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Strain-level characterization without culture enrichment? Easing and accelerating outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling
metagenomics and adaptive sampling using other databases. It allowed strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating ...
Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
contaminant present in the sample at once, possibly also at the SNP level. At the time this study started, shotgun metagenomics for the study of food contaminants was in its infancy. Moreover, strain-level ...
Shotgun metagenomics for strain-level food-borne outbreak investigation
Publication Type: Scientific poster, presentation or proceeding Authors: Florence E Buytaers Source: FoodMicro (2022) Service: Activités transversales en génomique appliquée Transversale activiteiten in toegepaste genomica Transversal activities in appli ...
Shotgun metagenomics as a ONE Health tool for better protecting human health
laboratories, however without isolation and in a shorter time-frame. This could be achieved to the strain level even in samples with several E. coli strains. The method was also used to solve a Salmonella ...
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After ...
Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies
Sigrid C.J. De Keersmaecker Source: Frontiers in Microbiology, Volume 12 (2021) Keywords: Flongle food surveillance Metagenomics nanopore outbreak SNP analysis STEC strain-level Abstract: The current ...
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.
Keersmaecker Source: Int J Mol Sci, Volume 21, Issue 16 (2020) Keywords: foodborne outbreak investigation public health strain-level metagenomics Abstract: Culture-independent diagnostics, such as metagenomic ...
A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.
Sigrid C.J. De Keersmaecker Source: Microorganisms, Volume 8, Issue 8 (2020) Keywords: food surveillance Metagenomics outbreak SNP analysis STEC whole genome Abstract: The management of a foodborne ...