Search Results (2,145)

Staphylococcus species are saprophytic, opportunistic, and nosocomial pathogens that frequently co-infect with other microorganisms, causing severe infections in birds. Some of the notable examples include bacterial chondronecrosis with osteomyelitis (BCO), cellulitis, dermatitis, and systemic infections. Understanding of how Staphylococcus spp. cause infections evading the host immune system is crucial for helping farmers and veterinarians develop long-term solutions for poultry production system management. The aim of this review is to broaden the understanding of Staphylococcus spp. epidemiology, virulence, genomic adaptability and coinfection patterns. The peer-reviewed articles were obtained from various databases, including Google Scholar, Web of Science, and PubMed. The review primarily focused on papers published between 1999 and 2025. The review presents an opportunity to identify research gaps and apply this knowledge to develop innovative approaches to address staphylococcal infections in broiler chickens. Additionally, BCO is often attributed to coinfection with Staphylococcus species and other pathogens. Full article

Staphylococcus aureus has been recognized as an important foodborne pathogen and methicillin-resistant S. aureus (MRSA) can cause fatal infections worldwide. Of great concern is that MRSA have been found in animals and non-healthcare settings; however, knowledge about the prevalence and genetic characteristics of S. aureus, especially MRSA from animals, retail meats and market shared shopping vehicles in the same district, is limited. In this study, we collected 423 samples including handrail swabs (n = 226) of shopping trolleys and baskets from 18 supermarkets, retail meats (n = 137) and swine nasal swabs (n = 60) between 2018 and 2020 in China. S. aureus isolates were isolated and identified by PCR, and then the mecA was used to confirm the MRSA. The antibiotic resistance and virulence genes among S. aureus were also analyzed, followed by whole genome sequencing (WGS). S. aureus isolates were widely distributed in shared shopping vehicles (8.0%, 18/226), retail meats (14.6%, 20/137) and swine (18.3%, 11/60). In total, 49 S. aureus were obtained and 20 of the 49 isolates were MRSA. We firstly reported a high prevalence of MRSA in shared shopping vehicles (7.5%, 17/226), followed by raw meats (2.2%, 3/137), and 44.4% (8/18) of the 18 supermarkets possessed MRSA-positive shopping vehicles. All 20 MRSA isolates were SCCmec IVa MRSA clones. Enterotoxin genes (sea/seb) associated with S. aureus food poisoning were present in 45.0% of the 20 S. aureus isolates from retail meats and 25.0% of the 20 MRSA isolates carried enterotoxin genes. Retail meats in this study carried ST6-MRSA, a common ST type of S. aureus from food-poisoning outbreaks in China. WGS showed that the MRSA from meats harbored enterotoxin gene sea and immune evasion genes (sak and scn) associated with human infections, and were clustered with previously reported MRSA isolates from animals and humans. The MRSA isolates carrying multiple virulence genes from shopping vehicles were also clustered with previously reported MRSA isolates from humans and animals, suggesting that the exchange of MRSA isolates might occur among different niches. Our results highlighted the risk of retail meats and shared shopping vehicles in spreading antimicrobial-resistant pathogens including MRSA. To our knowledge, this is the first report of the wide spread of MRSA in shared shopping vehicles in China. Full article

Background: Tracheobronchopathia osteochondroplastica (TO) is a rare benign disorder characterized by submucosal cartilaginous and osseous nodules of the tracheobronchial tree, typically sparing the posterior membranous wall. Involvement of the vocal cords is exceedingly rare and may result in critical airway obstruction. The underlying genetic and molecular mechanisms of TO remain largely unexplored. Case presentation: We report a rare case of TO extending from the vocal cords to the bronchi in a 76-year-old man who initially presented with pneumonia and later developed acute respiratory failure due to severe airway narrowing, necessitating emergency tracheostomy. Bronchoscopy and computed tomography revealed diffuse calcified nodules involving the anterior and lateral airway walls, including the subglottic region. Histopathology demonstrated chronic inflammatory cell infiltration with squamous metaplasia. To explore the molecular basis of this condition, whole-genome sequencing (WGS) was performed using peripheral blood samples—the first such application in TO. WGS identified 766 germline mutations (including 27 high-impact variants) and 66 structural variations. Candidate genes were implicated in coagulation and inflammation (KNG1), arachidonic acid metabolism and extracellular matrix remodeling (PLA2G4D), ciliary dysfunction and mineralization (TMEM67), vascular calcification (CDKN2B-AS1), smooth muscle function (MYLK4), abnormal calcification (TRPV2, SPRY2, BAZ1B), fibrotic signaling (AHNAK2), and mucosal barrier integrity (MUC12/MUC19). Notably, despite systemic germline mutations, calcification was restricted to the airway. Conclusions: This case highlights that TO with vocal cord involvement can progress beyond a benign course to cause life-threatening airway obstruction. Integrating clinical, histological, and genomic findings, we propose a novel pathophysiological model in which systemic genetic susceptibility interacts with local immune cell infiltration and fibroblast-driven extracellular matrix remodeling, resulting in airway-restricted dystrophic calcification. This first genomic characterization of TO provides new insights into its pathogenesis and suggests that multi-omics approaches may enable future precision medicine strategies for this rare airway disease. Full article

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of diseases originating from hematopoietic stem cell transformation, characterized by the clonal proliferation of hematopoietic progenitors. A specific subset includes myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase (TK) gene fusions, particularly involving PDGFR A or B, which are sensitive to TK inhibitor treatment. We report a case of a 21-year-old patient with a myeloproliferative/myelodysplastic neoplasm, presenting with hyperleukocytosis, anemia, thrombocytopenia, and elevated LDH. The peripheral blood smear showed hypogranular neutrophils, eosinophils, basophils, and myeloid precursors. The absence of BCR::ABL1 and mutations in JAK2, CALR, and MPL excluded common MPNs. Cytogenetic analysis revealed a rearrangement between chromosomes 5 and 14. FISH analysis confirmed an inverted insertion from chromosome 5 to chromosome 14, involving the PDGFRB gene. WGS and RNAseq identified a fusion between PDGFRB and CCDC88C, causing the constitutive activation of PDGFRB. The fusion gene was confirmed by sequencing. This allowed for targeted therapy with a tyrosine kinase inhibitor (TKI), leading to molecular remission monitored by RT-qPCR. This case highlights how a multidisciplinary approach can identify atypical transcripts in MPN, guiding targeted therapy with TK inhibitors, thus resulting in effective treatment and molecular remission. Full article

The Yan goose (YE, Anser cygnoides) is a valuable indigenous poultry genetic resource, renowned for its superior meat quality and environmental adaptability. Despite its economic importance, the genetic basis underlying these adaptive traits remains unclear. In this study, we employed whole-genome resequencing (WGS) to perform high-throughput sequencing on a conserved population of 15 samples. Bioinformatic analyses were conducted to systematically evaluate the population’s genetic structure, and a genome-wide scan for selection signals related to economically significant traits was performed using the integrated haplotype score (iHS) method. An average of 4.43 million high-quality SNPs were identified, which were predominantly located in intergenic and intronic regions. Population structure analysis revealed a close genetic relationship within the conserved population of YE, with no significant lineage stratification observed. Pairwise sequentially Markovian coalescent (PSMC) analysis indicated that the YE underwent a severe genetic bottleneck during the Last Glacial Maximum (LGM), followed by gradual population recovery in the early Neolithic period. Genome-wide selection signal scanning identified multiple genomic regions under strong selection, annotating key genes associated with growth and development (e.g., GHRL, AKT1, and MAPK3), lipid deposition (e.g., PLPP4, SAMD8, and LPIN1), and disease resistance and stress resilience (e.g., TP53, STAT3). Functional enrichment analysis revealed significant enrichment of these genes in pathways related to glycerophospholipid metabolism (p < 0.01), purine metabolism (p < 0.01), and immune response (p < 0.01). This study not only provides a theoretical foundation for the scientific conservation of the YE germplasm resources but also offers valuable genomic resources for identifying functional genes underlying important economic traits and advancing molecular breeding strategies. Full article

This is the first WGS study of the hawksbill sea turtle (Eretmochelys imbricata) from the Persian Gulf. Sequencing of 17 individuals from four nesting islands in the southern part of Iran’s coastline revealed population-level genetic differentiation with consistently low rates of nucleic diversity and differentiated demographic footprints in sampling populations in the Persian Gulf. In a population structure analysis, four populations were discovered; Shidvar had long-term isolation and Nakhiloo demonstrated admixture and higher heterogeneity. ROH and LD profiles are consistent with past bottlenecks, rather than recent inbreeding, and reflect each island’s demographic history. The observed fine-scale genomic divergence (e.g., even between sites in close proximity, such as Ommolgorm and Nakhiloo) suggests that natal homing and local environmental selection are meaningful drivers of genetic differentiation, and that specific conservation strategies should be implemented at each site. Full article

In this study, the synergistic effects of dietary Bacillus velezensis AAHM-BV2301, silica nanoparticles (SiNPs), and chitosan (CS) on the growth performance, innate immunity, gut microbiota, and disease resistance of Asian seabass (Lates calcarifer) fingerlings were evaluated. A total of 400 fish (11.25 ± 2.12 g) were assigned to five dietary treatments for 30 days: control, BV (1 × 10⁸ CFU/kg feed), BVSiNP (1 × 10⁸ CFU/kg + 2 mg SiNP/kg), BVCS (1 × 10⁸ CFU/kg + 15 g CS/kg), and BVSiNPCS (combined additives at the same concentrations). The growth indices (WG, SGR, RGR, and FCR) significantly increased in the fish fed BVSiNPs, whereas the level of innate immunity increased across all the supplemented groups, with BVCS and BVSiNPCS having the strongest respiratory burst and lysozyme activities. The tissue-specific modulation of immune-related genes (α2M, HSP70, Mx, and C3) was most pronounced in BVSiNP-fed fish, particularly in the gills and liver. Gut microbiome profiling revealed enrichment of Cetobacterium somerae in response to BV-based treatments, whereas BVSiNPCS induced the greatest increase in microbial richness and network connectivity. Postchallenge survival against Vibrio vulnificus was significantly greater in the BV and BVSiNP groups (p < 0.05). Overall, SiNPs acted as functional enhancers of the B. velezensis probiotic, supporting improved growth, immune activation, and microbiota restructuring. These results highlight the potential of nanoparticle-integrated synbiotics for microbiome-targeted health management in aquaculture. Full article

Enterotoxigenic Escherichia coli (ETEC)-induced neonatal calf diarrhea (NCD) causes significant economic losses to the cattle industry; therefore, understanding its antibiotic resistance is crucial for developing targeted prevention and treatment strategies. However, reports on antibiotic resistance in bovine ETEC are currently limited. This study conducted whole-genome sequencing (WGS) and antimicrobial susceptibility testing on ETEC F5- and F5-F41-positive strains isolated from neonatal calf diarrhea samples in Inner Mongolia, China. The results showed that both ETEC F5- and ETEC F5-F41-positive strains are multidrug-resistant, containing ceftriaxone (CRO), ceftazidime (CAZ)) and ciprofloxacin (CIP), which are listed as the highest priority critically important antimicrobial (HP-CIAs) by the World Health Organization (WHO). Combined analysis using the Comprehensive Antibiotic Resistance Database (CARD) and ResFinder 4.1 predictive analysis revealed that the chromosomes and plasmids of the 2 ETEC-positive strains contained 11 classes of antibiotic resistance genes, with the top 3 categories in terms of the number of resistance genes being aminoglycosides, β-lactamases, and chloramphenicols. In addition, various bacterial efflux pumps, including RND, MFS, SMR, and the ABC efflux pump family, were detected. A total of 74 antimicrobial resistance genes were identified in the 2 strains, belonging to 5 categories of drug resistance mechanisms; the antimicrobial resistance phenotype was consistent with the genotype. This study provides a reference for the prevention and treatment of diarrhea caused by ETEC. Full article

This study aimed to produce the hydrolysates of Xuanwei ham bone using enzymatic hydrolysis assisted by microwave and ultrasound pretreatment. A back propagation artificial neural network (BP-ANN) model was utilized to predict the optimal conditions, which involved 15 W/g bone for 15 min of ultrasound pretreatment and 5 W/g bone for 30 min of microwave pretreatment, achieving the highest degree of hydrolysis (DH). The model predicted a DH of 27.69, closely aligning with the experimentally measured actual DH of 28.33. DPPH radical scavenging and TBARS demonstrated that hydrolysates prepared by ultrasound combined microwave pretreatment (UMH) exhibited the highest antioxidant activity and significantly inhibited lipid oxidation. GC-MS analysis revealed that the UMH showed removal of bitter volatile flavor compounds, such as o-Cresol and m-Cresol, the retention of aromatic volatile compounds, such as 2-pentylfuran, formation of new aromatic volatile compounds such as 3-methylbutanal, and the reduction in certain aldehyde and ketone compounds. Pearson correlation analysis elucidated that the reduction in aldehyde and ketone compounds was positively linked to the enhanced antioxidant capacity of UMH. The results obtained hold substantial significance for enhancing the added value of Xuanwei ham within the food industry. Full article

Bacteriophage therapy, which employs bacterial viruses to selectively eliminate pathogenic bacteria, has re-emerged as a promising strategy in the face of increasing antimicrobial resistance. However, its widespread clinical implementation is constrained by concerns regarding safety, standardisation, and predictable efficacy. In this review, we examine the key role of genomics in transforming phage therapy from an empirical practice into a standardised and personalised modality of contemporary medicine. We describe how whole-genome sequencing (WGS) provides a basis for safety assessment by enabling systematic screening to exclude virulence factors, antibiotic resistance genes, and markers of lysogeny. WGS also facilitates the prediction of therapeutic efficacy and supports more rational phage selection by identifying receptor-binding proteins and characterising bacterial defence systems. In clinical settings, WGS data are increasingly used to monitor the evolution of bacterial populations and to adapt phage cocktails during treatment, thereby supporting personalised, adaptive phage therapy. Looking ahead, further progress is likely to come from integrating synthetic biology and artificial intelligence to engineer phage-based therapeutics with programmable specificity and predictable properties. Together, these developments are shaping a new paradigm of phage therapy as a scientifically grounded, standardised and controlled strategy to treat infections caused by antibiotic-resistant bacteria. Full article

DeepVariant has revolutionized the field of genetic variant identification by reframing variant detection as an image classification problem. However, despite its wide adoption in bioinformatics workflows, the tool continues to evolve mainly through the expansion of training datasets, while its core neural network architecture—Inception V3—has remained unchanged. In this study, we revisited the DeepVariant design and presented a prototype of a modernized version that supports alternative neural network backbones. As a proof of concept, we replaced the legacy Inception V3 model with a mid-sized EfficientNet model and evaluated its performance using the benchmark dataset from the Genome in a Bottle (GIAB) project. Alternative architecture demonstrated faster convergence, a twofold reduction in the number of parameters, and improved accuracy in variant identification. On the test dataset, updated workflow achieved consistent improvements of +0.1% in SNP F1-score, enabling the detection of up to several hundred additional true variants per genome. These results show that optimizing the neural architecture alone can enhance the accuracy, robustness, and efficiency of variant calling, thereby improving the overall quality of sequencing data analysis. Full article

Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022–2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of bla_OXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The bla_OXA-48 and bla_OXA-244 genes were chromosomally located, while bla_OXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the bla_OXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all bla_OXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored bla_CTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried bla_OXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far. Full article

Targeted next-generation sequencing (tNGS) closes the gap between point-of-care rapid tests and phenotypic drug susceptibility testing (pDST) in drug-resistant tuberculosis (DR-TB). The 2025 World Health Organization (WHO) consolidated guidelines and the operational handbook place tNGS after initial automated nucleic acid amplification tests (aNAATs) for the delivery of catalogue-linked molecular drug susceptibility testing (DST) for a broad drug panel, reserving whole-genome sequencing (WGS) and/or pDST for discordance resolution, confirmation, and surveillance. This review summarizes (i) the core tNGS principles and panel design; (ii) platform-specific workflows for Illumina and Nanopore, including direct-from-sample implementations and typical turnaround times; (iii) catalogue-based interpretation against the 2023 WHO Mycobacterium tuberculosis mutation catalogue, with emphasis on bedaquiline/clofazimine (BDQ/CFZ) resistance and management of uncertain variants; (iv) pooled accuracy and sources of genotype–phenotype discordance; and (v) practical requirements for bioinformatics, quality assurance/external quality assessment (QA/EQA), and standardized reporting. We summarize operational and economic considerations (throughput, batching, and network design) to clarify where tNGS adds value compared with alternative strategies and to outline priority research needs, including (i) performance standards for culture-free tNGS, (ii) robust heteroresistance detection, (iii) standardized variant curation, and (iv) data-sharing frameworks to refine genotype–phenotype links. When embedded within validated QA/EQA frameworks and catalogue-linked reporting systems, tNGS can shorten the time to effective therapy by rapidly informing fluoroquinolone (FQ) susceptibility and providing early, tiered resistance signals for newer agents (e.g., BDQ), with indeterminate findings prompting reflex pDST/WGS. Full article

Nanoparticles based on gallium ferrite are explored as potential agents for magnetic fluid hyperthermia due to their magnetic performance and biocompatibility. In this study, Ga_xFe_3−xO₄ systems (0 ≤ x ≤ 1) were synthesized by co-precipitation of iron chlorides, with part of the series modified by a chitosan shell. Structural analysis confirmed single-phase formation across the studied range, while microscopy revealed irregular morphology, broad size distribution, and aggregation into mass-fractal-like assemblies. Chitosan was observed to coat groups of particles rather than single crystallites. Under an alternating magnetic field, all samples exhibited efficient heating, with specific absorption rate values generally increasing with gallium content. The composition Ga_0.73Fe_2.27O₄ showed the highest SAR—83.4 ± 2.2 W/g at 2.8 mg/mL, 532 kHz, 15.3 kA/m, and SAR values rose with decreasing concentration. Cytotoxicity assays without magnetic activation indicated no harmful effect, while chitosan-coated nanoparticles enhanced fibroblast viability and lowered metabolic activity of HeLa cells. Higher Ga content (x = 0.66) combined with chitosan modification was identified as optimal for hyperthermia. The results demonstrate the biomedical potential of these nanoparticles, while emphasizing the need to reduce shape heterogeneity, aggregation, and sedimentation for improved performance. Full article

Background/Objectives: Rapid and accurate pathogen identification and antimicrobial susceptibility testing (AST) are critical for the proper management of patients with bloodstream infection (BSI). Real-time whole-genome sequencing (WGS) represents an attractive opportunity for exhaustive pathogen identification and antimicrobial susceptibility prediction (ASP). This feasibility study introduces BacT-Seq, a WGS-based prototype assay for the rapid and accurate identification of pathogens and the prediction of antimicrobial susceptibility from positive blood cultures using Oxford Nanopore Technologies (ONT) sequencing. Methods: A total of 200 positive blood culture samples from patients with a confirmed BSI were included in this study. DNA isolation from blood cultures was optimized prior to GridION (ONT) sequencing. Pathogen identification and several ASP methods were compared to conventional identification and phenotypic AST methods. Results: Most of the mono-microbial (89%) and poly-microbial (88%) samples were identified by BacT-Seq in less than 10 min of sequencing. While identification of poly-microbial samples remains challenging, identification of mono-microbial samples by sequencing was non-inferior to that of the conventional approach, even revealing an added value in terms of exhaustivity and/or taxonomic resolution. Machine-learning-based ASP models yielded 80% predictions in 2.5 h of sequencing. Their ability to predict resistance phenotypes varied with the microbial species evaluated, from 55/57 (96.5%) for Escherichia coli to 24/48 (50.0%) for Pseudomonas aeruginosa. Conclusions: This study demonstrates the feasibility of implementation of the BacT-Seq platform for the fast and accurate identification of pathogens from positive blood cultures. BacT-Seq performance of resistance predictions by bioinformatics tools is promising but requires further optimization and validation before clinical implementation. Full article