Search Results (6,302)

Shigella spp., and Escherichia coli exhibit notable genomic and phenotypic similarities, including serologically and genetically related somatic antigens. For example, the relationship among pathogenic strains E. coli 64474, O179, O188, and S. boydii O16 suggests a shared clonal origin. To evaluate their genomic proximity, a comparative genomics study was conducted using whole-genome sequencing. Comparative genomics involved rfb gene cluster regions and whole-genome comparisons. Phylogenomic inferences were performed using the virtual genome fingerprint (VGF) method with bootstrap support. The results revealed a high degree of genomic similarity and a close evolutionary relationship among E. coli strains, which also demonstrated genetic associations with clinically relevant pathotypes through the presence of virulence genes. Furthermore, serogroups 64474, O188, and S. boydii O16 exhibited close genetic relationships, suggesting that serotype 64474 could represent a novel serogroup, although its similarity to O188 indicates the influence of divergent factors. These findings support the hypothesis that these E. coli strains originated from a common clonal lineage, enhancing our understanding of serogroup diversity and the evolutionary dynamics within enteric pathogens. Full article

Oral squamous cell carcinoma (OSCC) typically develops in individuals with established risk factors such as tobacco and alcohol use, yet an increasing number of cases occur in young non-smoking, non-drinking (NSND) patients. We report a case of oral tongue OSCC in a 33-year-old woman who is a never-smoker and never-drinker without identifiable environmental or local risk factors. The patient underwent surgical treatment followed by adjuvant radiotherapy and remains disease-free 15 months after therapy. Whole-exome sequencing (WES) revealed a pathogenic truncating TP53 mutation together with additional somatic alterations affecting genes involved in DNA repair, hypoxia adaptation, mitochondrial function, and epigenetic regulation. The heterogeneous mutational profile suggests branched tumor evolution and the involvement of non-classical tumorigenic pathways. This report contributes to the growing evidence that OSCC in young NSND patients represents a biologically distinct subgroup and demonstrates the value of comprehensive genomic profiling for improving understanding of tumor heterogeneity and potential molecular drivers in the absence of traditional carcinogenic exposures. Full article

Bluetongue (BT) is an infectious, non-contagious, arthropod-borne viral disease of ruminants, and has a severe impact on livestock. It is caused by Bluetongue virus (BTV), a double-stranded (ds) RNA virus with a segmented genome (10 segments), belonging to the Seoreoviridae family, Orbivirus genus. Over the last 25 years, Europe has suffered multiple incursions of different BTV serotypes with serious consequences, which have mainly been controlled thanks to vaccination. In the case of Spain, from 2000 to 2023, BTV serotypes 1, 2, 4 and 8 have caused epidemics, and, sporadically, BTV-1 and -4 were detected in the same area and period. In 2024, BTV serotypes 1, 3 and 8 circulated simultaneously in the southwest of the country, causing a severe clinical impact in sheep but also in cattle and a multitude of outbreaks. Additionally, despite vaccination, serotype 4 also circulated that year, especially in areas where the other serotypes were already circulating. Whole-genome sequencing and phylogenetic analyses allowed us to confirm that serotypes 1 and 4 were homologous to viruses circulating in the country since 2000s, while serotypes 3 and 8 were homologous to BTVs recently notified in neighboring countries. In this context, many BTV co-infections of two or more different serotypes were confirmed by serotype-specific RT-PCRs, both in farms and individual animals. An epidemic caused by four serotypes coinciding in space and time had never occurred before in Spain, being a challenge for the diagnosis and control of this disease. Moreover, it could have favored the appearance of reassortant viruses with an unknown virulence, posing an additional risk. The data presented here raise the question of whether the co-circulation of different BTV strains, an exceptional situation, could become the new normal in certain areas of Europe. Full article

Ascosphaera apis is a fungal pathogen of honeybee larvae and the primary cause of chalkbrood disease, which weakens bee colonies, impairing their ability to function effectively and making them more susceptible to other pathogens and environmental stressors. This study aimed to develop and validate an in-house matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral library for A. apis. A new MALDI-TOF MS library was constructed using reference Ascosphaera species and validated through whole-genome-based confirmation of 31 clinical isolates of A. apis. Three different protein extraction methods were tested and compared: liquid cultivation, formic acid–ethanol extraction and extended direct transfer. Our findings demonstrate that MALDI-TOF MS is a rapid and reliable tool for identifying A. apis under the tested laboratory conditions and within the analyzed strain set, with no misidentifications observed for the liquid cultivation and formic acid–ethanol extraction methods. The extended direct mycelium transfer method was slightly less effective but still showed a high sensitivity of 83.9%. This study provides a foundation for improving diagnostic approaches in the management of honeybee fungal diseases. Full article

Background: Brucellosis is a globally distributed zoonotic disease characterized by highly variable clinical manifestations that may mimic systemic autoimmune and inflammatory disorders. In Europe, where the incidence of brucellosis is relatively low, limited clinical awareness may contribute to delayed diagnosis and inappropriate management. In addition to zoonotic transmission, Brucella species are a well-recognized cause of laboratory-acquired infections (LAIs) among microbiology laboratory personnel. Methods: We report a case of laboratory-acquired Brucella abortus infection in a young woman presenting with undulant fever, arthralgia, systemic inflammation, elevated ferritin levels, and antinuclear antibody (ANA) positivity. Microbiological confirmation was achieved through serological testing (ELISA), repeat blood cultures, species-specific quantitative PCR, and whole-genome sequencing (WGS) followed by core genome multilocus sequence typing (cgMLST). Results: Initial laboratory evaluation revealed elevated C-reactive protein, mildly increased ferritin levels (146 ng/mL), abnormal liver enzyme levels, and rising ANA titers (from 1:160 to 1:320), raising suspicion of a systemic autoimmune disorder and prompting consideration of corticosteroid therapy. Although the initial blood culture was negative, subsequent molecular diagnostics and repeat cultures confirmed B. abortus infection. Epidemiological investigation suggested a possible occupational exposure in a diagnostic microbiology laboratory, consistent with a laboratory-acquired infection. Genomic analysis classified the isolate as sequence type 1 (ST1) and demonstrated zero allelic differences compared with the ST1 reference strain. Targeted antimicrobial therapy resulted in complete clinical recovery, supporting an infection-triggered immune response rather than primary autoimmunity. Conclusions: Acute brucellosis should be considered in the differential diagnosis of febrile syndromes accompanied by autoimmune-like laboratory abnormalities, even in low-incidence regions. This case highlights the diagnostic challenges posed by laboratory-acquired brucellosis and underscores the importance of early microbiological investigation and strict biosafety awareness in laboratory settings. Full article

Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects. Full article

Candidozyma auris (C. auris) is an emerging healthcare-associated yeast of major epidemiological concern because of its multidrug resistance and outbreak potential. We report the recovery of a single C. auris isolate from a used face mask collected in May 2025 during a blinded dental medicine quality-control programme assessing microbial contamination in the working environment. To contextualise this finding, we analysed routine diagnostic laboratory data from 2017 to 2025. The isolate underwent whole-genome sequencing for molecular characterisation, including analysis of the ERG11 gene, and antifungal susceptibility testing by EUCAST broth microdilution. In addition, 53,802 patient-related Candida spp. isolates collected between 2017 and 2025 were reviewed retrospectively; species identification had been performed by MALDI-TOF. The environmental isolate belonged to clade III and carried the V125A/F126L substitutions in ERG11, consistent with African clade isolates and associated with intrinsically high fluconazole minimum inhibitory concentrations. No C. auris was detected in routine patient specimens during the study period, whereas Candida albicans remained the predominant species in clinical samples. These findings provide no evidence of ongoing C. auris transmission at the Medical University of Innsbruck, but highlight the need for continued vigilance and robust infection-prevention measures to limit the risk posed by isolated introductions. Full article

The DNA methyltransferases inhibitor 5-azacytidine (5AzC), clinically used to treat hematopoietic malignancies, can elevate genomic mutational burden, raising safety concerns. To define the epigenetic specificity and mutagenic consequences of 5AzC, we performed multi-omics analyses in Neurospora crassa. Our data showed that 5AzC caused a non-selective, genome-wide reduction in both 5-methylcytosine (5mC; ~50% decrease) and the heterochromatin mark H3K9me3 (~65% decrease), indicating broad off-target demethylation that may transiently benefit therapy yet compromise genome stability. Whole-genome sequencing (WGS) revealed a ~290-fold increase in mutation rate under 5AzC, with a pronounced C->G transversion bias, a spectrum typically associated with higher functional burden. Strikingly, 5AzC-induced mutations were enriched in H3K9me3-marked domains, particularly pericentromeric regions characterized by low 5mC but high H3K9me3. Genetic analyses showed that the loss of DNA methyltransferase DIM-2 reduced 5AzC-induced mutations by ~64%, while individual or combined knockout of the histone methyltransferase DIM-5 with DIM-2 led to an 85% reduction. Thus, mutagenesis was markedly amplified by DIM-2 and DIM-5, with DIM-2 activity dependent on DIM-5. Collectively, DIM-2 and DIM-5 accounted for nearly all A/T-site and ~80% of G/C-site mutations. These results reveal that 5AzC drives genome-wide loss of 5mC and H3K9me3, with mutagenesis preferentially targeting H3K9me3-enriched regions via DIM-2 and DIM-5. This work clarifies a mechanistic basis for 5AzC-associated genomic risk and highlights strategies for next-generation epigenetic therapies that preserve heterochromatin integrity while minimizing mutational load. Full article

Genetic diversity and antifungal susceptibility profiles of Aspergillus fumigatus are critical for understanding the evolution of resistance in clinical and environmental settings. We performed comprehensive genomic characterization of A. fumigatus isolates using whole-genome sequencing combined with phenotypic susceptibility assays. SnpEff-based variant annotation identified 76,079 single-nucleotide polymorphisms, revealing a high proportion of mutations (78.8%) in upstream and downstream regulatory regions, whereas high-impact coding variants remained rare (0.083%). Several key mutations were identified, including the well-established cyp51A M220V and HMG1 S212P/Y564H mutations. Moreover, a diverse array of peripheral cyp51A polymorphisms (M39I, E402D, N248K, and K372N) was detected, although these variants did not correlate with the resistant phenotypes. Our comparative genomic analysis identified a novel A586T substitution in the FKS1 gene in an isolate with an elevated minimum effective concentration of caspofungin, suggesting its possible association with reduced susceptibility, although functional validation is required. In isolates lacking canonical target-site mutations, the high frequency of regulatory-region variants indicated the involvement of non–target-site mechanisms. This study provides a detailed map of the genomic landscape of A. fumigatus and identifies candidate loci for future functional validation. Our results demonstrate the utility of high-throughput genomic surveillance for monitoring emerging resistance trends and characterizing the genetic background of clinical fungal pathogens. Full article

Linezolid represents a critical last-resort treatment for severe multidrug-resistant (MDR) Gram-positive bacterial infections. Rising linezolid resistance in Enterococcus isolates threatens its efficacy; this study characterized the molecular features and transfer potential of plasmid-encoded linezolid resistance genes optrA and poxtA in a linezolid-resistant Enterococcus asini isolate from chickens. An E. asini strain was isolated during a surveillance program focusing on drug-resistant Gram-positive bacteria in poultry. PCR screened linezolid resistance genes, conjugation and plasmid stability assays evaluated gene transferability and stability, and whole-genome sequencing (WGS) was performed using both the Illumina and Nanopore platforms. We present the first detection of optrA and poxtA genes in E. asini recovered from chicken feces in China. Sequence analysis of the complete genome showed that poxtA and optrA were situated on two distinct plasmids. The poxtA positive plasmid, pHNGXN23C145Ea-1, also carried multiple resistance genes, including tet(S), fexB, erm(B), ant(6)-Ia, aph(3′)-III. Furthermore, the poxtA gene was flanked by IS1216E mobile elements. The optrA bearing plasmid, pHNGXN23C145Ea-2, harbours a common genetic array of ‘IS1216E fexA-optrA-erm(A)-IS1216E’. Conjugation experiments indicated that neither the poxtA- nor the optrA-bearing plasmid was transferred to recipient strains, which was consistent with sequence analysis showing that both plasmids lacked intact conjugative transfer regions. Stability assays confirmed that poxtA and optrA remained highly stable in the absence of selective pressure. Notably, this discovery was made in a livestock sample, despite the non-use of linezolid in food animals, suggesting that such niches may act as silent reservoirs for resistance genes, which could persist and potentially transfer to clinically relevant MDR pathogens. Full article

Background: Translocation morphology renal cell carcinoma (tRCC) accounts for nearly half of all pediatric RCC cases. Biological study AREN14B4-Q aimed to characterize the molecular landscape of tRCC using samples acquired from patients enrolled in the Children’s Oncology Group Risk Classification and Biobanking study AREN03B2. Methods: From 2006 to 2014, patients <30 yr old with renal tumors were prospectively enrolled in AREN03B2, a Central IRB-approved biobanking study. All pediatric RCC cases underwent a detailed central pathology review and molecular diagnostics to accurately classify RCC subtypes. Samples with confirmed tRCC and appropriate informed consent were identified with adequate tissue for RNA and DNA extraction, along with germline DNA, for whole-genome sequencing (WGS), RNA sequencing, and DNA methylation analyses. Results: From 41 patients, high-quality samples allowed for 18 tumors and non-tumor DNA to be analyzed via WGS, 19 via DNA methylation, and 36 RNA samples via transcriptome sequencing. Consistent with and extending clinical cytogenetic findings, WGS and fusion transcript analyses confirmed very few additional mutations beyond the tRCC translocation. No recurrent genomic copy number gains/losses were found. RNA and WGS analyses enabled sub-classification of tRCC, closely aligning with the different TFE3 fusion partners. DNA methylation analyses demonstrated less tRCC sub-stratification compared with RNA analyses. Pathways activated in tRCC were involved in epithelial differentiation, extracellular matrix organization, apoptosis, immune regulation, signal transduction, and angiogenesis. Conclusions: Arrested epithelial differentiation is the overarching driver in tRCC and is strongly correlated with the specific subclasses of fusion transcript generated by the genetic translocation TFE fusion partner. Negative regulation of apoptosis, increased M2 macrophage expression, and enhanced angiogenesis also appear to be functional features of tRCCs, as are increased expression of matrix metalloproteinases, PI3K-AKT/mTOR/MAPK signaling, and mitochondrial metabolism, highlighting potential therapeutic options beyond direct targeting of the oncogenic driver fusions. Full article

Background: Resistance to first-line anti-tuberculosis drugs in Mycobacterium tuberculosis represents a significant public health challenge, particularly in high-burden tuberculosis (TB) settings such as Pakistan, where multidrug-resistant (MDR) forms further complicate disease control efforts. Drug resistance is primarily associated with mutations in rpoB, inhA, katG, embA, embB, embC, and pncA. The emergence of novel, region-specific variants underscores the urgent need for integrating genomic surveillance into routine TB diagnostics and regional control programs. This study aimed to identify the spectrum of mutations contributing to first-line drug resistance in MDR-TB isolates from Khyber Pakhtunkhwa, Pakistan. Methods: Whole-genome sequencing was performed on 16 clinical isolates (12 MDR and 4 drug-susceptible) to identify resistance-associated mutations in rpoB, inhA, katG, embA, embB, embC, and pncA. Detected variants were interpreted using the World Health Organization (WHO) mutation catalogue to determine their association with drug resistance. Phylogenetic relationships were inferred using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) platform. Results: A total of 16 M. tuberculosis isolates were analyzed to evaluate resistance to first-line anti-tuberculosis drugs. In rpoB, 76 distinct variants were identified, including canonical mutations such as Ser450Leu and His445Arg, as well as a potentially novel substitution, Ser431Phe, predicted to confer high-level rifampicin resistance. The katG and inhA genes harbored 24 and 27 mutations, respectively, including well-characterized substitutions such as Ser315Thr and Ala114Glu, which are strongly associated with isoniazid resistance. Mutations in embA and embB were linked to ethambutol resistance, with several variants localized within conserved transmembrane domains critical for drug interaction. Phylogenetic analysis revealed substantial genetic diversity and evidence of local transmission among MDR-TB isolates. Conclusions: This study suggests that the genetic landscape of drug resistance in M. tuberculosis is highly dynamic in endemic regions. The findings highlight the importance of integrating region-specific mutation profiles into molecular diagnostic frameworks to enhance early detection, guide individualized therapeutic interventions, and strengthen strategies aimed at controlling the transmission of MDR-TB. Full article

Achromobacter spp. are opportunistic pathogens in people with cystic fibrosis (PwCF), yet the role of the upper airways in their persistence and adaptation remains poorly understood. We investigated whether the sinonasal compartment may act as reservoir and evolutionary niche for Achromobacter spp. during airway infection. Twenty-two isolates obtained from paired nasal lavage and sputum samples of seven PwCF were analysed by whole-genome sequencing. Within each PwCF, identical clone types were detected in both airway compartments, supporting bacterial exchange between upper and lower airways. Despite clonal relatedness, substantial genomic diversification was observed between paired isolates. Genomic signatures indicative of elevated mutation rates were detected in a high number of isolates (73%) and in both airway compartments, highlighting widespread genomic diversification across the respiratory tract. Mobilome analysis revealed compartment-specific variations in insertion sequences, prophages, and integrative elements, suggesting genome plasticity. Additionally, mutation in an aspartate kinase gene was consistently associated with loss of biofilm formation in vitro, highlighting a potential link between this pathway and biofilm phenotype. Overall, our findings indicate that upper and lower airways represent interconnected but partially independent ecological niches where Achromobacter populations can diverge during colonization, supporting the view that both compartments contribute to their persistence and evolution in CF airways. Full article

X-linked dystrophin-deficient muscular dystrophy (DD-MD) is an uncommon neuromuscular disorder in cats. We described an adult male cat with chronic tongue protrusion, dysphagia, muscle hypertrophy, and a history of rhabdomyolysis associated with anesthesia. Clinical pathology revealed markedly increased CK activity, muscle histopathology demonstrated a dystrophic phenotype, and an absence of dystrophin protein was confirmed by immunofluorescent staining. Whole genome sequencing identified two potential disease-causing variants, including a new missense variant in the DMD gene (c.2207T>C; p.Gln736Arg), which was considered causative of the clinical phenotype. A second variant in the CLIC2 gene was also detected but was considered unlikely to cause myopathic signs. The clinical course remained stable over 1.5 years with supportive management and dietary modification, and no further episodes of rhabdomyolysis occurred. This case expands the known spectrum of feline DMD variants and highlights the value of genetic testing combined with muscle histopathology for diagnosing chronic presentations of MD. Avoidance of inhalant anesthetics may be important in managing affected cats due to the risk of acute muscle injury. Full article

Bovine rotavirus (BRV) poses a major threat to the global cattle industry, driving significant morbidity and mortality in young calves. In Yunnan Province, China, BRV is the primary cause of neonatal calf diarrhea (NCD), yet the molecular epidemiology of circulating strains remains poorly understood. This study aimed to investigate the molecular characteristics of bovine rotavirus strains associated with a severe outbreak of the NCD on a local farm. Fecal samples were collected from 396 calves and screened for BRV by RT-PCR targeting the VP6 gene. Positive samples were subjected to virus isolation in MA104 cells, followed by whole-genome sequencing, phylogenetic analysis, and pathogenicity assessment in suckling mice. Of 396 samples, 85 tested positive for BRV, corresponding to an animal-level prevalence of 21.5% (95% CI: 17.5–25.8%), with four fatalities recorded. A strain designated as BRV-YN1-2021 was successfully isolated, exhibiting characteristic cytopathic effects, specific immunofluorescence, and typical rotavirus morphology by electron microscopy. Genomic analysis revealed the constellation G8-P[¹]-I2-R2-C2-M2-A3-N2-T6-E2-H3, identified as genotype G8P[¹]. BLAST analysis showed that four genomic segments shared the highest identity with deer rotavirus strains, five with human rotavirus strains, and two with bovine rotavirus strains. Phylogenetic analysis demonstrated close relationships with US deer strains, Japanese bovine strains, and human strains circulating in China. Experimental infection in suckling mice induced diarrhea and significant intestinal histopathology, degeneration of villous epithelial cells, goblet cell hyperplasia, and inflammatory infiltration. This study reports the first isolation of a G8P[¹] bovine rotavirus from a diarrhea outbreak in Chinese cattle. The multi-host genetic composition provides evidence of interspecies reassortment events, highlighting the zoonotic potential of BRV and emphasizing the need for continuous molecular surveillance to inform effective control strategies. Full article