Search Results (1,239)

An outbreak characterized by clinical signs of diarrhea and paralysis, occasionally progressing to fatal outcomes, occurred at an ostrich breeding facility. Conventional antibiotic treatments proved ineffective. To investigate the etiology of the disease, brain and liver specimens were collected for diagnostic analysis. An Escherichia coli (E. coli) isolate, designated strain HZDC01, was obtained from cerebral tissues, and whole-genome sequencing was performed for genomic characterization. Genomic analysis revealed that the chromosomal DNA harbors numerous resistance genes, conferring multidrug resistance through complex mechanisms. Furthermore, a p0111-type plasmid carrying the bla_CTX-M-55 gene and an IncX1-type plasmid harboring rmtB, sul1, APH(6)-Id, tet(A), AAC(3)-IIc, aadA2, bla_TEM-1B, and floR genes were identified. These plasmids carry numerous mobile genetic elements that can disseminate via horizontal gene transfer, thereby amplifying the risk of resistance-gene spread within bacterial populations. Additionally, the ibeB and ibeC genes, which encode proteins involved in the invasion of brain microvascular endothelial cells, were identified. These genes may facilitate E. coli penetration of the blood–brain barrier, potentially leading to meningitis and posing a life-threatening risk to the host. This is the first report of the isolation and characterization of extended-spectrum beta-lactamase E. coli from the brain of an ostrich with paralysis. The findings provide valuable genomic insights into the antimicrobial resistance profiles and pathogenic mechanisms of ostrich-derived E. coli isolates. Full article

Background: The emergence and spread of the tigecycline resistance gene tet(A)-v1 in carbapenem-resistant Klebsiella pneumoniae (CRKP) poses significant public health challenges. However, the prevalence of tet(A)-v1-positive CRKP, especially in pediatric patients, remains poorly understood. This study aims to address the gap by performing an in-depth analysis of isolates collected from a children’s hospital in China. Methods: A 4-year retrospective study was conducted in the children’s hospital in Suzhou, China. Non-duplicated specimens were obtained from pediatric patients, and antimicrobial susceptibility profiles were assessed. Whole-genome sequencing and bioinformatics analyses were conducted to characterize the genetic background, antimicrobial resistance determinants, hypervirulence-associated genes, diversity of tet(A)-v1-carrying plasmids, the genetic environment of tet(A)-v1, and the potential for clonal transmission. Conjugative transferability of tet(A)-v1-carrying plasmids was also evaluated via conjugation assays. Results: Of the 73 tet(A)-v1-positive CRKP isolates from pediatric patients, 10.96% were non-susceptible to tigecycline. These isolates exhibited high genetic diversity, spanning across 13 STs (sequence types), with ST17 being predominant. Three carbapenemases were identified, with IMP being the most common. Isolates from diverse backgrounds, such as ST17, ST20, ST323, ST792, and ST3157, demonstrated evidence of clonal transmission. The tet(A)-v1 gene was located on 14 distinct plasmids across seven replicon types, with IncFIA/IncHI1 and IncFII being most commonly detected. All tet(A)-v1-carrying plasmids were multidrug-resistant, and 68.49% were conjugatively transferable, indicating a high potential for horizontal transfer. Four genetic contexts bordering tet(A)-v1 were identified, which points to active clonal dissemination. Conclusions: Although limited to a single hospital, this study represents one of the first in-depth investigations of tet(A)-v1-positive CRKP in pediatric patients, providing valuable insights into the prevalence and spread of tet(A)-v1 in this vulnerable group. These findings emphasize the urgent need for enhanced surveillance and infection control measures to curb the spread of tet(A)-v1-positive CRKP in pediatric healthcare environments, offering critical insights to mitigate its public health impact. Full article

Salmonella is a major foodborne pathogen that poses an increasing threat due to the emergence of mcr-1-mediated colistin resistance. However, data on mcr-1-positive Salmonella in pork products are limited. In this study, 457 samples collected in 2023 from pig slaughterhouses in Guangdong province were investigated to determine the prevalence and genomic characteristics of mcr-1-positive Salmonella isolates. We found that 92 Salmonella isolates (20.1%, 92/457) were recovered, representing six serotypes, including Salmonella Typhimurium (n = 29) and Salmonella Rissen (n = 29). High resistance to tetracycline (90.2%, 83/92) and multidrug resistance (58.7%, 54/92) were observed. Critically, two colistin-resistant Salmonella Kentucky ST198 isolates (2.2%) harboring mcr-1 on transferable IncI2 plasmids were identified. Genomic analysis revealed a novel multidrug resistance region (MRR, ~57 kb) inserted into the bcfH locus (containing floR, qnrS1, bla_CTX-M-55, and aph (3’)-Ia) and a variant Salmonella Genomic Island 1 (SGI1-KI, containing tet (A), sul1, qacEΔ1 and aadA7) in these isolates. The MRR and SGI1-KI may enhance bacterial survival under antibiotic selection pressure. Phylogenetic analysis showed close relatedness to human clinical strains, suggesting food chain transmission. The findings highlight a high antimicrobial resistance burden, the emergence of transferable last-resort colistin resistance (mcr-1), and acquisition of complex resistance determinants (MRR, SGI1-KI), underscoring an urgent need for enhanced “One Health” surveillance. Full article

Epigenetic regulation is critical to B cell development, guiding gene expression via DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. In mature B cell neoplasms, particularly diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), and chronic lymphocytic leukemia (CLL), these mechanisms are frequently disrupted. Recurrent mutations in key epigenetic regulators such as EZH2, KMT2D, CREBBP, and TET2 lead to altered chromatin states, repression of tumor suppressor genes, and enhanced oncogenic signaling. Dysregulation of specific microRNAs (e.g., miR-155, miR-21) further contributes to pathogenesis and therapeutic resistance. In DLBCL, hypermethylation of SMAD1 and CREBBP mutations are associated with immune evasion and chemoresistance. In FL, EZH2 gain-of-function and KMT2D loss-of-function mutations alter germinal center B cell programming, while in CLL, DNA hypomethylation patterns reflect the cell of origin and correlate with clinical outcome. Targeted therapies such as the EZH2 inhibitor tazemetostat have demonstrated efficacy in EZH2-mutant FL, while HDAC and BET inhibitors show variable responses across B cell malignancies. The limitations of current epigenetic therapies reflect the complexity of targeting epigenetic dysregulation rather than therapeutic futility. These challenges nonetheless highlight the relevance of epigenetic alterations as biomarkers and therapeutic targets, with potential to improve the management of mature B cell neoplasms. Full article

Background/Objectives: This study investigates genomic alterations (GA) between NPM1-mutated (NPM1mut) and wild-type (NPM1wt) acute myeloid leukemia (AML), aiming to better understand the AML genomic profile. NPM1mut AML represents a distinct clinical AML subtype with high relapse rates despite initial responsiveness to chemotherapy. Methods: A total of 4206 AML cases from 2019 to 2024 were analyzed using the FoundationOne Heme assay, incorporating comprehensive DNA and RNA sequencing. Patients were stratified into NPM1mut and NPM1wt cohorts, and genomic differences were systematically compared between the two groups. Results: Among 4206 cases, 633 (15.1%) featured NPM1 GA, with over 99% exhibiting short variant mutations. NPM1mut AML was more common in females (53.4% vs. 41.5%) and associated with a slightly higher median age (62 vs. 60 years). GA was more frequent in NPM1mut AML compared to the NPM1wt and included DNMT3A (39.2% vs. 12.6%; p < 0.0001), PTPN11 (18.3% vs. 7.5%; p < 0.0001), FLT3 (54.5% vs. 14.7%; p < 0.0001), IDH1 (16.1% vs. 5.6%; p < 0.0001), IDH2 (19.0% vs. 9.0%; p < 0.0001), TET2 (23.4% vs. 13.5%; p < 0.0001), and WT1 (12.5% vs. 9.4%; p = 0.02). GA was more frequent in NPM1wt AML and included ASXL1 (17.1% vs. 3.6%; p 0.0001), BCOR (7.5% vs. 1.6%; p < 0.0001), KMT2A (14.7% vs. 0.2%; p < 0.0001), RUNX1 (22.5% vs. 1.9%; p 0.0001), STAG2 (6.9% vs. 1.6%; p < 0.0001) and TP53 (19.1% vs. 4.1%; p < 0.0001). Conclusions: Mutations linked to therapy targets in AML, such as (FLT3 and IDH1/2), PTPN11, and DNMT3A (both associated with inferior outcomes), are more commonly observed in NPM1mut AML, whereas KMT2A, TP53, and myelodysplastic-related mutations are more commonly observed in NPM1wt AML. Full article

The biocontrol strain Streptomyces pratensis S10 was isolated from tomato leaf mold. The fermentation broth of strain S10 can effectively control Fusarium head blight (FHB), caused by Fusarium graminearum. Enhancing antifungal activity is essential in advancing its commercialization. In this study, we aimed to improve the antifungal activity of S10 by integrating fermentation optimization and genetic engineering. Single-factor experiments revealed that seven parameters, namely corn flour, yeast extract, NaNO₃, CaCO₃, K₂HPO₄, KCl, ZnSO₄·7H₂O, and MnCl₂·4H₂O, were identified as significant components. A Plackett–Burman design (PDB) indicated that corn flour, yeast extract, and ZnSO₄·7H₂O were the most critical variables affecting its inhibitory activity and mycelial biomass. The fermentation medium was further determined based on the steepest climbing experiment and a Box–Behnken design (BBD), and the mycelial dry weight of S. pratensis S10 was improved from 2.13 g/L in Gauze’s synthetic No. 1 medium to 8.12 g/L in the optimized medium, closely aligning with the predicted value of 7.98 g/L. Under the optimized medium, the antifungal rate of F. graminearum increased from 67.36 to 82.2%. The spore suspension of strain S10 cultured in the optimized medium substantially improved its biocontrol efficacy against FHB. Moreover, disruption of the key gene tetR led to increased antifungal activity of strain S10 against F. graminearum. Importantly, the antifungal activity of ΔtetR was greatly increased under the optimized fermentation medium. This study suggests that the gene tetR negatively regulates bioactive compound biosynthesis, and the optimized medium provides favorable conditions for the growth of S10. These observations establish an extended basis for the large-scale bioactive metabolite secretion of S. pratensis S10, providing a strong foundation for sustainable FHB management in agriculture. Full article

Autologous stem cell transplantation (ASCT) after high-dose chemo-therapy (HDCT) is an option of consolidation therapy in patients with AML, lymphoma, or myeloma. Clonal hematopoiesis (CH) is a premalignant state, associated with an increased risk of hematological cancer. The incidence of CH in patients with AML, myeloma, and lymphoma and its effect on the outcome after HDCT/ASCT remain poorly studied. Here we screened 142 patients treated with HDCT/ASCT between 2002 and 2021 at Bern University Hospital for somatic gene mutations in ASXL1, DNMT3A, JAK2, TET2, and TP53. CH-associated somatic gene mutations were detected in 14/31 AML patients (45%), 13/64 myeloma patients (20%), and 9/47 lymphoma patients (19%). Clinical characteristics, treatment modalities, and responses to treatment were similar in patients with and without CH. Patients with CH-associated gene mutations had higher relapse rates and reduced progression free survival, most evident in lymphoma patients (p = 0.007). Overall survival tended to be shorter in lymphoma patients with CH-associated mutations (p = 0.078), whereas this was not observed in AML and myeloma patients. Survival in lymphoma patients with CH was inferior, which may have an impact on post-transplant surveillance strategies in the future. In contrast, survival outcomes were not associated significantly with CH in AML and myeloma patients in our study. Longer follow-ups and larger cohorts will be needed to validate our observations. Full article

The capability to generate induced pluripotent stem cells (iPSCs) from adult somatic cells, enabling them to differentiate into any cell type, has been demonstrated in several studies. In humans and mice, iPSCs have been shown to differentiate into primordial germ cells (PGCs), spermatozoa, and oocytes. However, research on iPSCs in deer is novel. Despite the necessity for establishing germplasm banks from endangered cervid species, the collection and cryopreservation of gametes and embryos have proven complex for this group. Therefore, the focus of this study was to establish protocols for deriving stable iPSC lines from Blastocerus dichotomus (Marsh deer) using primary cells derived from antler, adipose tissue, or skin, with the ultimate goal of producing viable gametes in the future. To achieve this, two main reprogramming approaches were tested: (1) transfection using PiggyBac transposons (plasmid PB-TET-MKOS) delivered via electroporation and (2) lentiviral transduction using the STEMCCA system with either human (hOSKM) or murine (mOSKM) reprogramming factors. Both systems utilized murine embryonic fibroblasts (MEFs) as feeder cells. The PiggyBac system was further supplemented with a culture medium containing small molecules to aid reprogramming, including a GSK inhibitor, MEK inhibitor, ALK/TGF inhibitor, and thiazovivin. Initial colony formation was observed; however, these colonies failed to expand post-selection. Despite these challenges, important insights were gained that will inform and guide future studies toward the successful generation of iPSCs in deer. Full article

Fetal exposure to antiseizure medications (ASMs) can impact organogenesis, resulting in elevated risk of congenital malformations. Despite longstanding clinical awareness of the teratogenic potential of ASMs, the molecular mechanisms remain largely unexplored. To address this multisystem impact of ASMs, an OMIC-based approach was considered to understand the impact of ASMs on methylome and subsequently on proteome and how folic acid (FA) supplementation can counter the teratogenic impact. The study employed an established in vitro embryonic cell line model system, treated with varying concentrations of first-generation ASMs, alone and in combination with FA. Integrated analyses included quantification of global DNA methylation, expression analysis of key epigenetic regulators (DNMTs and TETs), genome-wide methylation profiling using the 935K EPIC array, and LC-MS/MS-based proteomics analysis. The study identified that ASMs can induce global DNA hypomethylation, which was likely to be impacted by dysregulation of DNMT and TET expression. Interestingly, FA co-treatment partially restored DNA methylation as evidenced by global DNA methylation and epigenetic gene expression, and also by compensatory effect via one-carbon metabolism. Genome-wide DNA methylation revealed site-specific hypermethylation at key developmental genes, several of which were reversed with FA. Proteomics analysis identified downregulation of developmentally critical proteins, including those linked to key metabolic processes, while FA co-treatment reversed expression of several such proteins. Integrative methylome–proteome analysis revealed the coordinated regulation of target genes that are linked to congenital abnormalities. Together, these findings offer mechanistic insight into ASM-induced teratogenesis and support FA’s potential to mitigate epigenetic and proteomic disruptions. This integrated OMICs based approach identifies key biomarkers which can be used for therapeutic monitoring and help in optimizing maternal epilepsy management. Full article

Background: Robust evidence supports the role of tetrahydrobiopterin (BH4) metabolism in sustaining inflammation; however, the mechanisms underlying the persistent upregulation of the BH4 pathway remain incompletely understood. This study investigated the epigenetic regulation of BH4 metabolism following a single injection of lipopolysaccharide (LPS) in the mouse hippocampus. Methods: Male C57BL/6J mice received either saline or LPS (0.33 mg/kg, i.p.) and were sacrificed at 4 h or 24 h post injection. Behavioral assessments and analyses of hippocampal neurotransmitter metabolism, DNA methylation profile, oxidative stress, and inflammasome activation were performed. Neopterin levels, a marker of immune system activation, were measured in both the plasma and hippocampus. Results: LPS-treated mice exhibited sickness behavior, including reduced locomotor and exploratory activity at both 4 and 24 h. While exploratory behavior showed partial recovery by 24 h, locomotor activity remained impaired. Neopterin levels increased in both the plasma and hippocampus following LPS administration but returned to baseline in the hippocampus by 24 h. Despite the normalization of neopterin, a persistent pro-inflammatory state in the hippocampus was evident at 24 h, as shown by increased expression of Ikbkb and components of the NLRP3 inflammasome, along with elevated oxidative stress markers. Upregulation of Nrf-2 and Hmox1 suggested activation of a protective antioxidant response. Dopaminergic metabolism was disrupted, indicating impaired BH4-dependent dopamine turnover. Epigenetic analysis revealed increased expression of DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) and Tet2, along with reduced expression of Tet1 and Tet3. Promoter hypomethylation of Gch1 and Ptps was observed, correlating with increased hippocampal expression and potentially elevated BH4 levels. Conclusions: Together, these findings show that a single LPS challenge was sufficient to induce the activation of the BH4 synthesis pathway during the late acute inflammatory phase, both systemically and in the hippocampus, potentially driven by epigenetic modifications such as promoter hypomethylation. This may contribute to the perpetuation of neuroinflammation. Full article

Salmonella is a zoonotic foodborne pathogen that affects poultry health and reaches consumers through the food chain via contaminated products. A cross-sectional study was conducted to isolate and identify Salmonella and to detect antibiotic resistance genes in Salmonella isolates from retail meat shops in Chitwan, Nepal. The antimicrobial susceptibility test was carried out using the Kirby–Bauer disc diffusion method. Antibiotic resistance genes were detected by using multiplex polymerase chain reaction (PCR). A total of 216 samples, chicken meat (108) and water (108), were tested for the presence of Salmonella. Out of the 216 samples tested, 38 samples were positive, giving an overall prevalence of 17.59%. A higher prevalence of Salmonella was found in meat samples, 29.62% (32/108), compared with the water samples, 5.55% (6/108), which was statistically significant (p < 0.05). The antibiogram profile showed maximum resistance to doxycycline (88%), followed by tetracycline (86%), erythromycin (79%), ampicillin + sulbactam (76%), ceftriaxone (22%), levofloxacin (21%), gentamicin (18%), chloramphenicol (13%), and amikacin (15%). The prevalence of the tetB gene and ere(A) gene was 23.68% (9/38) and 18.42% (7/38), respectively, and the association was statistically non-significant (p > 0.05). However, mcr1, catA1, and blaTEM genes were not detected. The study recommends integrated surveillance encompassing human health, food safety, and animal health under the ‘One Health’ approach, highlighting the need for effective strategies involving poultry farms, retail meat shops, and consumers to minimize contamination and reduce the transmission of Salmonella along the food chain from primary production to consumption on a global scale. Full article

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation rate: 28.72%). Fourteen serotypes were identified, with S. Typhimurium (23.68%), S. Indiana (21.93%), S. Kentucky (18.42%), and S. Enteritidis (12.28%) being predominant. Most isolates showed high resistance to β-lactams, tetracyclines, quinolones, and sulfonamides, with extensive multidrug resistance (MDR) observed—especially in S. Indiana, S. Typhimurium, and S. Kentucky. Among the 23 detected resistance genes, tet(B) had the highest prevalence (75.44%), particularly in S. Indiana. Biofilm formation was observed in 99.12% of isolates, with 84.21% demonstrating moderate to strong capacity. Eighteen virulence genes were detected; S. Enteritidis carried more spvB/C, sipB, and sodC1, while S. Indiana had higher cdtB carriage. PFGE revealed substantial genetic diversity among strains. This comprehensive analysis highlights the high AMR and biofilm potential of duck-derived Salmonella in China, emphasizing the urgent need for enhanced surveillance and control measures to mitigate public health risks. Full article

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article

The perianal skin is a unique “skin–gut” boundary that serves as a critical hotspot for the exchange and evolution of antibiotic resistance genes (ARGs). However, its role in the dissemination of antimicrobial resistance (AMR) has often been underestimated. To characterize the resistance patterns in the perianal skin environment of patients with perianal diseases and to investigate the drivers of AMR in this niche, a total of 51 bacterial isolates were selected from a historical strain bank containing isolates originally collected from patients with perianal diseases. All the isolates originated from the skin site and were subjected to antimicrobial susceptibility testing, whole-genome sequencing, and co-occurrence network analysis. The analysis revealed a highly structured resistance pattern, dominated by two distinct modules: one representing a classic Staphylococcal resistance platform centered around mecA and the bla operon, and a broad-spectrum multidrug resistance module in Gram-negative bacteria centered around tet(A) and predominantly carried by IncFIB and other IncF family plasmids. Further analysis pinpointed IncFIB-type plasmids as potent vehicles driving the efficient dissemination of the latter resistance module. Moreover, numerous unexplained resistance phenotypes were observed in a subset of isolates, indicating the potential presence of emerging and uncharacterized AMR threats. These findings establish the perianal skin as a complex reservoir of multidrug resistance genes and a hub for mobile genetic element exchange, highlighting the necessity of enhanced surveillance and targeted interventions in this clinically important ecological niche. Full article

Contaminated poultry is one of the major sources of food-borne non-typhoidal Salmonella (NTS). The aim of this study was to evaluate the presence of Salmonella along the slaughter process in low- and high-throughput poultry abattoirs in South Africa and to determine their characteristics. Samples were collected from 500 chicken carcass rinsates at various processing stages in three abattoirs. Salmonella detection and identification was conducted in accordance with the ISO 6579 methodology. NTS serotyping was performed with serotype-specific PCRs. The Kirby–Bauer disk diffusion method was used to determine antimicrobial resistance in Salmonella. PCR was used to analyze thirteen antimicrobial genes and four virulence genes. Salmonella spp. was detected in 11.8% (59/500; CI: 9.5–15) of the samples tested. The predominant serovars were Salmonella Enteritidis (n = 21/59; 35.59%) and Salmonella Typhimurium (n = 35; 59.32%). Almost all Salmonella isolates were susceptible to all tested antimicrobials except three. Despite the low resistance to tetracyclines at the phenotypic level, approximately half of the strains carried tetA genes, which may be due to “silent” antimicrobial resistance genes. Diverse virulence genes were detected among the confirmed NTS serotypes. We found a predominance of S. Enteritidis and S. Typhimurium from chicken carcasses with diverse virulence and resistance genes. As we detected differences between the slaughterhouses, an in-depth study should be performed on the risk of Salmonella in low- and high-throughput abattoirs. The integrated monitoring and surveillance of NTS in poultry is warranted in South Africa to aid in the design of mitigation strategies. Full article