem-resistant A. baumannii (CRAB) has intensified interest in novel antimicrobial agents such as cefiderocol, eravacycline, and imipenem–relebactam. Methods: A total of 80 multidrug-resistant (MDR) A. baumannii isolates recovered from various clinical specimens between April 2019 and October 2023 were included. Antimicrobial susceptibility testing was performed using disk diffusion, gradient test, and broth microdilution methods in accordance with EUCAST and CLSI recommendations. The minimum inhibitory concentrations (MIC’s) for cefiderocol were evaluated with broth microdilution using iron-depleted cation-adjusted Mueller–Hinton broth as the reference method. The presence of carbapenem resistance–associated genes (blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, blaIMP, and tetA) was investigated by polymerase chain reaction. Results: All isolates were resistant to imipenem and meropenem. Colistin resistance was detected in 7.5% of isolates. According to EUCAST criteria, cefiderocol susceptibility was observed in 77.5% of isolates by microdilution and in 81.25% by disk diffusion. Eravacycline demonstrated low MIC values, with MIC₅₀ and MIC₉₀ of 0.25 mg/L and 0.75 mg/L, respectively. In contrast, all isolates were resistant to imipenem–relebactam. The blaOXA-23 gene was detected in 82.5% and blaOXA-24 in 17.5% of isolates, while no blaOXA-58, blaIMP, or tetA genes were identified. No statistically significant association was found between cefiderocol resistance and OXA-type carbapenemase genes. Conclusions: Cefiderocol and eravacycline demonstrated promising in vitro activity against MDR A. baumannii, including colistin-resistant isolates, whereas imipenem–relebactam showed no activity. These findings support the potential role of cefiderocol and eravacycline as alternative treatment options for CRAB infections and highlight the multifactorial nature of cefiderocol resistance beyond OXA-type carbapenemase production. Full article

The coexistence of antibiotic resistance genes (ARGs), particularly those conferring resistance to last-resort antibiotics, is increasingly present in lesser-studied bacterial species. Tigecycline is currently one of the last important barriers in the treatment of carbapenem-resistant bacterial infections, whose resistance gene, tet(X), is prevalent across multiple bacterial genera, but the coexistence of tet(X3) and tet(X4) in Acinetobacter sp. is rarely observed. Here, we report a strain co-harboring the chromosomal tet(X3) and plasmid-borne tet(X4) isolated from a commercial beef cattle farm in Henan province, China. The strain exhibited resistance to ampicillin, gentamicin, chloramphenicol, sulfamethoxazole, tetracycline, doxycycline, tigecycline, and omadacycline. Based on whole-genome sequencing (WGS), the strain was identified as A. indicus using Average Nucleotide Identity (ANI) and digital DNA–DNA hybridization (dDDH). Chromosomal tet(X3) was identified in the genetic context, ISVsa3-XerD-tet(X3)-res-ISVsa3. The plasmid-located tet(X4) with the genetic context, ISVsa3-abh-tet(X4)-ISVsa3, and 14 additional resistance genes were located in multiple pdif modules. Two different typing methods, the Rep-based strategy (designed for A. baumanii) and MOB-typer, identified the tet(X4)-positive plasmid as GR31 and rep_cluster_1656, respectively. Conjugation assay failed to observe the transfer of the tet(X4)-positive plasmid into recipients, E. coli J53 and Salmonella LGJ2. The co-occurrence of tet(X3) and tet(X4) in Acinetobacter may suggest a risk of rapid dissemination of tigecycline resistance and the hidden presence of numerous undetected bacteria co-carrying high-risk ARGs in the agroecological system, both of which should cause particular concern. Full article