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2025
4CMenB vaccine coverage of invasive serogroup B meningococci collected in Belgium between 2016 and 2022, Goeders, Nathalie, Vanneste Kevin, Roosens Nancy, Bogaerts Bert, and Mattheus Wesley , Human Vaccines & Immunotherapeutics, Jul-12-2027, Volume 21, Issue 1, (2025)
Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches, Van Laere, Yari, Fraiture Marie-Alice, Gobbo Andrea, De Keersmaecker Sigrid C. J., Marchal Kathleen, Roosens Nancy, and Vanneste Kevin , Frontiers in Microbiology, Jul-01-2027, Volume 16, (2025)
BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows., Nikolaos, Strepis, Dennis Dollee, Donny Vrins, Vanneste Kevin, Bogaerts Bert, Catherine Carrillo, Amrita Bharat, Kristy Horan, L Sherry, Norelle, Torsten Seemann, et al. , BMC Genomics, 2025 Jan 10, Volume 26, Issue 1, (2025)
be.Prepared: Setting up a cloud-based bioinformatics platform and coupled NRC usability platform for integrated genomic-epidemiological analysis at a national level, Gori, A., Kelchtermans Michael, Millis Kato, Van Laer Amber, Mairiaux Eric, initiative Members of the H. E. R., Van den Bossche An, Ceyssens Pieter-Jan, Mattheus Wesley, Mathys Vanessa, et al. , Applied Bioinformatics and Public Health Microbiology, 22/05/2025, Hixton, UK, (2025)
Development of a shotgun metagenomics workflow for the comprehensive surveillance of biological impurities in vitamin-containing food products, Orval, Rik, Jolien D'aes, De Keersmaecker Sigrid C. J., Vanneste Kevin, Deforce Dieter, Roosens Nancy, and Fraiture Marie-Alice , LWT, Jan-09-2025, Volume 231, (2025)
Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection., Bogaerts, Bert, Van Braekel Julien, Van Uffelen Alexander, D'aes Jolien, Godfroid Maxime, Delcourt Thomas, Kelchtermans Michael, Milis Kato, Goeders Nathalie, De Keersmaecker Sigrid C. J., et al. , BMC Genomics, 2025 Jan 08, Volume 26, Issue 1, (2025)
Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases., Winand, Raf, Elizabet D'hooge, Van Uffelen Alexander, Bogaerts Bert, Van Braekel Julien, Hoffman Stefan, Roosens Nancy, Pierre Becker, De Keersmaecker Sigrid C. J., and Vanneste Kevin , BMC Genomics, 2025 Aug 06, Volume 26, Issue 1, (2025)
Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible in broilers., Moniek, Ringenier, Boyen Filip, Bogaerts Bert, Gand Mathieu, Vanneste Kevin, De Keersmaecker Sigrid C. J., Ilias Chantziaras, Nelima Ibrahim, Devreese Mathias, and Dewulf Jeroen , Front Vet Sci, 2025, Volume 12, (2025)
Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products, D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, Van Laere Yari, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Food Chemistry: Molecular Sciences, June-2025, Volume 10, (2025)
Molecular and WGS-based characterization of invasive Neisseria meningitidis isolates collected in Belgium (2016-2022) and MenB-FHbp vaccine coverage estimation of serogroup B., Goeders, Nathalie, Vanneste Kevin, Roosens Nancy, Bogaerts Bert, and Mattheus Wesley , Vaccine, 2025 May 10, Volume 55, (2025)
Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance., Bloemen, Bram, Gand Mathieu, Moniek Ringenier, Bogaerts Bert, Vanneste Kevin, Marchal Kathleen, Roosens Nancy, Dewulf Jeroen, Boyen Filip, and De Keersmaecker Sigrid C. J. , Front Microbiol, 2025, Volume 16, (2025)
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of and when accounting for methylation-related errors., Bogaerts, Bert, Margo Maex, Florian Commans, Goeders Nathalie, Van den Bossche An, De Keersmaecker Sigrid C. J., Roosens Nancy, Ceyssens Pieter-Jan, Mattheus Wesley, and Vanneste Kevin , J Clin Microbiol, 2025 Oct 08, Volume 63, Issue 10, (2025)
Salmonella spp. as a be.Prepared Case Study for Integrating Microbial Genomic and Health Data in Public Health Surveillance, Van Laer, Amber, Commans Florian, Mattheus Wesley, Van den Bossche An, Ceyssens Pieter-Jan, Vanneste Kevin, De Keersmaecker Sigrid C. J., Gori A., Kelchtermans Michael, Milis Kato, et al. , Scientific seminar for Infectious Diseases, 22/05/2025, Brussels, Belgium, (2025)
2024
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities, Van Uffelen, Alexander, Posadas Andrés, Roosens Nancy, Marchal Kathleen, De Keersmaecker Sigrid C. J., and Vanneste Kevin , Scientific Data, 2024/08/10, Volume 11, Issue 1, (2024)
be.Prepared: An architecture to increase Belgian integration of health data as a way of strengthening preparedness for infectious diseases, Van Laer, Amber, Kelchtermans Michael, Millis Kato, Gori A., Van Cauteren Dieter, Brondeel Ruben, De Keersmaecker Sigrid C. J., Herman Philippe, Roosens Nancy, De Ridder Karin, et al. , The Belgian Presidency of the Council of the European Union, March 2024, (2024)
be.Prepared to increase Belgian integration of health data as a way of strengthening preparedness for infectious diseases, Masset, Heleen, Van Laer Amber, Kelchtermans Michael, Millis Kato, Gori A., Winand Raf, De Keersmaecker Sigrid C. J., Roosens Nancy, Herman Philippe, Brondeel Ruben, et al. , ESCMID Global 2024, 27/04/2024, Barcelona, (2024)
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert, Van den Bossche An, Verhaegen Bavo, Delbrassinne Laurence, Mattheus Wesley, Nouws Stéphanie, Godfroid Maxime, Hoffman Stefan, Roosens Nancy, De Keersmaecker Sigrid C. J., et al. , J Clin Microbiol, 2024 Mar 05, (2024)
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)
Genomic comparison between and and analysis of peptide-based biomarkers for serodiagnosis., Moens, Charlotte, Bogaerts Bert, Lorente-Leal Victor, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Mostin Laurent, Fretin David, and Marché Sylvie , Front Vet Sci, 2024, Volume 11, (2024)
An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material., Liu, Lihong, Mikhayil Hakhverdyan, Wallgren Per, Vanneste Kevin, Qiang Fu, Pierrick Lucas, Blanchard Yannick, de Graaf Miranda, Oude Munnink Bas B., van Boheemen Sander, et al. , Microbiol Spectr, 2024 Oct 03, Volume 12, Issue 10, (2024)
Phage-Mediated Digestive Decolonization in a Gut-On-A-Chip Model: A Tale of Gut-Specific Bacterial Prosperity., Van Nieuwenhuyse, Brieuc, Merabishvili Maya, Goeders Nathalie, Vanneste Kevin, Bogaerts Bert, de Jode Mathieu, Ravau Joachim, Wagemans Jeroen, Belkhir Leïla, and Van der Linden Dimitri , Viruses, 2024 Jun 28, Volume 16, Issue 7, (2024)
Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GM Bacillus licheniformis producing alpha-amylase, Fraiture, Marie-Alice, Gobbo Andrea, Guillitte Chloé, Marchesi Ugo, Verginelli Daniela, De Greve Joke, D'aes Jolien, Vanneste Kevin, Papazova N., and Roosens Nancy , Food Chemistry: Molecular Sciences, Jan-07-2024, Volume 8, (2024)
Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling, Buytaers, Florence E., Verhaegen Bavo, Van Nieuwenhuysen Tom, Roosens Nancy, Vanneste Kevin, Marchal Kathleen, and De Keersmaecker Sigrid C. J. , Frontiers in Microbiology, (2024)

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