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In this work, Oxford Nanopore sequencing is tested as an accessible method for quantifying heterogeneity of amplified DNA. This method enables rapid quantification of deletions, insertions, and substitutions, the probability of each mutation error, and …
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Read PDF<h4>Objective</h4>Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used to subtype pathogens causing foodborne and waterborne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae …
Read PDFWastewater-based epidemiology (WBE) offers valuable insight into viral circulation at the community level. In this study, we combined digital PCR (dPCR) with molecular typing to investigate the prevalence and diversity of human adenoviruses (HAdVs) in …
Read PDF<h4>Background</h4>Molecular diagnosis has become highly significant for patient management in oncology.<h4>Methods</h4>Here, 30 well-characterized clinical germline samples were studied with adaptive sampling to enrich the full sequence of 152 cancer predisposition genes. Sequencing was performed on …
Read PDFMorus mongolica is a wild mulberry native to China and North Korea. In the current study, we assembled a high-quality telomere-to-telomere genome sequence of M. mongolica using NGS, HiFi, ONT, and Hi-C technologies. The genome …
Read PDF<i>Enterobacter roggenkampii</i> VT5-1 was isolated from rice noodles, an imported food product from Vietnam. The chromosome and plasmid from the strain were sequenced using Oxford Nanopore sequencing. Total genomes are approximately 4.9 Mbp long, and …
Read PDFThis announcement reports the complete genome sequences, created by combined Illumina and Oxford Nanopore sequencing, of two carbapenemase-producing Enterobacterales (<i>Escherichia coli</i> [LaAc-1-20] and <i>Enterobacter hormaechei</i>, strain 19632-21) isolated from dogs in the United States. Both …
Read PDF<h4>Background/aim</h4>Osteoporosis is a multifactorial skeletal disease that predominantly affects postmenopausal women and is characterized by reduced bone mass and an increased risk of fractures. Growing evidence suggests that the gut microbiota plays a pivotal role …
Read PDF<i>Alternaria</i> is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection …
Read PDFWe present the genome sequence of <i>Lacticaseibacillus rhamnosus</i> isolated from human gut using Oxford Nanopore technology sequencing. The annotated draft genome of <i>L. rhamnosus</i> A20T1A showed the presence of probiotics and psychobiotics genomic traits relevant …
Read PDFGastric dysbiosis, characterized by shifts in the microbial composition, has been increasingly associated with the development of gastric cancer, the fifth leading cause of cancer-related deaths worldwide and the second in Chile, yet its characterization …
Read PDFGenomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor …
Read PDFAn entomopathogenic fungus, <i>Amphichorda felina</i> (formerly classified as <i>Beauveria felina</i>), was sequenced through Illumina MiSeq short reads and Oxford Nanopore long reads. The hybrid assembly resulted in a genome of approximately 29.6 Mb with 9 …
Read PDFOnychostoma macrolepis is an emerging commercial fish with high edible value. Due to overfishing and environmental pollution, the wild population of Onychostoma macrolepis is declining sharply. In this study, we successfully assembled a chromosome-level genome …
Read PDFAdvances in Oxford Nanopore Technologies (ONT) with the introduction of the r10.4.1 flow cell have reduced the sequencing error rates to <1%. When a reference sequence is known, this allows for accurate variant calling comparable …
Read PDF<h4>Background</h4>Breeding of genetically polled animals is a desirable approach in modern cattle husbandry for welfare and economic reasons. At least four different genetic variants associated with polledness in cattle have been identified, suggesting genetic heterogeneity. …
Read PDFExtended 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. …
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