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Staphylococcal enterotoxin gene cluster: prediction of enterotoxin (SEG and SEI) production and of the source of food poisoning based on Saβ typing.

animal) were investigated applying bioinformatics methods (phylogenetic analysis using the core genome and different alignments). SEG and SEI expression was tested using a sandwich ELISA method.Strains ...

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection.

the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of ...

NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Strains Responsible for FoodBorne Outbreaks.

Christos; Daskalov, Hristo; Mistou, Michel-Yves; Hennekinne, Jacques-Antoine Source: Front Microbiol, Volume 11 (2020) Keywords: bioinformatics tool; gene detection genomic staphylococcal enterotoxins genes ...

Listeria surveillance in Belgium

evolution in molecular typing, the NRC completely switched to Whole-Genome-Sequencing (WGS) for cluster detection. Therefore, an in-house Galaxy-based bio-informatic pipeline was developed. For the strain ...

Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:.

PLoS One, Volume 13, Issue 2 (2018) Keywords: bacterial phylogeny; food-borne; genes; NGS; WGS; computational biology/bioinformatics; disease outbreaks; outbreak; performance evaluation; pipeline; ...

Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016.

funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was ...

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