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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 ...
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.
successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same ...
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 ...
Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019
receiving further training. Main concerns were related to the cost of sequencing technologies, data sharing, data integration, interdisciplinary working, and bioinformatics expertise. Conclusions Belgian ...
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 ...
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: as a Proof-of-Concept.
bioinformatics resources and/or expertise. Moreover, many national reference laboratories and centers, as well as other laboratories working under a quality system, require extensive validation to demonstrate that ...
Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study.
Publication Type: Peer reviewed scientific article Authors: Vanneste, Kevin; Garlant, Linda; Broeders, Sylvia; Steven Van Gucht; Nancy Roosens Source: BMC Bioinformatics, Volume 19, Issue 1 (2018) ...
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 ...