Browsing by author "Vanneste, Kevin"
Now showing items 1-18 of 18
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A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches
Bogaerts, Bert; Delcourt, Thomas; Soetaert, Karine; Boarbi, Samira; Ceyssens, Pieter-Jan; Winand, Raf; Van Braekel, Julien; De Keersmaecker, Sigrid C. J.; Roosens, Nancy H. C.; Marchal, Kathleen; Mathys, Vanessa; Vanneste, Kevin (2021) -
A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products
Buytaers, Florence E.; Fraiture, Marie-Alice; Berbers, Bas; Vandermassen, Els; Hoffman, Stefan; Papazova, Nina; Vanneste, Kevin; Marchal, Kathleen; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J. (2021) -
Application of a strain- level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
Buytaers, Florence E.; Saltykova, Assia; Mattheus, Wesley; Verhaegen, Bavo; Roosens, Nancy H. C.; Vanneste, Kevin; Laisnez, Valeska; Hammami, Naiima; Pochet, Brigitte; Cantaert, Vera; Marchal, Kathleen; Denayer, Sarah; De Keersmaecker, Sigrid C. J. (2021) -
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities
Van Uffelen, Alexander; Posadas, Andres; Roosens, Nancy H. C.; Marchal, Kathleen; De Keersmaecker, Sigrid C. J.; Vanneste, Kevin (2024) -
Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
Bloemen, Bram; Gand, Mathieu; Vanneste, Kevin; Marchal, Kathleen; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J. (2023) -
Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations
Bogaerts, Bert; Winand, Raf; Van Braekel, Julien; Hoffman, Stefan; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.; Marchal, Kathleen; Vanneste, Kevin (2021) -
First detection of a plasmid located carbapenem resistant blaVIM-1 gene in E.coli isolated from meat products at retail in Belgium in 2015
Garcia-Graells, C.; Berbers, Bas; Verhaegen, B.; Vanneste, Kevin; Marchal, Kathleen; Roosens, N.H.C.; Botteldoorn, N.; De Keersmaecker, S.C.J. (2020-07) -
First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin
Yehouenou, Carine; Bogaerts, Bert; Vanneste, Kevin; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.; Marchal, Kathleen; Affolabi, Dissou; Soleimani, Reza; Rodriguez-Villalobos, Hector; Van Bambeke, Francoise; Dalleur, Olivia; Simon, Anne (2021) -
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
Nouws, Stephanie; Bogaerts, Bert; Verhaegen, Bavo; Denayer, Sarah; Pierard, Denis; Marchal, Kathleen; Roosens, Nancy H. C.; Vanneste, Kevin; De Keersmaecker, Sigrid C. J. (2020) -
Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
Buytaers, Florence E.; Verhaegen, Bavo; Gand, Mathieu; D'aes, Jolien; Vanneste, Kevin; Roosens, Nancy H. C.; Marchal, Kathleen; Denayer, Sarah; De Keersmaecker, Sigrid C. J. (2022) -
Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation
Bogaerts, Bert; Winand, Raf; Van Braekel, Julien; Mattheus, Wesley; De Keersmaecker, Sigrid C. J.; Roosens, Nancy H. C.; Marchal, Kathleen; Vanneste, Kevin; Ceyssens, Pieter-Jan (2021) -
Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies
Buytaers, Florence E.; Saltykova, Assia; Denayer, Sarah; Verhaegen, Bavo; Vanneste, Kevin; Roosens, Nancy H. C.; Pierard, Denis; Marchal, Kathleen; De Keersmaecker, Sigrid C. J. (2021) -
Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices
Nouws, Stephanie; Verhaegen, Bavo; Denayer, Sarah; Crombe, Florence; Pierard, Denis; Bogaerts, Bert; Vanneste, Kevin; Marchal, Kathleen; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J. (2023) -
Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium
Berbers, Bas; Vanneste, Kevin; Roosens, Nancy H. C. J.; Marchal, Kathleen; Ceyssens, Pieter-Jan; De Keersmaecker, Sigrid C. J. (2023) -
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin- producing Escherichia coli using a reference collection extensively characterized with conventional methods
Bogaerts, Bert; Nouws, Stephanie; Verhaegen, Bavo; Denayer, Sarah; Van Braekel, Julien; Winand, Raf; Fu, Qiang; Crombe, Florence; Pierard, Denis; Marchal, Kathleen; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.; Vanneste, Kevin (2021) -
Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks
Nouws, Stephanie; Bogaerts, Bert; Verhaegen, Bavo; Denayer, Sarah; Laeremans, Lasse; Marchal, Kathleen; Roosens, Nancy H. C.; Vanneste, Kevin; De Keersmaecker, Sigrid C. J. (2021) -
Whole- genome- based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance
Van Poelvoorde, Laura A. E.; Bogaerts, Bert; Fu, Qiang; De Keersmaecker, Sigrid C. J.; Thomas, Isabelle; Van Goethem, Nina; Van Gucht, Steven; Winand, Raf; Saelens, Xavier; Roosens, Nancy; Vanneste, Kevin (2021) -
Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
Yehouenou, Carine Laurence; Bogaerts, Bert; De Keersmaecker, Sigrid C. J.; Roosens, Nancy H. C.; Marchal, Kathleen; Tchiakpe, Edmond; Affolabi, Dissou; Simon, Anne; Dossou, Francis Moise; Vanneste, Kevin; Dalleur, Olivia (2021)