Works by Bogaerts, Bert

Results: 25

Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1614301

By:

Bloemen, Bram;
Gand, Mathieu;
Ringenier, Moniek;
Bogaerts, Bert;
Vanneste, Kevin;
Marchal, Kathleen;
Roosens, Nancy H. C.;
Dewulf, Jeroen;
Boyen, Filip;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

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.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11917-y

By:

Winand, Raf;
D'hooge, Elizabet;
Van Uffelen, Alexander;
Bogaerts, Bert;
Van Braekel, Julien;
Hoffman, Stefan;
Roosens, Nancy H. C. J.;
Becker, Pierre;
De Keersmaecker, Sigrid C. J.;
Vanneste, Kevin

Publication type:

Article

Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin.

Published in:

Microorganisms, 2023, v. 11, n. 8, p. 1954, doi. 10.3390/microorganisms11081954

By:

Laurence Yehouenou, Carine;
Bogaerts, Bert;
Vanneste, Kevin;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.;
Kpangon, Arsène A.;
Affolabi, Dissou;
Simon, Anne;
Dossou, Francis Moise;
Dalleur, Olivia

Publication type:

Article

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation.

Published in:

Microorganisms, 2021, v. 9, n. 4, p. 767, doi. 10.3390/microorganisms9040767

By:

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

Publication type:

Article

Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products.

Published in:

Life (2075-1729), 2022, v. 12, n. 12, p. 1971, doi. 10.3390/life12121971

By:

D'aes, Jolien;
Fraiture, Marie-Alice;
Bogaerts, Bert;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C. J.;
Vanneste, Kevin

Publication type:

Article

BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-024-11158-5

By:

Strepis, Nikolaos;
Dollee, Dennis;
Vrins, Donny;
Vanneste, Kevin;
Bogaerts, Bert;
Carrillo, Catherine;
Bharat, Amrita;
Horan, Kristy;
Sherry, Norelle L.;
Seemann, Torsten;
Howden, Benjamin P.;
Hiltemann, Saskia;
Chindelevitch, Leonid;
Stubbs, Andrew P.;
Hays, John P.

Publication type:

Article

Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-024-11182-5

By:

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.;
Roosens, Nancy H. C.;
Winand, Raf;
Vanneste, Kevin

Publication type:

Article

Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products.

Published in:

Foods, 2021, v. 10, n. 11, p. 2637, doi. 10.3390/foods10112637

By:

D'aes, Jolien;
Fraiture, Marie-Alice;
Bogaerts, Bert;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.;
Vanneste, Kevin

Publication type:

Article

The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country.

Published in:

Foods, 2020, v. 9, n. 8, p. 1030, doi. 10.3390/foods9081030

By:

Nouws, Stéphanie;
Bogaerts, Bert;
Verhaegen, Bavo;
Denayer, Sarah;
Crombé, Florence;
De Rauw, Klara;
Piérard, Denis;
Marchal, Kathleen;
Vanneste, Kevin;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices.

Published in:

Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1204630

By:

Nouws, Stéphanie;
Verhaegen, Bavo;
Denayer, Sarah;
Crombé, Florence;
Piérard, Denis;
Bogaerts, Bert;
Vanneste, Kevin;
Marchal, Kathleen;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B<sub>2</sub> products sold on the Belgian market using whole-genome sequencing.

Published in:

Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1173594

By:

Bogaerts, Bert;
Fraiture, Marie-Alice;
Huwaert, Astrid;
Van Nieuwenhuysen, Tom;
Jacobs, Bram;
Van Hoorde, Koenraad;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.;
Vanneste, Kevin

Publication type:

Article

Phage-Mediated Digestive Decolonization in a Gut-On-A-Chip Model: A Tale of Gut-Specific Bacterial Prosperity.

Published in:

Viruses (1999-4915), 2024, v. 16, n. 7, p. 1047, doi. 10.3390/v16071047

By:

Van Nieuwenhuyse, Brieuc;
Merabishvili, Maya;
Goeders, Nathalie;
Vanneste, Kevin;
Bogaerts, Bert;
de Jode, Mathieu;
Ravau, Joachim;
Wagemans, Jeroen;
Belkhir, Leïla;
Van der Linden, Dimitri

Publication type:

Article

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-71207-3

By:

Nouws, Stéphanie;
Bogaerts, Bert;
Verhaegen, Bavo;
Denayer, Sarah;
Piérard, Denis;
Marchal, Kathleen;
Roosens, Nancy H. C.;
Vanneste, Kevin;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

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: Neisseria meningitidis as a Proof-of-Concept.

Published in:

Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.00362

By:

Bogaerts, Bert;
Winand, Raf;
Fu, Qiang;
Van Braekel, Julien;
Ceyssens, Pieter-Jan;
Mattheus, Wesley;
Bertrand, Sophie;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.;
Vanneste, Kevin

Publication type:

Article

Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019.

Published in:

Acta Clinica Belgica, 2022, v. 77, n. 5, p. 853, doi. 10.1080/17843286.2021.1999588

By:

Soetaert, Karine;
Ceyssens, Pieter-Jan;
Boarbi, Samira;
Bogaerts, Bert;
Delcourt, Thomas;
Vanneste, Kevin;
De Keersmaecker, Sigrid C.J.;
Roosens, Nancy H.C.;
Vodolazkaia, Alexandra;
Mukovnikova, Marina;
Mathys, Vanessa

Publication type:

Article

Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 1, p. 298, doi. 10.3390/ijms21010298

By:

Winand, Raf;
Bogaerts, Bert;
Hoffman, Stefan;
Lefevre, Loïc;
Delvoye, Maud;
Van Braekel, Julien;
Fu, Qiang;
Roosens, Nancy HC;
De Keersmaecker, Sigrid CJ;
Vanneste, Kevin

Publication type:

Article

Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019.

Published in:

2022

By:

Timmermans, Michaël;
Bogaerts, Bert;
Vanneste, Kevin;
Keersmaecker, Sigrid C J De;
Roosens, Nancy H C;
Kowalewicz, Carole;
Simon, Guillaume;
Argudín, Maria A;
Deplano, Ariane;
Hallin, Marie;
Wattiau, Pierre;
Fretin, David;
Denis, Olivier;
Boland, Cécile;
De Keersmaecker, Sigrid C J

Publication type:

journal article

Isolation of Drug-Resistant Gallibacterium anatis from Calves with Unresponsive Bronchopneumonia, Belgium.

Published in:

2020

By:

Van Driessche, Laura;
Vanneste, Kevin;
Bogaerts, Bert;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H.;
Haesebrouck, Freddy;
De Cremer, Lieze;
Deprez, Piet;
Pardon, Bart;
Boyen, Filip

Publication type:

journal article

Genomic comparison between Mycobacterium bovis and Mycobacterium microti and in silico analysis of peptide-based biomarkers for serodiagnosis.

Published in:

Frontiers in Veterinary Science, 2024, p. 1, doi. 10.3389/fvets.2024.1446930

By:

Moens, Charlotte;
Bogaerts, Bert;
Lorente-Leal, Victor;
Vanneste, Kevin;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.;
Mostin, Laurent;
Fretin, David;
Marché, Sylvie

Publication type:

Article

Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-63987-5

By:

Fraiture, Marie-Alice;
Bogaerts, Bert;
Winand, Raf;
Deckers, Marie;
Papazova, Nina;
Vanneste, Kevin;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H. C.

Publication type:

Article

Population Analysis of O26 Shiga Toxin-Producing Escherichia coli Causing Hemolytic Uremic Syndrome in Italy, 1989–2020, Through Whole Genome Sequencing.

Published in:

Frontiers in Cellular & Infection Microbiology, 2022, v. 12, p. 1, doi. 10.3389/fcimb.2022.842508

By:

Michelacci, Valeria;
Montalbano Di Filippo, Margherita;
Gigliucci, Federica;
Arancia, Silvia;
Chiani, Paola;
Minelli, Fabio;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.;
Bogaerts, Bert;
Vanneste, Kevin;
Morabito, Stefano

Publication type:

Article

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.

Published in:

Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.752883

By:

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

Publication type:

Article

Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks.

Published in:

Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.750278

By:

Nouws, Stéphanie;
Bogaerts, Bert;
Verhaegen, Bavo;
Denayer, Sarah;
Laeremans, Lasse;
Marchal, Kathleen;
Roosens, Nancy H. C.;
Vanneste, Kevin;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

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.

Published in:

Annals of Clinical Microbiology & Antimicrobials, 2021, v. 20, n. 1, p. 1, doi. 10.1186/s12941-020-00411-w

By:

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, Françoise;
Dalleur, Olivia;
Simon, Anne

Publication type:

Article

Shifting national surveillance of Shigella infections toward geno‐serotyping by the development of a tailored Luminex assay and NGS workflow.

Published in:

MicrobiologyOpen, 2019, v. 8, n. 8, p. N.PAG, doi. 10.1002/mbo3.807

By:

Ventola, Eleonora;
Bogaerts, Bert;
De Keersmaecker, Sigrid C. J.;
Vanneste, Kevin;
Roosens, Nancy H. C.;
Mattheus, Wesley;
Ceyssens, Pieter‐Jan

Publication type:

Article