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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)
Review on current scientific literature and overview of commercially available methods for on-site DNA isolation, AbuOun, Manal, Navickaite Indre, De Keersmaecker Sigrid C. J., Gand Mathieu, Persson Søren, Michelacci Valeria, Marotta Francesca, Di Domenico Marco, Garofolo Giuliano, and Brouwer Michael , 28/04/2021, Zenodo, p.15, (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)
Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution., Van Poelvoorde, Laura, Gand Mathieu, Fraiture Marie-Alice, De Keersmaecker Sigrid C. J., Verhaegen Bavo, Van Hoorde Koenraad, Cay Ann Brigitte, Balmelle Nadège, Herman Philippe, and Roosens Nancy , Curr Issues Mol Biol, 2021 Nov 06, Volume 43, Issue 3, (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)
Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance., Van Poelvoorde, Laura, Bogaerts Bert, Qiang Fu, De Keersmaecker Sigrid C. J., Thomas Isabelle, Van Goethem Nina, Van Gucht Steven, Winand Raf, Saelens Xavier, Roosens Nancy, et al. , Microb Genom, 2021 09, Volume 7, Issue 9, (2021)
2020
The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country., Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Crombé Florence, De Rauw Klara, Piérard Denis, Marchal Kathleen, Vanneste Kevin, Roosens Nancy, et al. , Foods, 2020 Aug 01, Volume 9, Issue 8, (2020)
Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus, Berbers, Bas, Saltykova Assia, Garcia-Graells Cristina, Philipp Patrick, Arella Fabrice, Marchal Kathleen, Winand Raf, Vanneste Kevin, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Scientific Reports, Jan-12-2020, Volume 10, Issue 1, (2020)
Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination., Berbers, Bas, Ceyssens Pieter-Jan, Bogaerts Pierre, Vanneste Kevin, Roosens Nancy, Marchal Kathleen, and De Keersmaecker Sigrid C. J. , Antibiotics (Basel), 2020 Aug 11, Volume 9, Issue 8, (2020)
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, Cristina, Berbers Bas, Verhaegen Bavo, Vanneste Kevin, Marchal Kathleen, Roosens Nancy, Botteldoorn N, and De Keersmaecker Sigrid C. J. , International Journal of Food Microbiology, Jan-07-2020, Volume 324, (2020)
Food Chemistry, Function and AnalysisDNA Techniques to Verify Food Authenticity CHAPTER 8. GMO Detection and Identification Using Next-generation Sequencing, Fraiture, Marie-Alice, Papazova N., Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , 2020, Cambridge, p.96 - 106, (2020)
Gender‐dependent association between exhaled nitric oxide and the CC16 38AA genotype in young school children, Nauwelaerts, S., Roosens Nancy, De Cremer Koen, Bernard Alfred, and De Keersmaecker Sigrid C. J. , Immunity, Inflammation and Disease, Jun-08-2020, (2020)
Genomic epidemiology of emerging ESBL-producing Kentucky in Europe., Coipan, Claudia E., Westrell Therese, van Hoeck Angela H. A. M., Alm Erik, Kotila Saara, Berbers Bas, De Keersmaecker Sigrid C. J., Ceyssens Pieter-Jan, Borg Maria Louise, Chattaway Marie, et al. , Emerg Microbes Infect, 2020 Dec, Volume 9, Issue 1, (2020)
A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium., Gand, Mathieu, Mattheus Wesley, Roosens Nancy, Dierick Katelijne, Marchal Kathleen, Bertrand Sophie, and De Keersmaecker Sigrid C. J. , Food Microbiol, 2020 Oct, Volume 91, (2020)
Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing., Fraiture, Marie-Alice, Bogaerts Bert, Winand Raf, Deckers Marie, Papazova N., Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , Sci Rep, 2020 04 27, Volume 10, Issue 1, (2020)
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates, Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Piérard Denis, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Scientific Reports, Jan-12-2020, Volume 10, Issue 1, (2020)
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates., Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Piérard Denis, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Sci Rep, 2020 09 04, Volume 10, Issue 1, (2020)
Isolation of Drug-Resistant Gallibacterium anatis from Calves with Unresponsive Bronchopneumonia, Belgium., Van Driessche, Laura, Vanneste Kevin, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, Haesebrouck Freddy, De Cremer Lieze, Deprez Piet, Pardon Bart, and Boyen Filip , Emerg Infect Dis, 2020 04, Volume 26, Issue 4, (2020)
A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay, Gand, Mathieu, Mattheus Wesley, Roosens Nancy, Dierick Katelijne, Marchal Kathleen, De Keersmaecker Sigrid C. J., and Bertrand Sophie , Food Microbiology, Jan-05-2020, Volume 87, (2020)
NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program, Delcourt, Thomas, Vanneste Kevin, Soumali Mohamed Rida, Coucke Wim, Ghislain V, Hébrant Aline, Van Valckenborgh Els, De Keersmaecker Sigrid C. J., Roosens Nancy, Van de Walle P, et al. , Cancers, Jan-11-2020, Volume 12, Issue 11, (2020)
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, Van Goethem, Nina, Struelens M. J., De Keersmaecker Sigrid C. J., Roosens Nancy, Robert A., Quoilin Sophie, Van Oyen Herman, and Devleesschauwer Brecht , BMC Public Health, Jan-12-2020, Volume 20, Issue 1, (2020)

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