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18 pages, 1942 KiB  
Article
Surveillance and Characterization of Vancomycin-Resistant and Vancomycin-Variable Enterococci in a Hospital Setting
by Claudia Rotondo, Valentina Antonelli, Alberto Rossi, Silvia D’Arezzo, Marina Selleri, Michele Properzi, Silvia Turco, Giovanni Chillemi, Valentina Dimartino, Carolina Venditti, Sara Guerci, Paola Gallì, Carla Nisii, Alessia Arcangeli, Emanuela Caraffa, Stefania Cicalini and Carla Fontana
Antibiotics 2025, 14(8), 795; https://doi.org/10.3390/antibiotics14080795 - 4 Aug 2025
Abstract
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple [...] Read more.
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections. Full article
(This article belongs to the Special Issue Hospital-Associated Infectious Diseases and Antibiotic Therapy)
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22 pages, 11006 KiB  
Article
Supervised Machine-Based Learning and Computational Analysis to Reveal Unique Molecular Signatures Associated with Wound Healing and Fibrotic Outcomes to Lens Injury
by Catherine Lalman, Kylie R. Stabler, Yimin Yang and Janice L. Walker
Int. J. Mol. Sci. 2025, 26(15), 7422; https://doi.org/10.3390/ijms26157422 - 1 Aug 2025
Viewed by 134
Abstract
Posterior capsule opacification (PCO), a frequent complication of cataract surgery, arises from dysregulated wound healing and fibrotic transformation of residual lens epithelial cells. While transcriptomic and machine learning (ML) approaches have elucidated fibrosis-related pathways in other tissues, the molecular divergence between regenerative and [...] Read more.
Posterior capsule opacification (PCO), a frequent complication of cataract surgery, arises from dysregulated wound healing and fibrotic transformation of residual lens epithelial cells. While transcriptomic and machine learning (ML) approaches have elucidated fibrosis-related pathways in other tissues, the molecular divergence between regenerative and fibrotic outcomes in the lens remains unclear. Here, we used an ex vivo chick lens injury model to simulate post-surgical conditions, collecting RNA from lenses undergoing either regenerative wound healing or fibrosis between days 1–3 post-injury. Bulk RNA sequencing data were normalized, log-transformed, and subjected to univariate filtering prior to training LASSO, SVM, and RF ML models to identify discriminatory gene signatures. Each model was independently validated using a held-out test set. Distinct gene sets were identified, including fibrosis-associated genes (VGLL3, CEBPD, MXRA7, LMNA, gga-miR-143, RF00072) and wound-healing-associated genes (HS3ST2, ID1), with several achieving perfect classification. Gene Set Enrichment Analysis revealed divergent pathway activation, including extracellular matrix remodeling, DNA replication, and spliceosome associated with fibrosis. RT-PCR in independent explants confirmed key differential expression levels. These findings demonstrate the utility of supervised ML for discovering lens-specific fibrotic and regenerative gene features and nominate biomarkers for targeted intervention to mitigate PCO. Full article
(This article belongs to the Section Molecular Informatics)
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15 pages, 3534 KiB  
Article
Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt
by Ahmed M. Soliman, Hazem Ramadan, Toshi Shimamoto, Tetsuya Komatsu, Fumito Maruyama and Tadashi Shimamoto
Microorganisms 2025, 13(8), 1769; https://doi.org/10.3390/microorganisms13081769 - 29 Jul 2025
Viewed by 469
Abstract
This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The blaNDM-19 was identified by PCR screening and DNA sequencing. The [...] Read more.
This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The blaNDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes blaNDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (blaTEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding blaNDM-19 includes ISAba125-IS5-blaNDM-19-bleMBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of blaNDM and its related variants. To our knowledge, this is the first genomic report of a blaNDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article
(This article belongs to the Special Issue Gut Microbiota of Food Animal)
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16 pages, 1591 KiB  
Article
Molecular and Drug Resistance Characteristics of Haemophilus influenzae Carried by Pediatric Patients with Adenoid Hypertrophy
by Nan Xiao, Jia-Hao Qin, Xiu-Ying Zhao and Lin Liu
Microorganisms 2025, 13(8), 1764; https://doi.org/10.3390/microorganisms13081764 - 29 Jul 2025
Viewed by 217
Abstract
Purpose: The adenoid microbiota plays a key role in adenoid hypertrophy (AH). This study explored the molecular epidemiology and antimicrobial resistance of Haemophilus. Influenzae (H. influenzae) strains in pediatric AH patients. Methods: Retrospective analysis of pediatric AH patients undergoing endoscopic adenoidectomy. [...] Read more.
Purpose: The adenoid microbiota plays a key role in adenoid hypertrophy (AH). This study explored the molecular epidemiology and antimicrobial resistance of Haemophilus. Influenzae (H. influenzae) strains in pediatric AH patients. Methods: Retrospective analysis of pediatric AH patients undergoing endoscopic adenoidectomy. Adenoid tissue samples were cultured to screen for pathogens. H. influenzae strains were identified by 16S rRNA sequencing and serotyped via q-PCR. Multilocus sequence typing (MLST) and ftsI gene analysis were conducted using PubMLST. β-lactamase genes (blaTEM-1, blaROB-1) were detected by PCR, and antibiotic susceptibility testing (AST) was performed using the Etest method. For imipenem-resistant strains, the acrRAB efflux pump gene cluster and ompP2 porin gene were sequenced and compared with those of the wild-type strain Rd KW20. Results: Over 8 months, 56 non-duplicate H. influenzae strains were isolated from 386 patients. The detection rate was highest in children under 5 years (30.5%) compared to those aged 5–10 years (13.4%) and 10–15 years (8.7%). Of 49 sub-cultured strains, all were non-typeable H. influenzae (NTHi). MLST identified 22 sequence types (STs) and 13 clonal complexes (CCs), with CC11 (26.5%), CC3 (14.3%), and CC107 (14.3%) being predominant. Common STs included ST103 (22.4%), ST57 (10.2%), and ST107 (10.2%). Most strains belonged to the ftsI group III-like+ (57.1%). β-lactamase positivity was 98.0% (48/49), with blaTEM-1 (95.9%) and blaROB-1 (18.4%) detected. AST showed low susceptibility to ampicillin (10.2%), amoxicillin–clavulanate (34.7%), azithromycin (12.2%), and trimethoprim–sulfamethoxazole (14.3%). Among the β-lactamase-positive strains, 44/48 were β-lactamase-positive ampicillin-resistant (BLPAR); none were β-lactamase-negative ampicillin-resistant (BLNAR). Imipenem susceptibility was 91.8% (45/49). No carbapenemases were found in the imipenem-resistant strains, but mutations in acrRAB (88.12–94.94% identity) and ompP2 (77.10–82.94% identity) were observed. Conclusions: BLPAR NTHi strains of CC11 are major epidemic strains in pediatric AH. Imipenem resistance in H. influenzae likely results from porin mutations rather than carbapenemase activity. Enhanced surveillance of H. influenzae’s role in AH and its resistance patterns is warranted. Full article
(This article belongs to the Section Medical Microbiology)
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20 pages, 2552 KiB  
Article
Environmental Dispersion of Multiresistant Enterobacteriaceae in Aquatic Ecosystems in an Area of Spain with a High Density of Pig Farming
by Javier Díez de los Ríos, Noemí Párraga-Niño, María Navarro, Judit Serra-Pladevall, Anna Vilamala, Elisenda Arqué, María Baldà, Tamar Nerea Blanco, Luisa Pedro-Botet, Óscar Mascaró and Esteban Reynaga
Antibiotics 2025, 14(8), 753; https://doi.org/10.3390/antibiotics14080753 - 25 Jul 2025
Viewed by 298
Abstract
Background: This study aimed to (a) assess the prevalence of multidrug-resistant (MDR) Enterobacteriaceae in the waters of two rivers and wastewater treatment plants (WWTPs) in a region of Catalonia, Spain; (b) genetically characterize the MDR strains; and (c) compare extended-spectrum β-lactamase (ESBL)-producing [...] Read more.
Background: This study aimed to (a) assess the prevalence of multidrug-resistant (MDR) Enterobacteriaceae in the waters of two rivers and wastewater treatment plants (WWTPs) in a region of Catalonia, Spain; (b) genetically characterize the MDR strains; and (c) compare extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from environmental and human sources. Methods: A total of 62 samples were collected from the influent and effluent of 31 WWTPs and 29 river water samples from 11 sites. Simultaneously, 382 hospitalized patients were screened for MDR Enterobacteriaceae using rectal swabs. All isolates underwent antibiotic susceptibility testing and whole-genome sequencing. Results: MDR Enterobacteriaceae were detected in 48.4% of WWTP samples, with 18.5% ESBL-producing E. coli and 1.5% (one sample) OXA-48-producing K. pneumoniae in influents, and 12.8% ESBL-producing E. coli in effluents. In river waters, 5.6% of samples contained ESBL-producing E. coli and 1.4% (1 sample) contained VIM-producing Enterobacter cloacae complex strains. Among patients, 10.2% (39/382) carried MDR Gram-negative bacilli, of which 66.7% were ESBL-producing E. coli. In aquatic ecosystems E. coli ST131 (13.3%) and ST162 (13.3%) were the most common strains, while in humans the common were E. coli ST131 (33.3%), ST69 (11.1%) and ST410 (7.4%) in humans. The most frequent environmental antibiotic resistance genes (ARG) were blaCTX-M-15 (24%) and blaTEM-1B (20%), while the most common ARGs were blaTEM-1B (20.4%), blaCTX-M15 (18.4%) and blaCTX-M-27 (14.3%). IncF plasmids were predominant in environmental and human strains. Conclusions: ESBL-producing E. coli and carbapenemase-producing Enterobacteriaceae are present in aquatic environments in the region. Phylogenetic similarities between environmental and clinical strains suggest a possible similar origin. Further studies are necessary to clarify transmission routes and environmental impact. Full article
(This article belongs to the Special Issue A One Health Approach to Antimicrobial Resistance, 2nd Edition)
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16 pages, 1234 KiB  
Article
Genomic Insights of Emerging Multidrug-Resistant OXA-48-Producing ST135 Proteus mirabilis
by Angeliki Mavroidi, Elisavet Froukala, Nick Spanakis, Aikaterini Michelaki, Maria Orfanidou, Vasiliki Koumaki and Athanasios Tsakris
Antibiotics 2025, 14(8), 750; https://doi.org/10.3390/antibiotics14080750 - 25 Jul 2025
Viewed by 293
Abstract
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. [...] Read more.
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. Methods: Characterization of Pm GR-1 was performed by the Vitek® Compact and Mass Spectrometry systems, antimicrobial susceptibility testing, detection of beta-lactamases, multilocus-sequence typing (MLST), and whole-genome sequencing (WGS). In silico prediction of mobile genetic elements (MGEs), genomic islands (GIs), antimicrobial resistance genes (ARGs) and virulence factors (VFs), and phylogenetic, core-genome SNP and comparative genomics analyses were executed using bioinformatic tools. Results: Pm GR-1 was isolated from a urine sample of an outpatient in a Greek hospital. It exhibited a multidrug-resistant phenotype, being susceptible only to amikacin and ceftazidime/avibactam. It co-carried several beta-lactamase genes on the chromosome (blaOXA-48, blaCTX-M-14, blaTEM-1) and a plasmid (blaTEM-2) and several other ARGs, but also mutations associated with quinolone resistance in the DNA gyrase and topoisomerase IV subunits. It belonged to the international clone ST135 that has also been detected among OXA-48-producing P. mirabilis strains from Germany and the USA. Pm GR-1 was genetically related to those from Germany, sharing highly similar MGEs, GIs, ARGs and VFs, including the chromosomal blaOXA-48 genetic structure, the O-antigen locus, the flagella locus, the MR/P fimbriae operon, and the urease gene cluster. Conclusions: To our knowledge, this is the first report from Greece of a blaOXA-48-possessing P. mirabilis strain. The emergence of blaOXA-48 among P. mirabilis strains of the international clone ST135 in different geographical regions is worrying. Close monitoring of these strains is required in One Health settings. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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24 pages, 9486 KiB  
Article
StMAPKK1 Enhances Thermotolerance in Potato (Solanum tuberosum L.) by Enhancing Antioxidant Defense and Photosynthetic Efficiency Under Heat Stress
by Xi Zhu, Yasir Majeed, Kaitong Wang, Xiaoqin Duan, Nengkang Guan, Junfu Luo, Haifei Zheng, Huafen Zou, Hui Jin, Zhuo Chen and Yu Zhang
Plants 2025, 14(15), 2289; https://doi.org/10.3390/plants14152289 - 24 Jul 2025
Viewed by 297
Abstract
The functional role of MAPKK genes in potato (Solanum tuberosum L.) under high-temperature stress remains unexplored, despite their critical importance in stress signaling and yield protection. We characterized StMAPKK1, a novel group D MAPKK localized to plasma membrane/cytoplasm. Quantitative real-time polymerase chain [...] Read more.
The functional role of MAPKK genes in potato (Solanum tuberosum L.) under high-temperature stress remains unexplored, despite their critical importance in stress signaling and yield protection. We characterized StMAPKK1, a novel group D MAPKK localized to plasma membrane/cytoplasm. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed cultivar-specific upregulation in potato (‘Atlantic’ and ‘Desiree’) leaves under heat stress (25 °C, 30 °C, and 35 °C). Transgenic lines overexpressing (OE) StMAPKK1 exhibited elevated antioxidant enzyme activity, including ascorbate peroxidase (APX), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), mitigating oxidative damage. Increased proline and chlorophyll accumulation and reduced oxidative stress markers, hydrogen peroxide (H2O2) and malondialdehyde (MDA), indicate improved cellular redox homeostasis. The upregulation of key antioxidant and heat stress-responsive genes (StAPX, StCAT1/2, StPOD12/47, StFeSOD2/3, StMnSOD, StCuZnSOD1/2, StHSFA3 and StHSP20/70/90) strengthened the enzymatic defense system, enhanced thermotolerance, and improved photosynthetic efficiency, with significant improvements in net photosynthetic rate (Pn), transpiration rate (E), and stomatal conductance (Gs) under heat stress (35 °C) in StMAPKK1-OE plants. Superior growth and biomass (plant height, plant and its root fresh and dry weights, and tuber yield) accumulation, confirming the positive role of StMAPKK1 in thermotolerance. Conversely, RNA interference (RNAi)-mediated suppression of StMAPKK1 led to a reduction in enzymatic activity, proline content, and chlorophyll levels, exacerbating oxidative stress. Downregulation of antioxidant-related genes impaired ROS scavenging capacity and declines in photosynthetic efficiency, growth, and biomass, accompanied by elevated H2O2 and MDA accumulation, highlighting the essential role of StMAPKK1 in heat stress adaptation. These findings highlight StMAPKK1’s potential as a key genetic target for breeding heat-tolerant potato varieties, offering a foundation for improving crop resilience in warming climates. Full article
(This article belongs to the Special Issue Cell Physiology and Stress Adaptation of Crops)
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39 pages, 1137 KiB  
Review
Spatial Transcriptomics Decodes Breast Cancer Microenvironment Heterogeneity: From Multidimensional Dynamic Profiling to Precision Therapy Blueprint Construction
by Aolong Ma, Lingyan Xiang, Jingping Yuan, Qianwen Wang, Lina Zhao and Honglin Yan
Biomolecules 2025, 15(8), 1067; https://doi.org/10.3390/biom15081067 - 24 Jul 2025
Viewed by 578
Abstract
Background: Breast cancer, the most prevalent malignancy among women worldwide, exhibits significant heterogeneity, particularly in the tumor microenvironment (TME), which poses challenges for treatment. Spatial transcriptomics (ST) has emerged as a transformative technology, enabling gene expression analysis while preserving tissue spatial architecture. This [...] Read more.
Background: Breast cancer, the most prevalent malignancy among women worldwide, exhibits significant heterogeneity, particularly in the tumor microenvironment (TME), which poses challenges for treatment. Spatial transcriptomics (ST) has emerged as a transformative technology, enabling gene expression analysis while preserving tissue spatial architecture. This provides unprecedented insights into tumor heterogeneity, cellular interactions, and disease mechanisms, offering a powerful tool for advancing breast cancer research and therapy. This review aims to synthesize the applications of ST in breast cancer research, focusing on its role in decoding tumor heterogeneity, characterizing the TME, elucidating progression and metastasis dynamics, and predicting therapeutic responses. We also explore how ST can bridge molecular profiling with clinical translation to enhance precision therapy. The key scientific concepts of review included the following: We summarize the technological advancements in ST, including imaging-based and sequencing-based methods, and their applications in breast cancer. Key findings highlight how ST resolves spatial heterogeneity across molecular subtypes and histological variants. ST reveals the dynamic interplay between tumor cells, immune cells, and stromal components, uncovering mechanisms of immune evasion, metabolic reprogramming, and therapeutic resistance. Additionally, ST identifies spatial prognostic markers and predicts responses to chemotherapy, targeted therapy, and immunotherapy. We propose that ST serves as a hub for integrating multi-omics data, offering a roadmap for precision oncology and personalized treatment strategies in breast cancer. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Breast Cancer)
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20 pages, 6555 KiB  
Article
Construction of a Genetic Prognostic Model in the Glioblastoma Tumor Microenvironment
by Wenhui Wu, Wenhao Liu, Zhonghua Liu and Xin Li
Genes 2025, 16(8), 861; https://doi.org/10.3390/genes16080861 - 24 Jul 2025
Viewed by 295
Abstract
Background: Glioblastoma (GBM) is one of the most challenging malignancies in all of neoplasms. These malignancies are associated with unfavorable clinical outcomes and significantly compromised patient wellbeing. The immunological landscape within the tumor microenvironment (TME) plays a critical role in determining GBM prognosis. [...] Read more.
Background: Glioblastoma (GBM) is one of the most challenging malignancies in all of neoplasms. These malignancies are associated with unfavorable clinical outcomes and significantly compromised patient wellbeing. The immunological landscape within the tumor microenvironment (TME) plays a critical role in determining GBM prognosis. By mining data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and correlating them with immune responses in the TME, genes associated with the immune microenvironment with potential prognostic value were obtained. Method: We selected GSE16011 as the training set. Gene expression profiles were substrates scored by both ESTIMATE and xCell, and immune cell subpopulations in GBM were analyzed by CIBERSORT. Gene expression profiles associated with low immune scores were performed by lasso regression, Cox analysis and random forest (RF) to identify a prognostic model for the multiple genes associated with immune infiltration in GBM. Then we constructed a nomogram to optimize the prognostic model using GSE7696 and TCGA-GBM as validation sets and evaluated these data for gene mutation and gene enrichment analysis. Result: The prognostic correlation between the six genes (MEOX2, PHYHIP, RBBP8, ST18, TCF12, and THRB) and GBM was finally found by lasso regression, Cox regression, and RF, and the online database obtained that all six genes were differentially expressed in GBM. Therefore, a prognostic correlation model was constructed based on the six genes. Kaplan–Meier (KM) survival analysis showed that this prognostic model had excellent prognostic ability. Conclusions: Prognostic models based on tumor microenvironment and immune score stratification and the construction of related genes have potential applications for prognostic analysis of GBM patients. Full article
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19 pages, 2677 KiB  
Article
Role of StAR Gene in Sex Steroid Hormone Regulation and Gonadal Development in Ark Shell Scapharca broughtonii
by Wenjing Wang, Zhihong Liu, Huaying Zhang, Zheying Gao, Sudong Xia, Xiujun Sun, Liqing Zhou, Zhuanzhuan Li, Peizhen Ma and Biao Wu
Biology 2025, 14(8), 925; https://doi.org/10.3390/biology14080925 - 23 Jul 2025
Viewed by 427
Abstract
This study elucidates the role of the steroidogenic acute regulatory protein (StAR) in sex steroid hormone dynamics and the gonadal development of the commercially important marine bivalve ark shell Scapharca broughtonii. The sequence of the StAR gene was obtained and [...] Read more.
This study elucidates the role of the steroidogenic acute regulatory protein (StAR) in sex steroid hormone dynamics and the gonadal development of the commercially important marine bivalve ark shell Scapharca broughtonii. The sequence of the StAR gene was obtained and verified from the transcriptome of ark shell, then the tissue localization and expression pattern during the gonad development of the StAR gene were detected by in situ hybridization and quantitative real-time PCR, respectively. Additionally, the concentrations of three critical sex steroid hormones (progesterone, testosterone, and estradiol) were measured throughout gonadal development using enzyme-linked immunosorbent assay (ELISA). The results showed that the length of the coding region of StAR was 1446 bp, encoding 481 amino acids. The results of qRT-PCR showed that the expression of the StAR gene varied with gonadal development, increased from the early active stage to the development stage, and decreased from the mature stage to the spent stage. Notably, the expression level in ovaries was higher than that in testes, suggesting the potential involvement of StAR in sex differentiation and gonadal development. Additionally, the results indicated that progesterone, testosterone, and estradiol accounted for 80%, 10%, and 10% of the total hormone content in the gonads, respectively. Correlation analysis revealed a highly significant strong positive correlation between progesterone/estradiol levels and StAR gene expression, demonstrating that StAR serves as a key regulator in sex steroid hormone biosynthesis. These findings provide crucial molecular evidence for StAR-mediated steroidogenesis in bivalve reproduction, offering fundamental insights into invertebrate endocrinology. Full article
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15 pages, 3311 KiB  
Article
Induction of Triploid Grass Carp (Ctenopharyngodon idella) and Changes in Embryonic Transcriptome
by Zixuan E, Han Wen, Yingshi Tang, Mingqing Zhang, Yaorong Wang, Shujia Liao, Kejun Chen, Danqi Lu, Haoran Lin, Wen Huang, Xiaoying Chen, Yong Zhang and Shuisheng Li
Animals 2025, 15(15), 2165; https://doi.org/10.3390/ani15152165 - 22 Jul 2025
Viewed by 295
Abstract
Grass carp is an economically important cultured species in China. Triploid embryo production is widely applied in aquaculture to achieve reproductive sterility, improve somatic growth, and reduce ecological risks associated with uncontrolled breeding. In this study, a simple cold shock method for inducing [...] Read more.
Grass carp is an economically important cultured species in China. Triploid embryo production is widely applied in aquaculture to achieve reproductive sterility, improve somatic growth, and reduce ecological risks associated with uncontrolled breeding. In this study, a simple cold shock method for inducing triploid grass carp was developed. The triploid induction rate of 71.73 ± 5.00% was achieved by applying a cold treatment at 4 °C for 12 min, starting 2 min after artificial fertilization. Flow cytometry and karyotype analysis revealed that triploid individuals exhibited a 1.5-fold increase in DNA content compared to diploid counterparts, with a chromosomal composition of 3n = 72 (33m + 36sm + 3st). Additionally, embryonic transcriptome analysis demonstrated that, in the cold shock-induced embryos, genes associated with abnormal mesoderm and dorsal–ventral axis formation, zygotic genome activation (ZGA), and anti-apoptosis were downregulated, whereas pro-apoptotic genes were upregulated, which may contribute to the higher abnormal mortality observed during embryonic development. Overall, this study demonstrates optimized conditions for inducing triploidy in grass carp via cold shock and provides insights into the transcriptomic changes that take place in cold shock-induced embryos, which could inform future grass carp genetic breeding programs. Full article
(This article belongs to the Section Aquatic Animals)
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7 pages, 186 KiB  
Case Report
Spontaneous Improvement of Hypogonadotropic Hypogonadism in a Patient with PCSK1 and HS6ST1 Mutations: A Case Report
by Alanna Asgeirsson, Eujean Park, Vinicius Seidel, Mathew Shedd, Matheni Sathananthan, Tania Arous, Kevin Codorniz, Silvana Giannelli, Justin Do, Wyut Yi Thin, Arsenije Jelovac and Scott Lee
Life 2025, 15(7), 1151; https://doi.org/10.3390/life15071151 - 21 Jul 2025
Viewed by 264
Abstract
Kallmann syndrome (KS) is a form of hypogonadotropic hypogonadism (HH) characterized by gonadotropin-releasing hormone (GnRH) deficiency and anosmia due to defective neuronal migration. While traditionally considered irreversible, cases of spontaneous improvement of HH have been reported, suggesting residual GnRH neuronal function in some [...] Read more.
Kallmann syndrome (KS) is a form of hypogonadotropic hypogonadism (HH) characterized by gonadotropin-releasing hormone (GnRH) deficiency and anosmia due to defective neuronal migration. While traditionally considered irreversible, cases of spontaneous improvement of HH have been reported, suggesting residual GnRH neuronal function in some individuals. We present a case of a 29-year-old man with KS who exhibited spontaneous recovery of endogenous testosterone production following the cessation of long-term androgen therapy without the use of alternative hormonal agents. After ceasing testosterone therapy for several months, the patient’s total testosterone levels normalized (407–424 ng/dL), accompanied by increased secondary sexual characteristics, stable gonadotropin levels, and normal testicular volume. Persistent anosmia was noted, suggesting that restoration of reproductive endocrine function can occur independently of olfactory recovery. Genetic testing identified heterozygous mutations in PCSK1 and HS6ST1, genes implicated in GnRH regulation and KS pathogenesis. This case highlights the potential role of genetic variation in spontaneous HH improvement and underscores the need for individualized management strategies, including periodic reassessment of gonadal function and fertility potential. Further research is needed to elucidate the mechanisms driving spontaneous HH improvement, identify predictive biomarkers of reversibility, and explore therapeutic strategies that may promote endogenous GnRH activity in select patients with KS. Full article
(This article belongs to the Section Medical Research)
16 pages, 2268 KiB  
Article
Epichloë Endophyte Alters Bacterial Nitrogen-Cycling Gene Abundance in the Rhizosphere Soil of Perennial Ryegrass
by Munire Maimaitiyiming, Yanxiang Huang, Letian Jia, Mofan Wu and Zhenjiang Chen
Biology 2025, 14(7), 879; https://doi.org/10.3390/biology14070879 - 18 Jul 2025
Viewed by 254
Abstract
Perennial ryegrass (Lolium perenne), an important forage and turfgrass species, can establish a mutualistic symbiosis with the fungal endophyte Epichloë festucae var. lolii. Although the physiological and ecological impacts of endophyte infection on ryegrass have been extensively investigated, the response of [...] Read more.
Perennial ryegrass (Lolium perenne), an important forage and turfgrass species, can establish a mutualistic symbiosis with the fungal endophyte Epichloë festucae var. lolii. Although the physiological and ecological impacts of endophyte infection on ryegrass have been extensively investigated, the response of the soil microbial community and nitrogen-cycling gene to this relationship has received much less attention. The present study emphasized abundance and diversity variation in the AOB-amoA, nirK and nosZ functional genes in the rhizosphere soil of the endophyte–ryegrass symbiosis following litter addition. We sampled four times: at T0 (prior to first litter addition), T1 (post 120 d of 1st litter addition), T2 (post 120 d of 2nd litter addition) and T3 (post 120 d of 3rd litter addition) times. Real-time fluorescence quantitative PCR (qPCR) and PCR amplification and sequencing were used to characterize the abundance and diversity of the AOB-amoA, nirK and nosZ genes in rhizosphere soils of endophyte-infected (E+) plants and endophyte-free (E−) plants. A significant enhancement of total Phosphorus (P), Soil Organic Carbon (SOC), Ammonium ion (NH4+) and Nitrate ion (NO3) contents in the rhizosphere soil was recorded in endophyte-infected plants at different sampling times compared to endophyte-free plants (p ≤ 0.05). The absolute abundance of the AOB-amoA gene at T0 and T1 times was higher, as was the absolute abundance of the nosZ gene at T0, T1 and T3 times in the E+ plant rhizophere soils relative to E− plant rhizosphere soils. A significant change in relative abundance of the AOB-amoA and nosZ genes in the host rhizophere soils of endophyte-infected plants at T1 and T3 times was observed. The experiment failed to show any significant alteration in abundance and diversity of the nirK gene, and diversity of the AOB-amoA and nosZ genes. Analysis of the abundance and diversity of the nirK gene indicated that changes in soil properties accounted for approximately 70.38% of the variation along the first axis and 16.69% along the second axis, and soil NH4+ (p = 0.002, 50.4%) and soil C/P ratio (p = 0.012, 15.8%) had a strong effect. The changes in community abundance and diversity of the AOB-amoA and nosZ genes were mainly related to soil pH, N/P ratio and NH4+ content. The results demonstrate that the existence of tripartite interactions among the foliar endophyte E. festucae var. Lolii, L. perenne and soil nitrogen-cycling gene has important implications for reducing soil losses on N. Full article
(This article belongs to the Collection Plant Growth-Promoting Bacteria: Mechanisms and Applications)
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20 pages, 489 KiB  
Article
Genomic Analysis of Antibiotic Resistance and Virulence Profiles in Escherichia coli Linked to Sternal Bursitis in Chickens: A One Health Perspective
by Jessica Ribeiro, Vanessa Silva, Catarina Freitas, Pedro Pinto, Madalena Vieira-Pinto, Rita Batista, Alexandra Nunes, João Paulo Gomes, José Eduardo Pereira, Gilberto Igrejas, Lillian Barros, Sandrina A. Heleno, Filipa S. Reis and Patrícia Poeta
Vet. Sci. 2025, 12(7), 675; https://doi.org/10.3390/vetsci12070675 - 17 Jul 2025
Viewed by 404
Abstract
Sternal bursitis is an underexplored lesion in poultry, often overlooked in microbiological diagnostics. In this study, we characterized 36 Escherichia coli isolates recovered from sternal bursitis in broiler chickens, combining phenotypic antimicrobial susceptibility testing, PCR-based screening, and whole genome sequencing (WGS). The genetic [...] Read more.
Sternal bursitis is an underexplored lesion in poultry, often overlooked in microbiological diagnostics. In this study, we characterized 36 Escherichia coli isolates recovered from sternal bursitis in broiler chickens, combining phenotypic antimicrobial susceptibility testing, PCR-based screening, and whole genome sequencing (WGS). The genetic analysis revealed a diverse population spanning 15 sequence types, including ST155, ST201, and ST58. Resistance to tetracycline and ciprofloxacin was common, and several isolates carried genes encoding β-lactamases, including blaTEM-1B. Chromosomal mutations associated with quinolone and fosfomycin resistance (e.g., gyrA p.S83L, glpT_E448K) were also identified. WGS revealed a high number of virulence-associated genes per isolate (58–96), notably those linked to adhesion (fim, ecp clusters), secretion systems (T6SS), and iron acquisition (ent, fep, fes), suggesting strong pathogenic potential. Many isolates harbored virulence markers typical of ExPEC/APEC, such as iss, ompT, and traT, even in the absence of multidrug resistance. Our findings suggest that E. coli from sternal bursitis may act as reservoirs of resistance and virulence traits relevant to animal and public health. This highlights the need for including such lesions in genomic surveillance programs and reinforces the importance of integrated One Health approaches. Full article
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15 pages, 1907 KiB  
Article
Plasma Soluble ST2 as a Prognostic Biomarker for Cardiovascular Events and Mortality in COVID-19 Patients
by Yongcui Yan, Yan Zhuang, Huihui Li and Dao Wen Wang
J. Cardiovasc. Dev. Dis. 2025, 12(7), 273; https://doi.org/10.3390/jcdd12070273 - 17 Jul 2025
Viewed by 329
Abstract
Background: Coronavirus disease 2019 (COVID-19) is frequently complicated by cardiovascular involvement. Soluble growth stimulation-expressed gene 2 (sST2) is a promising cardiovascular biomarker, but its prognostic value in COVID-19 remains unclear. Methods: This retrospective cohort study included 314 hospitalized COVID-19 patients classified into mild/moderate [...] Read more.
Background: Coronavirus disease 2019 (COVID-19) is frequently complicated by cardiovascular involvement. Soluble growth stimulation-expressed gene 2 (sST2) is a promising cardiovascular biomarker, but its prognostic value in COVID-19 remains unclear. Methods: This retrospective cohort study included 314 hospitalized COVID-19 patients classified into mild/moderate (n = 168) and severe/critical (n = 146). Plasma sST2 were measured using an enzyme-linked immunosorbent assay. Correlation analyses evaluated associations between sST2 and clinical parameters. Cox regression assessed the independent predictive value for cardiovascular events and all-cause mortality. Results: sST2 levels were significantly higher in severe/critical patients (16.877 ng/mL) than in mild/moderate cases (6.189 ng/mL) and healthy controls (4.003 ng/mL). sST2 positively correlated with cardiac injury markers (cTnI, CK-Mb, NT-proBNP), inflammatory indices (IL-1β, hsCRP), D-dimer, and inversely correlated with a left ventricular ejection fraction (r = −0.86). Elevated sST2 independently predicted cardiovascular events (HR = 2.972) and mortality (HR = 4.681). The Kaplan–Meier survival analysis demonstrated higher cardiovascular event rates and lower survival probabilities in patients with elevated sST2. The ROC curve indicated sST2 outperformed cTnI and NT-proBNP in predicting cardiovascular events (AUC = 0.898) and mortality (AUC = 0.871). Conclusion: Elevated sST2 is associated with myocardial injury, inflammation, and poor prognosis in COVID-19, supporting its value for risk stratification. Full article
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