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2022
Towards a new (H)ERA: Preparedness for outbreak detection and response, Van Laer, Amber, Nauwelaers Inne, Vanneste Kevin, Mairiaux Eric, Muyldermans Gaetan, Segers Nicolas, Klamer Sofieke, and Masset Heleen , 19/05/2022, (2022)
Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance, Van Poelvoorde, Laura, Vanneste Kevin, De Keersmaecker Sigrid C. J., Thomas Isabelle, Van Goethem Nina, Van Gucht Steven, Saelens Xavier, and Roosens Nancy , Frontiers in Microbiology, Jul-04-2023, Volume 13, (2022)
Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance., Van Poelvoorde, Laura, Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , Front Microbiol, 2022, Volume 13, (2022)
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, Vanneste Kevin, Laisnez Valeska, Hammami Naïma, Pochet Brigitte, Cantaert Vera, et al. , Microbial Genomics, Jul-04-2021, Volume 7, Issue 4, (2021)
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, Marchal Kathleen, et al. , J Clin Microbiol, 2021 Mar 31, (2021)
Case Report: Multidrug Resistant Raoultella ornithinolytica in a Septicemic Calf, Pas, Mathilde L., Vanneste Kevin, Bokma Jade, Van Driessche Laura, De Keersmaecker Sigrid C. J., Roosens Nancy, Haesebrouck Freddy, Boyen Filip, and Pardon Bart , Front Vet Sci, 2021, Volume 8, (2021)
Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products., D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Foods, 2021 Oct 30, Volume 10, Issue 11, (2021)
Concentrations and distribution of chlorinated paraffins in Belgian foods, McGrath, Thomas J., Limonier Franck, Poma Giulia, Bombeke Jasper, Winand Raf, Vanneste Kevin, Andjelkovic Mirjana, Van Hoeck Els, Joly Laure, and Covaci Adrian , Environmental Pollution, Jan-12-2021, Volume 291, (2021)
Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants, Gand, Mathieu, Vanneste Kevin, Thomas Isabelle, Van Gucht Steven, Capron Arnaud, Herman Philippe, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Genes, Jan-04-2021, Volume 12, Issue 4, (2021)
Evaluation of the added value of viral genomic information for predicting severity of influenza infection, Van Goethem, Nina, Robert Annie, Bossuyt Nathalie, Van Poelvoorde Laura, Quoilin Sophie, De Keersmaecker Sigrid C. J., Devleesschauwer Brecht, Thomas Isabelle, Vanneste Kevin, Roosens Nancy, et al. , BMC Infectious Diseases, Jan-12-2021, Volume 21, Issue 1, (2021)
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, De Keersmaecker Sigrid C. J., Marchal Kathleen, and Vanneste Kevin , Microb Genom, 2021 11, Volume 7, Issue 11, (2021)
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, De Keersmaecker Sigrid C. J., Marchal Kathleen, Dissou Affolabi, Soleimani Reza, Rodriguez-Villalobos Hector, Van Bambeke Françoise, et al. , Ann Clin Microbiol Antimicrob, 2021 Jan 06, Volume 20, Issue 1, (2021)
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market., Deckers, Marie, Van Braekel Julien, Vanneste Kevin, Deforce Dieter, Fraiture Marie-Alice, and Roosens Nancy , Database (Oxford), 2021 10 09, Volume 2021, (2021)
Key considerations for the implementation of high throughput sequencing based metagenomics (mNGS) in diagnostic clinical, food and veterinary labs : a no-nonsense pointer. the Metastava consortium, Van Borm, Steven, Vandenbussche Frank, De Clercq Kris, Haegeman Andy, De Keersmaecker Sigrid C. J., Vanneste Kevin, Peeters Michael, Van Gucht Steven, Blanchard Yannick, Pavio Nicole, et al. , 2021, (2021)
Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019., Timmermans, Michaël, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kowalewicz Carole, Simon Guillaume, M Argudín Angeles, Deplano Ariane, Hallin Marie, et al. , J Antimicrob Chemother, 2021 Oct 21, (2021)
Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019, Timmermans, Michaël, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kowalewicz Carole, Simon Guillaume, Argudín Maria A., Deplano Ariane, Hallin Marie, et al. , Journal of Antimicrobial Chemotherapy, Sep-10-2022, Volume 77, Issue 1, (2021)
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, Marchal Kathleen, Vanneste Kevin, and Ceyssens Pieter-Jan , Microorganisms, 2021 Apr 06, Volume 9, Issue 4, (2021)
Presence of chlorinated paraffins in foodstuffs and intake of the belgian population, Joly, Laure, McGrath Thomas J., Limonier Franck, Poma Giulia, Bombeke Jasper, Winand Raf, Vanneste Kevin, Andjelkovic Mirjana, Van Hoeck Els, and Covaci Adrian , LABINFO, 12/2021, Volume 20, Number 18, Brussels, Belgium, (2021)
Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019., Soetaert, Karine, Ceyssens Pieter-Jan, Boarbi Samira, Bogaerts Bert, Delcourt Thomas, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Vodolazkaia Alexandra, Mukovnikova Marina, et al. , Acta Clin Belg, 2021 Nov 09, (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 N., Vanneste Kevin, Marchal Kathleen, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Food Chemistry: Molecular Sciences, Jan-07-2021, Volume 2, (2021)
Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing, Van Poelvoorde, Laura, Delcourt Thomas, Coucke Wim, Herman Philippe, De Keersmaecker Sigrid C. J., Saelens Xavier, Roosens Nancy, and Vanneste Kevin , Frontiers in Microbiology, Jan-10-2022, Volume 12, (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, Piérard Denis, Marchal Kathleen, and De Keersmaecker Sigrid C. J. , Frontiers in Microbiology, May-11-2021, Volume 12, (2021)
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 Stéphanie, Verhaegen Bavo, Denayer Sarah, Van Braekel Julien, Winand Raf, Fu Qiang, Crombé Florence, Piérard Denis, Marchal Kathleen, et al. , Microbial Genomics, Jan-03-2021, Volume 7, Issue 3, (2021)
Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks, Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Laeremans Lasse, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Frontiers in Microbiology, Feb-11-2021, Volume 12, (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, Marchal Kathleen, Tchiakpe Edmond, Dissou Affolabi, Simon Anne, Dossou Francis Moise, Vanneste Kevin, et al. , Front Microbiol, 2021, Volume 12, (2021)

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