Dengue fever is one of the most widely distributed vector-borne infectious diseases globally, prevalent in tropical and subtropical regions. An estimated 3.9 billion people in 128 countries are at risk of infection globally, and the 2024 outbreak was the most severe. As a tropical region, Hainan Province in China serves as a significant endemic area for dengue fever, where epidemic prevention and control remain critical. To analyze the transmission dynamics and pathogen variation characteristics of the 2024 dengue fever outbreak in Hainan Province. Acute-phase serum samples from 18 confirmed dengue cases during the 2024 outbreak in Hainan Province were collected and serotyped using TaqMan real-time PCR. The viral envelope (E) gene and representative whole genomes were sequenced and compared with domestic reference strains to assess epidemic trends. Phylogenetic and molecular clock analyses were performed based on E gene and full-genome sequences to infer spatiotemporal transmission dynamics. Sequence alignment and homology modeling were used to identify E gene mutations and evaluate their potential effects on E protein functional domains and viral pathogenicity. Among the 18 samples, 17 were dengue virus (DENV)-1, and 1 was DENV-3. Phylogenetic analysis revealed that the primary strains in this outbreak were highly homologous to those circulating in Guangdong Province; however, two strains exhibited significant genetic differences, suggesting possible independent introduction. Additionally, two unique DENV-1 E gene mutations (D147N and S338L) were identified, which we hypothesize may be associated with viral characteristics, subject to further functional verification. This study systematically reveals the epidemiological characteristics of the 2024 dengue fever outbreak and provides a scientific basis for formulating local control strategies and a research foundation for further exploring the molecular-level pathogenicity and transmissibility of DENV.

The significant temperature variations across northern and southern China have driven the adaptive evolution of Chinese native cattle breeds, allowing them to thrive in diverse and extreme bioclimate environments. Understanding how these breeds have adapted to varying temperatures is essential for identifying genetic factors that contribute to their survival in such conditions. In this study, using whole-genome sequence data of 336 individuals (with an average sequencing depth of 30.12 ×) from 21 cattle breeds, including 8 breeds from cold regions, 3 from warm regions, and 10 from hot regions, clear genetic differentiation among the three groups of breeds was revealed. Using whole-genome SNP, InDel, and SV data, a series of selective genomic regions, genes, and variants/SVs associated with cold or hot temperature adaptability were identified. Key genes, including KLB, HSPA4, ECSCR, DNAJC18 and SLC9A1 are speculated to be responsible for cold/hot adaptability based on the extreme difference in allele frequency of the selective variants/SVs harbored by these genes, their known biological functions, protein-protein interaction network, findings from previous studies on their relation to environmental adaptation, and their tissue specificities. By integrating SNP, InDel, and SV data, this study provides a comprehensive genetic framework for understanding selective environmental adaptation. These findings enhance our understanding of the mechanisms underlying temperature adaptation in cattle and offer a molecular foundation for the development of new breeds.

Gene transfer from NDM-5-producing and OXA-48-producing Enterobacter hormaechei ST79 on contaminated dicloxacillin capsules to other Enterobacterales in Europe, 2020-23: a retrospective, observational, molecular epidemiological study.

Neurodevelopmental disorders (NDDs) often remain unexplained due to limited assessment of non-coding genomic elements. Motivated by recent reports implicating RNU4-2, which encodes a spliceosomal small nuclear RNA (snRNA), we analyzed whole-genome sequencing data from 15 450 Korean individuals, including 2797 unrelated NDD probands. Rare pathogenic RNU4-2 variants were identified in 20 probands (0.72%), including 17 (85%) with a recurrent n.64_65insT variant. RNA secondary structure modeling and molecular dynamics simulations demonstrated that n.64_65insT disrupts the U4/U6 snRNA duplex and impairs exposure of the U6 ACAGAGA motif required for 5' splice-site recognition. Whole-blood RNA-seq from carriers revealed increased alternative 5' splice-site usage and dysregulation of immune, chromosomal, and DNA metabolic gene programs. Clinically, affected individuals presented with global developmental delay, microcephaly, seizures, failure to thrive, and dysmorphic features. These findings establish RNU4-2, particularly n.64_65insT, as a cause of early-onset NDD. We advocate for routine assessment of spliceosomal RNA genes in genomic diagnostics and reanalysis of unsolved cases to improve yield and guide counseling in rare neurodevelopmental syndromes.

The study addresses the increasing resistance to the FDA-approved drug Bedaquiline (BDQ) in Mycobacterium tuberculosis (MTB). The absence of any defined resistance locus and the wide variation in the drug targets across clinical isolates have raised a big question about our understanding of the molecular basis of BDQ resistance acquisition. Using machine learning (ML) methods, BDQ resistance was predicted from whole-genome sequencing data for MTB clinical isolates. Variant calling format data generation involved several steps, including adapter trimming and alignment to the H37Rv reference genome. The ML models, namely, Multilayer Perceptron and Random Forest (RF), achieved high accuracies of 83.60% and 79.64%, respectively. The top 50 features were mapped to the H37Rv reference genome, and several new drug targets were identified. In addition to the coding regions, some non-coding intergenic regions were also obtained. Mapping of these features to the H37Rv genome revealed 15 new antibiotic-resistant genes. In addition, the use of explainable AI (XAI) methods, such as SHapley Additive exPlanations, facilitated the identification of mutations associated with BDQ resistance. In conclusion, the ML models demonstrated effective predictive capabilities for BDQ resistance, whereas XAI contributed to understanding key resistance features.

Putative novel β-lactamase-encoding genes are increasingly identified in whole-genome sequencing (WGS) data, often without phenotypic or biochemical characterization. Here, we characterized the chromosome-encoded GUA-1 Ambler class A β-lactamase from the clinical isolate Pseudomonas guariconensis-like 65411. Among the 40 P. guariconensis genomes available in the GenBank database, only 8 carried a blaGUA-like gene, whereas the others encoded an AmpC β-lactamase, suggesting the existence of two distinct subspecies. Notably, these eight isolates, despite originating from diverse geographical regions, all harbored the blaGUA-like gene inserted at the same chromosomal locus. Heterologous expression in Pseudomonas aeruginosa and Escherichia coli revealed a clavulanic-acid-inhibited cefotaximase-type ESBL. GUA-1 shared 72% amino acid sequence identity with putative Ambler class A β-lactamases from Pseudomonas fulva, Pseudomonas mosselii, and Pseudomonas soli, and 57% with LUT-1, a class A cephalosporinase from Pseudomonas luteola. Kinetic analyses showed that GUA-1 hydrolyzed cefotaxime but not ceftazidime, similarly to LUT-1 and CTX-M-1-type ESBLs. IC50 measurements indicated strong inhibition by clavulanic acid, tazobactam, and avibactam, but not by vaborbactam. Molecular modeling supported these findings, showing favorable binding of cefotaxime in the active site, whereas steric hindrance from Trp274 and electrostatic repulsion from Asp240 likely prevent ceftazidime binding. The blaGUA-1 gene was chromosomally located, with no obvious promoter identified in the immediate upstream region. RT-PCR experiments revealed expression levels comparable to other β-lactamase genes present (blaDHA, blaCMY, blaOXA-1, and blaOXA-204) and to the upstream-located Na+/H antiporter gene. 5' RACE experiments suggested that the blaGUA-1 gene is co-transcribed along with the Na+/H gene. Overall, this study highlights the diversity of β-lactamases within Pseudomonas species.

This study aimed to compare the microbial profiles between hospital wastewater and river water to assess the dissemination of clinical isolates into the environment. Two types of water samples were collected from sampling sites which were geographically close (wastewater from the University Hospital of Larissa and river water from the Pineios River). Gram-negative bacteria isolated from both sample types were identified using MALDI-TOF. Furthermore, the minimum inhibitory concentration (MIC) of antibiotics were evaluated. A total of 54 Gram-negative isolates, belonging to diverse species, were collected from wastewater sample and river sample. All isolates were classified as MDR, exhibiting resistance to at least one agent from more than three different antibiotic classes. Based on species identification and susceptibility profiles, 27 isolates (19 from wastewater and 8 from river-water) were selected to be further characterized by whole-genome sequencing (WGS). Analysis of WGS data, revealed the presence of different STs, even in isolates belonging to the same bacterial species. Additionally, WGS data showed that carbapenemase-encoding genes were identified in the majority of isolates. PlasmidFinder identified a huge variety of plasmid replicons among the isolates studied. In conclusion, both hospital wastewater and river water contained isolates carrying clinically relevant resistance determinants, such as carbapenemase-encoding genes. The presence of these pathogenic bacteria in the river poses a significant public health concern. Although we could not identify the origin of MDR bacteria in the river sample, these findings highlight the growing threat of antimicrobial resistance in the environment and underscore the urgent need for improved treatment methods and stricter surveillance to control its spread.

This study investigated the influence of the methylenetetrahydrofolate reductase (MTHFR) 677C > T polymorphism on bladder urothelial carcinoma (BLCA) using whole-genome bisulfite sequencing (WGBS) and The Cancer Genome Atlas (TCGA) data. The TT genotype was associated with reduced global DNA methylation, thereby altering the molecular landscape of BLCA. Differential methylation analysis identified three molecular subtypes of BLCA. Subtype 2, characterized by the lowest methylation levels, was associated with favorable prognosis, earlier disease stage, and a higher frequency of FGFR3 mutations, along with increased infiltration of plasma cells, memory B cells, and naive CD4+T cells. In contrast, Subtype 3 exhibited increased neutrophil infiltration and upregulation of immune checkpoint molecules, including PD-L1 and CTLA-4. Transcriptomic analysis indicated that low methylation and high expression of TRIM27 in Subtype 2 were associated with improved prognosis, whereas high methylation and low expression of RASSF1 in Subtype 3 were associated with poorer outcomes. Metabolic pathways were enriched in Subtype 2, whereas cell cycle-related genes were overexpressed in Subtype 3. These findings indicate that the MTHFR 677C > T polymorphism modulates DNA methylation and significantly influences the molecular characteristics, immune microenvironment, and prognosis of BLCA. Methylation-based subtyping may provide biomarkers for precise diagnosis and therapeutic stratification in BLCA.

A cross-sectional study of oxidative stress pathway genotypes and their interactions with environmental pollutant levels identifies associations with gene expression and lung function.

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300 kb and 200 kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein's function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation. This adaptive variation may be crucial to anchor adaptive responses facing future environmental change.

Global epidemiological survey and genomic analysis of multiple carbapenemases-producing Citrobacter freundii.

Genetic structure and plumage color candidate genes of Yunnan Partridge duck revealed by whole genome resequencing.

Clonal selection drives cancer development, but quantifying selection on noncoding somatic mutations remains largely unexplored. Here, we introduce dNdS-Fun, an extension of the dN/dS framework to quantify selection of both coding and noncoding somatic mutations, thereby enhancing the discovery of driver genes. Applying dNdS-Fun to whole-genome sequencing data from 14,886 cancer patients across 31 cancer types, we identify 175 genes under positive selection across multiple cancer types or datasets, as well as 20 previously known driver genes detected through noncoding mutations. Of these, 69 are previously unrecognized as drivers, and 30 are identified solely through noncoding mutations. Furthermore, we observe evidence of negative selection throughout the genome, with significant enrichment in essential and cancer-dependent genes. Sixteen genes exhibit an overall signature of negative selection but show positive selection in noncoding elements, indicating both their conserved functions and adaptive regulatory roles in tumorigenesis. Our study reveals evidence consistent with negative selection of noncoding mutations, providing important insights for future research on their roles in cancer progression.

Rising drug resistance necessitates genomic selection to enhance parasite resistance in sheep. Copy number variations (CNVs) constitute structural genomic alterations that influence livestock traits by modifying gene dosage. This study aimed to identify candidate CNVs that differentiate between Haemonchus contortus-resistant and susceptible Rideau Arcott ewe lambs through comprehensive whole genome sequencing (WGS) analysis. Fecal egg count (FEC) analysis of 32 inoculated animals across five time points (days 21, 28, 35, 42, and 56 post-infection) identified 16 individuals with consistent extreme parasite response phenotypes. The resistant group (n = 9) showed a 10.5-fold lower FEC at day 21 post-infection and maintained 3- to 14-fold lower FEC (p < 0.05) across multiple time points than the susceptible group (n = 7). Consensus calling across CNVpytor, DELLY, and Manta algorithms yielded 22,184 high-confidence CNVs from WGS data at 6.75X genome coverage. These CNVs were consolidated into 3,751 CNV regions (CNVRs) encompassing 65.0Mb (2.63%) of the sheep autosomal genome. Group-wise comparison identified 329 resistant-only and 133 susceptible-only differential CNVRs. The resistant group harboured 3.5-fold more gain category CNVRs and 13-fold more associated duplicated genes than susceptible animals. A 2.3Mb duplication containing CLCA1 appeared exclusively in resistant sheep, which is associated with mucus production. Functional enrichment analysis also confirmed that calcium-gated chloride channel activity was exclusively in the resistant group, which is associated with regulating mucus production. Additional resistance-associated gain CNVRs encompassed LTC4S, ROBO1, RASGRP1, PRKCQ, and MBL2. Conversely, susceptible animals exhibited metabolic dysfunction potentially due to PIK3CA and AGXT duplications, with an enrichment of pathways associated with diabetic cardiomyopathy and prion disease. The study suggests associations between resistance-linked CNVRs and genes involved in mucosal barriers, immune cell trafficking, and T-cell responses. In contrast, susceptible group-linked CNVRs are associated with metabolic disruption, suggesting that metabolic disturbance is a key factor in susceptibility. The first WGS-based CNV analysis successfully identified novel structural variants distinguishing resistant from susceptible Rideau Arcott ewe lambs. The discovery of resistance- and susceptibility-specific gene duplications and metabolic pathways offers new targets for genetic selection. However, the candidate CNVRs warrant validation in larger populations for implementation in breeding programs aimed at improving parasite resistance.

Multidimensional prophage profiling of carbapenem-resistant Enterobacteriaceae in Thailand: a nationwide, multicentre, genomic study.

Studies have reported conflicting findings regarding the contribution of germline variants or somatic genomic drivers to racial disparities in multiple myeloma (MM). To comprehensively investigate somatic drivers in relation to inherited genetics in MM, we combined newly sequenced whole-genome sequencing data with publicly available datasets (total n = 1,286). Overall, we did not identify germline or somatic genomic differences that explain the different risk of developing MM between patients with genetic similarity to African (AFR) or European (EUR) reference populations. A difference in the detectability and timing of APOBEC-associated and germinal center mutational activity was observed. Integrating epidemiological data and mutational signature-based temporal estimates, we challenge the assumption that individuals in the AFR group develop MM at a younger age. Finally, we demonstrate that, with equal access to efficacious therapies, patients in the AFR and EUR groups have equivalent clinical outcomes.

The Changthangi goat, native to the high-altitude Ladakh Plateau in northern India, thrives in oxygen-deficient environments above 4,000m. This study investigated the genetic basis of high-altitude adaptation in Changthangi goats by integrating comparative genomics and transcriptomics, using the tropical lowland Jamunapari goat as a comparative model. Whole-genome sequence data from 15 individuals per breed were analyzed using complementary selection sweep metrics, including nucleotide diversity, Tajima's D, iHS, CLR, XP-EHH, and FST. These analyses identified candidate genomic regions under strong selective pressure, encompassing genes involved in hypoxia sensing (HIF-1α, HIF-2α/EPAS1, EGLN1), angiogenesis (VEGFA, AGGF1, ZEB1), cardiovascular regulation (PRKCB, ESR1, RYR2), mitochondrial and energy metabolism (ACADSB, ACSS3, ACSL1), cellular stress tolerance (BCL2, ATM), and thermogenesis (UCP1, FGF21). Unlike previous caprine studies that primarily infer hypoxia adaptation from genomic signals alone, our study integrates cardiac transcriptomics to demonstrate that genomic selection in Changthangi goats is accompanied by coordinated transcriptional remodeling across interconnected physiological systems in a physiologically relevant tissue. Comparative cardiac transcriptomic profiling revealed concordant expression divergence in genes associated with oxygen transport, vascular remodeling, mitochondrial function, substrate utilization, redox balance, and genome maintenance. This integrative multi-omics framework provides a mechanistic view of caprine high-altitude adaptation and highlights the value of combining genomic selection analyses with tissue-specific transcriptional profiling to resolve complex adaptive traits.

Biodiversity and biogeography of the multi-kingdom cancer microbiome.

Germline variants in Ribosomal Protein S20 (RPS20) have been reported to predispose to colorectal cancer (CRC) based on occurrence in a total of 3455 CRC cases and co-segregation with disease in 3 families. RPS20 encodes a component of the ribosomal 40S subunit, but the mechanism by which the variants might influence CRC risk remains unclear. The current study assessed the association of RPS20 variants with CRC predisposition in whole-genome sequencing (WGS) data from 9738 CRC cases and 161,403 cancer-free controls from the COloRectal tumour Gene Identification consortium (CORGI) study, 100,000 Genomes (100kGP) and UK Biobank (UKB). One hundred and sixty-eight CORGI cases and 23 100kGP cases were recruited based on a family history of CRC. After excluding common polymorphisms, we identified one putative loss-of-function RPS20 variant in cases (p.Ile89fs), and none in controls. This individual was not from a multiplex family, and hence co-segregation analysis of the variant and disease was not possible. One in-frame deletion and one missense variant predicted to be probably pathogenic were found in controls. We also reviewed the evidence on RPS20 and CRC risk from the literature. We concluded that the combined data do not show conclusively that RPS20 is a proven CRC predisposition gene. Its inclusion in diagnostic gene panels for CRC cannot be justified until and unless stronger supporting evidence becomes available in the future.

Despite its high prevalence and the discovery of hundreds of genetic associations, the genetic determinants and heterogeneous manifestations of asthma remain incompletely understood. Incorporating polygenic risk scores (PRS) into asthma research offers a powerful approach to quantify inherited susceptibility, refine risk profiles, and advance mechanistic understanding of disease development. For this study, we leveraged whole-genome sequencing (WGS) data from two family-based cohorts of childhood asthma - the Genetics of Asthma in Costa Rica Study (GACRS) and the Childhood Asthma Management Program (CAMP) - to examine the transmission profiles of externally derived asthma PRS and their associations with clinical phenotypes in children with asthma. To further elucidate molecular mechanisms, we integrated large-scale external genome-wide association study (GWAS) summary statistics and genetic prediction models of protein abundance in a two-step proteome-wide association study (PWAS) of asthma. Our findings provide robust evidence supporting the validity of externally derived asthma PRS (asthma PRS association p-valuep= 10−24[GACRS and CAMP trios combined] for the Global Biobank Meta-analysis Initiative [GBMI]) and reveal consistent associations with spirometry measures and atopy markers across both studies, as 13 of 21 traits (62%) were significantly associated with the GBMI-PRS in the meta-analysis after multiple-testing correction. Moreover, the results of the integrative proteomic analysis implicate IL-1 signaling in the etiology of asthma, reinforcing the candidacy of IL1R1 antagonists for drug repurposing.