Oxford Nanopore long reads of simulated bacterial communities from fresh spinach and surface water were generated (R9.4.1+SQK-LSK109 and R10.4+SQK-LSK112; 0.5, one, and two million reads). serotype Heidelberg, Montevideo, or Typhimurium was included alone or in combination in the spinach community, while the water community harbored .
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http://dx.doi.org/10.1128/mra.00586-24 | DOI Listing |
BMC Res Notes
January 2025
Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain), Brussels, Belgium.
Objective: 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 isolates from whole-genome sequencing (WGS) data, and provide backward compatibility with traditional MLVA typing methods. The previous development and validation work was conducted using short (pair-end 300 and 150 nt long) reads from Illumina MiSeq and Hiseq sequencing.
View Article and Find Full Text PDFPlant Dis
January 2025
University of Minnesota Twin Cities, Department of Plant Pathology, 1991 Upper Buford circle, 495 Borlaug Hall, Saint Paul, Minnesota, United States, 55108;
Ginger (Zingiber officinale) is an herbaceous perennial in the Zingiberaceae family grown primarily in tropical to subtropical biomes as a culinary spice, a traditional medicine, and a landscaping plant. While ginger grows at soil temperatures above 20°C, several farmers in the upper Midwestern US farmers grows short-season ginger in high tunnels. In 2023 and 2024, growers in southeastern Minnesota reported a new disease of ginger.
View Article and Find Full Text PDFMicrobiol Resour Announc
January 2025
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
The complete genome of subsp. BI040-a human stool isolate, was sequenced using Illumina and Oxford Nanopore technologies. The BI040 genome is composed of a circular 1,944,141-bp chromosome which carries genes potentially involved in vitamin synthesis and gut health.
View Article and Find Full Text PDFJ Clin Virol
January 2025
Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:
Background: Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time.
View Article and Find Full Text PDFSci Data
January 2025
Department of Botany and Evolutionary Ecology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, Olsztyn, 10-719, Poland.
Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with a cosmopolitan distribution among a wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into the genetic aspects of this species is limited.
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