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Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
Salmonella SNP analysis strain-level Abstract: Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to ...
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 ...
Bluetongue Virus Infections in Cattle Herds of Manabí Province of Ecuador
death may occur depending on the strain of the virus and other factors; cattle act as a reservoir for the virus. Although the Ecuadorian coast has climatic conditions that favor the presence of the ...
Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs.
involved pyrazinamide, ethambutol, and ethionamide, and low-level rifampicin- or isoniazid-resistance mutations, all notoriously prone to phenotypic testing variability. Only 2 of 91 (2.2%) resistance ...
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.
chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain ...
NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Strains Responsible for FoodBorne Outbreaks.
To include the different divergence levels between SE-coding genes, parameters of coverage and identity were generated from 10,000 simulations and a dataset of 244 assembled genomes from strains ...
Human challenge trial workshop: Focus on quality requirements for challenge agents, Langen, Germany, October 22, 2019.
exposure studies need to be safe and results should be meaningful, e.g. contribute to a better cure. Both in the US and in Europe, the level of Good Manufacturing Practice required is related to the phase of ...
Development of a genoserotyping system for the identification of Salmonella serotypes
of the results in a database to improve the Salmonella surveillance in Belgium. The 4 modules and the DSS were validated by comparison with the classical method, including more than 1300 strains and ...
Molecular surveillance of anti-malarial drug resistance in Democratic Republic of Congo: high variability of chloroquinoresistance and lack of amodiaquinoresistance.
to 63.9% in 2014. The purpose of this study was to determine the prevalence of K76T mutations in circulating strains of Plasmodium falciparum, 16 years after CQ withdrawal in the DRC and to investigate ...