Search results - 21 results
Strain-level characterization without culture enrichment? Easing and accelerating outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling
outbreak. Additionally, the living S. aureus strain was spiked into mashed potatoes at a level of 10 5 CFU per 25 grams and three DNA extraction kits were tested, in combination with two databases for ...
Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
water, the DNA was extracted with two classical commercial kits or with a kit performing depletion of the host DNA. The extracted DNA also was amplified or not using Phi29 polymerase. We showed that all ...
Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteriaAbstractBackgroundResultsConclusion
Keywords: DNA extraction HMW DNA Long-read Metagenomics Method evaluation nanopore Abstract: Background: Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which ...
Shotgun metagenomics as a ONE Health tool for better protecting human health
each other, and also to the results obtained with conventional methods. Results: A commercial kit was selected and optimized for the extraction of sufficient high-molecular weight DNA, to match the needs ...
Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype.
assessed according to the OIE standards. To facilitate assay deployment, amplification conditions were optimized with different nucleic extraction systems and amplification kits. Performance of the new ...
Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks
C.J. De Keersmaecker Source: Frontiers in Microbiology, Volume 12 (2021) Keywords: DNA extraction kits enterotoxin gene profiling outbreak investigation relatedness determination Staphylococcus aureus, ...
A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.
Shiga toxin-producing (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
C.J. De Keersmaecker Source: Scientific Reports, Volume 10, Issue 1 (2020) Keywords: DNA extraction kits outbreak investigation Shiga toxin producing Escherichia coli (STEC) Whole genome sequencing (WGS) ...
Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?
Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping ...
Global transcriptional analyses of Mycobacterium tuberculosis using old and new drugs
of the drug. RNA was extracted combining bead-beating in TRI zol and the Direct-Zol purification kit. After quality control, the extracts were fragmented, barcoded and pooled, cDNA libraries were ...