Search Results (2,892)

Background: TCF20-associated neurodevelopmental disorder (TCF20-NDD) is a heterogeneous clinical condition resulting from defects in gene-encoding Transcription Factor 20, which plays a key role in neuronal development and synaptic function. Here, we present a novel case involving an 11-year-old boy who was referred to us for a neuro-developmental disorder characterized by attention deficit hyperactivity disorder (ADHD), tremor in the upper limbs, tilted head posture, motor delay, impaired executive functioning, and oculomotor dyspraxia. Methods: Genetic tests were performed, including CGH array, molecular analysis of the FMR1 gene, molecular analysis using a next-generation sequencing gene panel targeted for spinocerebellar diseases, and finally, WES including mitochondrial genome analysis. A neuroimaging study of brain and spine was performed using MRI. Results: Trio Whole Exome Sequencing revealed a de novo pathogenic frameshift variant NM_001378418.1:c.5009dup, p.(Thr1671Aspfs*5) in the TCF20 gene. The MRI scan of the brain, cervical, dorsal, and lumbosacral spine revealed Chiari type I malformation. Regarding the pathogenic mechanism underlying Chiari I malformation, it could be found in the homology between TCF20 and the RAI1 gene, the latter being associated with alterations in the posterior cranial fossa. Conclusions: We emphasize the use of exome sequencing in patients with unclear clinical presentations, with awareness of TCF20-associated neurodevelopmental disorder; paying attention to brain MRI findings would be useful to further expand the phenotype of TCF20-NDD. Full article

Breast cancer remains a major global health challenge. Yet, genomic data from Middle Eastern and North African (MENA) populations are limited, restricting insights into disease drivers and therapeutic opportunities in this demographic. To address this gap, we performed whole-exome sequencing (WES) on 52 breast cancer samples, including 51 from the MENA region, to characterize somatic mutations and potential therapeutic targets. Across the cohort, 37,369 somatic variants matched entries in the COSMIC database, and driver prediction tools (BoostDM and OncodriveMUT) identified 2451 predicted driver mutations, including 648 known driver variants in genes such as TP53, PIK3CA, GATA3, PTEN, SF3B1, and KMT2C. In addition, 1803 novel predicted drivers were detected, many affecting DNA repair pathways, including homologous recombination (BRCA2, RAD51C), mismatch repair (MLH1, MSH2), and nucleotide excision repair (ERCC2, ERCC3), as well as regulators such as TP53 and ATM. Mutational signature analysis revealed a predominance of C>T substitutions and subtype-specific patterns, with SBS22 and SBS43 enriched in Luminal A tumors. Therapeutic annotation using OncoKB identified 223 actionable or likely oncogenic variants, highlighting potential targets for precision oncology. This study provides a comprehensive characterization of the breast cancer mutational landscape in MENA patients and offers a valuable resource for advancing genomic and therapeutic research in this demographic. Full article

Whole-genome sequencing (WGS) is integral to precision oncology, yet most cancer biospecimens used for WGS are formalin-fixed paraffin-embedded (FFPE) due to their widespread availability in clinical practice. However, FFPE processing can degrade DNA quality. This study compares WGS outcomes from matched cryopreserved (CP) and FFPE tumor samples, hypothesizing that CP tissues yield superior sequencing quality and variant detection. Fifty matched pairs of CP and FFPE tumor samples spanning multiple cancer types were obtained from a biobank. DNA was extracted, and WGS was performed. We assessed sequencing quality metrics and variant analysis between the two preservation methods. Presequencing metrics favored CP tissue, with a significantly higher gDNA concentration, DIN, and DNA fragment size. The WGS results showed that the CP samples had a higher mean read depth and larger insert size. Although the mapping percentages were similar, FFPE exhibited higher tumor mutation burden (13.7 vs. 6.4 mutations/Mb) and lower concordance with CP in variant calls (43.5% overlap). CP samples detected more structural variants and enabled the improved identification of oncogenic driver mutations. Cryopreserved tissues consistently outperform FFPE in terms of DNA quality and WGS metrics, enabling the more accurate detection of clinically relevant mutations. These findings support prioritizing CP sample preservation for genomic profiling in cancer care. Full article

Background/Objectives: Due to the numerical dominance of environmental and commensal strains, understanding antimicrobial resistance (AMR) transmission in Escherichia coli requires consideration of non-clinical as well as pathogenic isolates. In this cross-sectional study, associations between the genetic context of non-clinical E. coli and AMR carriage are examined in isolates sampled from different niches within a One Health continuum. Methods: Two hundred eighty-eight E. coli isolates collected in Alberta, Canada (2018–2019) from wastewater, well water, feces of broiler chickens and feedlot cattle, and retail beef and chicken meat were selected from existing surveillance collections using a stratified random sampling structure. Using short-read whole genome assemblies, phylogenetic relationships were inferred from pan-genome multiple sequence alignments. Principal coordinate analysis and permutational analysis of variance (PERMANOVA) of a Jaccard dissimilarity matrix derived from gene presence/absence data were used to investigate contributions of source and AMR strata to observe genetic dissimilarity. Population clustering and gene under- or over-representation by source and cluster were also explored. Results: Minimal phylogenetic segregation of isolates was noted based on source or AMR strata, and both contributed significant but small proportions of observed genetic dissimilarity, with the largest proportion attributed to phylogroup. There was notable diversity of E. coli within and between sources; however, in some larger clusters, differential gene presence/absence was potentially linked to ecological niche rather than source of isolation. Conclusions: This study highlights the ecological complexity of AMR in E. coli in non-clinical contexts, offering a novel lens on how niche-specific factors can influence population structure and AMR carriage. It also provides insight into apparent discrepancies in the literature regarding clustering of E. coli by source. These findings support a more integrative One Health approach to AMR surveillance, emphasizing the need to account for microbial diversity and niche-specific adaptation across interconnected systems. Full article

The emergence of multidrug-resistant Shiga toxin-producing Escherichia coli (STEC) poses a major challenge to public health and necessitates the development of alternative antimicrobial strategies. This study aimed to isolate and characterize five lytic bacteriophages belonging to the genus Mosigvirus and evaluate their potential as biocontrol against MDR STEC strains and their biofilms. The five bacteriophages, designated vB_EcoM-pJBB (ΦB), vB_EcoM-pJBC (ΦC), vB_EcoM-pJBJ (ΦJ), vB_EcoM-pJBK (ΦK), and vB_EcoM-pJBL (ΦL), were isolated from sewage treatment plant samples using STEC ATCC 43895 as host. Biological characterization included host range determination against 19 MDR STEC strains, one-step growth analysis, environmental stability assays, bacteriolytic activity assessment, and antibiofilm efficacy testing. Whole-genome sequencing and phylogenetic analyses were performed to determine genomic features and taxonomic classification. The phages demonstrated varying infectious capacities, lysing between six and 12 strains, with ΦL exhibiting the broadest spectrum of activity. All phages showed MOI-independent antibiofilm activity, preventing biofilm formation by approximately 70% and disrupting pre-formed biofilms by up to 80.3%. Genomic analysis revealed the absence of lysogeny markers, virulence factors, and antimicrobial resistance genes, while identifying putative depolymerase genes associated with tail fiber proteins. Phylogenetic analysis confirmed the taxonomic position of these phages within the Mosigvirus genus in the Straboviridae family. Our findings indicate that the newly identified Mosigvirus phages are promising candidates for phage-based biocontrol applications. Full article

Tomato is one of the most important vegetable crops in Costa Rica, where favorable environmental conditions enabled year-round production but also promote bacterial diseases. In recent years, pith necrosis has been frequently observed; nevertheless, the causal agents remain unidentified in the country. This study evaluated bacteria associated with symptomatic plants collected in the Central Valley of Costa Rica. From 32 plants, 61 bacterial isolates were obtained, described morphologically, and characterized through basic biochemical tests. Partial sequencing of the 16S rRNA gene revealed diverse bacterial taxa, predominantly belonging to the genus Pseudomonas. Thirteen isolates were selected for pathogenicity assays, which confirmed variable virulence levels. Multilocus sequence analysis based on concatenated sequences of the 16S rRNA, gyrB, rpoD, and rpoB genes identified Pseudomonas alliivorans LTM 13.1.2, P. flavescens LTM 14.2.2, and P. capsici LTM 78.3.2 as causal agents of pith necrosis. Additionally, P. straminea LTM 78.2.1 and Cedecea sp. LTM 72.2.1 caused tissue discoloration. Whole-genome sequencing of the two most virulent isolates (LTM 13.1.2 and LTM 78.3.2) supported their taxonomic classification and revealed virulence-associated genes and biosynthetic clusters. This study represents the first report of these Pseudomonas species as tomato pathogens in Costa Rica and expands their known distribution and host ranges. Full article

Background/Objectives: Since its emergence in late 2019, SARS-CoV-2 has demonstrated remarkable genetic diversity driven by mutations and recombination events that shaped the course of the COVID-19 pandemic. Continuous genomic monitoring is essential to track viral evolution, assess the spread of variants of concern (VOCs), and inform public health strategies. The present study aimed to characterize the molecular epidemiology of SARS-CoV-2 in northern Greece from the first national case in February 2020 through early 2025. Methods: A total of 66 respiratory samples collected from hospitalized patients across Northern Greece were subjected to whole-genome sequencing using Oxford Nanopore Technologies’ MinION Mk1C platform and the ARTIC protocol. Sequences were analyzed with PANGO, Nextclade, and GISAID nomenclature systems for lineage and clade assignment, and the WHO nomenclature for VOCs. Results: Across 66 genomes, 34 PANGO lineages were identified. Early introductions included B.1 (2/66), B.1.177 (3/66), and B.1.258 (1/66). Alpha (5/66) and Beta (5/66) circulated in February–June 2021. Delta (AY.43) was detected in early 2022 (2/66; Jan–Feb) but was rapidly displaced by Omicron and reached 100% of the sequences by May 2022. Omicron diversified into BA.1/BA.1.1 (3/66), BA.2 (6/66), BA.4/BA.5 (14/66), BF.5 (1/66), EG.5 (1/66; designated a WHO Variant of Interest in 2023), JN.1 (4/66; globally dominant lineage prompting vaccine updates in 2024–2025), KS.1 (2/66; together with KS.1.1 are recognized PANGO lineages that were tracked internationally but remained less prevalent), KP.3 (5/66; together with KP.3.1.1, prominent “FLiRT” descendants circulating in 2024), and recombinants XDK, XDD, and XEC (5/66), reported by their PANGO names in accordance with the WHO’s current framework, which reserves Greek letters only for newly designated VOCs. Conclusions: This five-year genomic analysis provides an insight into the continuous evolution of SARS-CoV-2 in northern Greece. The findings underscore the importance of sustained genomic surveillance, integrated with epidemiological data, to detect emerging variants, monitor recombination, and strengthen preparedness for future coronavirus threats. Full article

Enterococcus faecalis (E. faecalis) is a significant zoonotic pathogen, primarily causing opportunistic infections in humans while often existing as a commensal in animal reservoirs, facilitating its dissemination. Current understanding of the resistance profiles, virulence mechanisms, and host–pathogen interactions of E. faecalis from ruminants, particularly unique species such as the plateau yak, remains limited. This knowledge gap hinders the accurate assessment of their transmission risk and the development of effective control strategies. This study presents a comprehensive analysis of a multidrug-resistant E. faecalis isolate from yak feces, integrating whole-genome sequencing (WGS), an animal challenge model, and transcriptomic profiling. Antimicrobial susceptibility testing revealed resistance to β-lactams, aminoglycosides, glycopeptides, tetracyclines, and fluoroquinolones. WGS identified numerous resistance genes (e.g., parC, gyrA, rpoB) and virulence-associated genes (e.g., prgB/asc10, cpsA/uppS). Phylogenetic analysis indicated a close relationship with a human urinary tract isolate (ASM3679337v1). Mouse challenge experiments demonstrated that this strain induced significant intestinal histopathological damage. A subsequent transcriptomic analysis of infected tissues identified the differential activation of key signaling pathways, including NF-κB and MAPK. Our findings provide crucial insights into the resistance and pathogenic mechanisms of ruminant-derived E. faecalis and establish an experimental foundation for optimizing clinical antimicrobial therapy against such strains. Full article

Background/Objectives: Bacteroides species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical Bacteroides isolates from southern Thailand. Methods: Sixteen isolates were collected from body fluids, tissues, and pus at Songklanagarind Hospital (2022–2024). Whole-genome sequencing was performed on the BGI platform, followed by genome assembly, annotation, average nucleotide identity (ANI), pairwise single-nucleotide polymorphism (SNP) analysis, antimicrobial resistance (AMR) gene profiling, plasmid prediction, virulence screening, and phylogenetic analysis. Results: ANI and SNP analysis revealed two clusters: one comprising B. ovatus, B. intestinigallinarum, and B. thetaiotaomicron, and another mainly B. fragilis with one B. hominis isolate. All isolates were resistant to ampicillin, cephalothin, and penicillin; six B. fragilis strains were resistant to all tested antibiotics. The β-lactamase gene cepA was detected in all B. fragilis isolates, and plasmids were predicted in two genomes. Three virulence types (capsule formation, lipopolysaccharide modification, and stress response) were identified. Phylogenomic analysis confirmed species-level assignments and revealed underrecognized lineages, emphasizing the value of genome-based approaches for accurate classification. Conclusions: Clinical Bacteroides isolates display diverse resistance and virulence profiles, highlighting the importance of strain-level genomic surveillance. Full article

Background/Objectives: A Petit Bleu de Gascogne (PBDG) dog presented with a progressive neurological disorder characterized by hind-limb weakness, anxiety and hallucinatory episodes, lip smacking, progressive vision loss, muscle atrophy, and ataxia. Magnetic resonance imaging revealed diffuse brain atrophy. The dog was euthanized at approximately 23 months of age due to the progression of neurological signs. A study was undertaken to identify the molecular genetic basis of the disorder in this dog. Methods: Microscopic analyses were performed to characterize the disease pathology and whole-genome sequencing was performed to identify the molecular genetic basis of the disorder. Results: The proband exhibited pronounced accumulations of autofluorescent intracellular inclusions in the brain, retina, and heart with ultrastructural appearances similar to those of lysosomal storage bodies that accumulate in the neuronal ceroid lipofuscinosis (NCLs), a group of progressive neurodegenerative disorders. Whole-genome sequence analysis of DNA from the proband identified homozygous missense variants in AP3B1 and TRAPPC9 that encode proteins involved in sorting and transport of proteins through the Golgi apparatus to lysosomes. Screening of unaffected PBDGs for these variants identified dogs that were homozygous for either variant, but no other dogs that were homozygous for both. Conclusions: These findings raise the possibility that the disease involves the combined influence of the two variants, and that the proteins encoded by these genes interact within the Golgi apparatus to mediate protein sorting and transport to lysosomes. An alteration in this interaction could underlie the NCL-like lysosomal storage disorder observed in the proband. Full article

Background/Objectives: Fresh frozen (FF) samples are routinely used to isolate high-molecular-weight intact genomic DNA. However, when FF samples are not available, archived formalin-fixed paraffin-embedded (FFPE) tissue samples often represent the only available material in clinical research. Due to formaldehyde-induced degradation of nucleic acids they pose special challenges for genetic investigations. In this study we compare whole-genome sequencing results on intact DNA versus fragmented DNA derived from FFPE samples of three dogs. Methods: We prepared matched libraries from FF and FFPE samples of three dogs affected by an inherited disease, EFNB3-related congenital mirror movement disorder 1 (CMM1). Paired-end short-read sequencing data were obtained on an Illumina sequencer and analyzed with adapted workflows for FF or FFPE data, respectively. Results: The data between FF and FFPE samples were largely consistent. FF data showed a superior variant call accuracy, as expected. However, the data quality from the FFPE samples was sufficient to correctly identify the causal variant in EFNB3. Conclusions: This pilot study demonstrates the feasibility of using FFPE samples from dogs for whole-genome sequencing and the detection of germline variants. Using FFPE samples in the analysis of suspected inherited diseases in domestic animals may represent a valuable approach in veterinary genetics if no other samples are available. Full article

Background: The Delta variant of SARS-CoV-2 virus, one of the alarming variants of concern (VOC) with a distinct mutation characteristic, was immensely detrimental and a significant cause of the prolonged pandemic waves. This study aimed to analyze the genetic characteristics of the predominant Delta variant in acute febrile illness (AFI) patients in Ethiopia. Method: Nasopharyngeal swab samples were collected from AFI patients in four hospitals from February 2021 to June 2022 and tested for SARS-CoV-2 by using RT-qPCR. Of 101 positive samples, 48 stored specimens were re-tested, and 26 with sufficient RNA quality (Ct < 30) were sequenced using whole-genome sequencing to identify variants of concern, specific virus lineages and mutation features. Result: Delta variants (21J clade) were found predominant among all the sequenced SARS-CoV-2 isolate (80.8%, 21/26). AY.120 (46.2%) and B.1.617.2 (26.9%) were the predominant sub-lineages of the Delta variant. Omicron (21k, Pango BA.1.1/BA.1.17/BA.1) and Alpha (20I, Pango B.1.1.7) variants accounted for 11.5% and 7.7% of the total sequenced samples. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Ethiopia. The number of mutations increases dramatically from Alpha (~35 avg) to Delta (~42 avg) to Omicron (~56 avg). The Delta variant revealed a spike mutation on L452R and T478K and P681R, and was characterized by the double deletion E156-F157- in Spike protein. Conclusions: The findings are indicative of a gradual change in the genetic coding of the virus underscoring the importance of ongoing genomic surveillance to track the evolution and spread of SARS-CoV-2 and other emerging virus. Full article

Background/Objectives: Family history is a known risk factor for multiple myeloma (MM) and its precursor condition, monoclonal gammopathy of undetermined significance (MGUS). Previous genome-wide association studies (GWASs) have identified 35 common loci associated with MM risk and 21 associated with MGUS. The objective of this study was to identify less common and rare genetic loci predisposing to MM/MGUS through whole-exome sequencing (WES)-based linkage analysis. Methods:Multipoint linkage analysis was conducted using the Multipoint Engine for Rapid Likelihood Inference (MERLIN) with the Lander–Green algorithm on germline WES data from 79 pedigrees with 2 or more affected relatives (120 MM, 86 MGUS, and 21 unaffected). Genome-wide linkage was evaluated using 12,946 independent single-nucleotide variants (linkage disequilibrium r² < 0.05). Results: Significant linkage was observed at chromosome 6q22.33–q24.2 by the non-parametric model (logarithm-of-odds (LOD) = 3.3) and suggestive linkage by the dominant parametric model (heterogeneity LOD (HLOD) = 2.5). Fourteen rare variants within this region were prioritized using family-specific partial LOD scores and in silico functional prediction tools. Nine of these variants, REPS1, THEMIS, TAAR6, AHI1, VNN1, VNN3, MTFR2/FAM54A, LAMA2, and PHACTR2, overlapped immune-regulatory regions in blood cell lines and were not previously identified in GWASs. Conclusions: This study demonstrates the utility of applying a linkage analysis framework to familial WES data for identifying genomic regions and candidate genes that may contribute to MM/MGUS predisposition. These findings provide new insight into the inherited risk and etiology of familial MM and MGUS. Full article

Background/Objectives: In an era of increasing bacterial resistance, Enterococcus, as a reservoir of antibiotic resistance genes, poses a serious threat to public health. Methods: This study conducted antibiotic susceptibility tests, whole-genome sequencing, and bioinformatics analysis on 89 Enterococcus isolates from chickens, pigs, cattle, and sheep in Ningxia Autonomous Region. Results: The resistance rates of Enterococcus to clindamycin, cefoxitin, sulfamethoxazole, and tamoxifen were all above 95%, and 96.6% (86/89) of the isolates were multi-antibiotic resistant. There were significant differences in resistance phenotypes among different species, with Enterococcus from pigs showing significantly higher resistance than those from other animals. optrA was commonly found in Enterococcus from pigs, accounting for 61.5% (8/13). ST480, ST16, ST116, and ST300 were the main MLST types, and ST16 was one of the important pathogenic Enterococcus types. Conclusions: The study revealed the occurrence of inter-species transmission events of Enterococcus. In conclusion, this study comprehensively described the resistance spectrum, sequence characteristics, and transmission features of resistance genes in Enterococcus isolated from farm animals, and emphasized the possibility of the spread of resistance genes carried by Enterococcus from farm animals to humans. Full article

The changes in charge distribution caused by mutations in the spike protein may play a crucial role in balancing infectivity and immune evasion during the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To explore how charge increments in spike protein variants influence viral evolution, a statistical analysis was conducted on 57 SARS-CoV-2 variants, examining relationships between charge distribution, lineage divergence, angiotensin-converting enzyme 2 (ACE2) affinity, immune evasion, and receptor-binding domain (RBD) expression. A phylogenetic tree was also reconstructed using only the charge properties of mutation sites. Results indicated that with increasing lineage divergence, overall positive charge initially rose sharply and then more gradually. Partitioning the spike protein into three domains—the RBD, the N-terminal flanking region (B-RBD), and the C-terminal flanking region (A-RBD)—revealed distinct patterns: positive charge increased in the RBD and A-RBD, whereas the B-RBD accumulated negative charge. Charge increments were negatively associated with ACE2 affinity and RBD expression but positively correlated with immune evasion. The k-mer-based tree derived from charge-reduced sequences showed a topology consistent with the whole-genome tree. These findings suggest that charge distribution in spike proteins is closely linked to viral evolution, with the opposing trends in the RBD and B-RBD potentially reflecting a balance between infectivity and immune escape. Full article