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Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study.
community obtained by in vitro spiking minced meat with a Shiga toxin-producing (STEC) isolate originating from a described outbreak. The more optimal tool Sigma was further evaluated using in silico ...
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 ...
The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country.
Vanneste; Nancy Roosens; Sigrid C.J. De Keersmaecker Source: Foods, Volume 9, Issue 8 (2020) Keywords: Food Safety foodborne outbreak investigation Shiga toxin-producing Escherichia coli STEC Surveillance WGS ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.
virulence and antimicrobial resistance genotyping) and phylogenetic relatedness (core genome multilocus sequence typing and single nucleotide polymorphism analysis). Shiga toxin-producing Escherichia coli ...