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Extended spectrum β-lactamase producing Escherichia coli (ESBL-Ec) is recognized as an opportunistic pathogen with zoonotic potential, posing a threat to public health. This study aimed to identify virulence factor genes (VFGs), determine ESBL-Ec pathotypes and …
Read PDFExtended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases represent a threat for public health. Their dissemination is often mediated by mobile genetic elements (MGEs), but plasmid identification and characterization could be hindered by sequencing limitations. …
Read PDFItalian ryegrass (Lolium multiflorum Lam.) is an important forage grass, providing a major source of feed for ruminants in temperate regions. Due to its highly heterozygous and repeat-rich genome, high-quality chromosome-level genome assemblies are scarce …
Read PDF<i>Leishmania panamensis</i> is a causative agent of leishmaniasis in Latin America, with significant incidence in Panama and Colombia. The first annotated genome draft for this parasite remained incomplete due to its highly repetitive nature. Here, …
Read PDFHighland potato areas in East Java, Indonesia-Sumber Brantas and Tosari-face severe late blight caused by <i>Phytophthora infestans</i>. We profiled phyllosphere fungal communities (phylloplane plus leaf endosphere) on symptomatic potato leaves and examined how management contexts …
Read PDFAutism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder marked by difficulties in communication, social interaction, and restricted, repetitive behaviors. The gut microbiota has emerged as a key factor in the gut-brain axis relevant to …
Read PDFNucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes …
Read PDFGenomics research is essential for understanding the transmission and evolution of bacterial antimicrobial resistance. The development of nanopore long-read sequencing has revolutionized our understanding of the prevalence, spread, and dynamic evolution of bacterial ARGs. This …
Read PDF<h4>Motivation</h4>Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to …
Read PDF<b>Background:</b> Structural variants (SVs) play a significant role in gene function and are implicated in numerous human diseases. With advances in sequencing technologies, identifying SVs through whole-genome sequencing (WGS) has become a key area of …
Read PDFThe community of microorganisms occurring in the animal gut, known as the gut microbiota, is closely connected to host health. It is essential for metabolic processes, digestion, and defense against pathogens. Knowledge about the composition …
Read PDFRNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted long non-coding …
Read PDF<i>Streptococcus pneumoniae</i> (pneumococcus) is a leading cause of community-acquired pneumonia and invasive diseases, particularly among children and the elderly. The introduction of pneumococcal conjugate vaccines has significantly reduced invasive pneumococcal disease, but the prevalence of …
Read PDFThis dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates …
Read PDF<i>Pseudomonas</i> sp. CBR-F is a bacterial species isolated from a water treatment plant targeting for per- and poly-fluoroalkyl substances, a difficult-to-degrade family of anthropogenic compounds. Here, we report a complete genome for <i>Pseudomonas</i> sp. CBR-F, …
Read PDFRespiratory syncytial virus (RSV) is a globally circulating virus, causing severe respiratory infections in infants and the elderly. Two RSV vaccines were recently approved, and passive immunization is now recommended in several countries for all …
Read PDFThe genus Ormosia is in the Fabaceae family. China is one of its centers of origin, with almost all species being endemic, suggesting the need for genomic studies to understand its evolution, conservation, and use. …
Read PDFAccurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related <i>Staphylococcus …
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