| Targeting the 16s rRNA gene for bacterial identification in complex mixed samples: Comparative evaluation of second (illumina) and third (oxford nanopore technologies … R Winand, B Bogaerts, S Hoffman, L Lefevre, M Delvoye, J Van Braekel, ... International journal of molecular sciences 21 (1), 298, 2019 | 211 | 2019 |
| 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 … B Bogaerts, R Winand, Q Fu, J Van Braekel, PJ Ceyssens, W Mattheus, ... Frontiers in microbiology 10, 362, 2019 | 55 | 2019 |
| Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates S Nouws, B Bogaerts, B Verhaegen, S Denayer, D Piérard, K Marchal, ... Scientific reports 10 (1), 14649, 2020 | 53 | 2020 |
| Isolation of drug-resistant Gallibacterium anatis from calves with unresponsive bronchopneumonia, Belgium L Van Driessche, K Vanneste, B Bogaerts, SCJ De Keersmaecker, ... Emerging infectious diseases 26 (4), 721, 2020 | 41 | 2020 |
| Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019 M Timmermans, B Bogaerts, K Vanneste, SCJ De Keersmaecker, ... Journal of Antimicrobial Chemotherapy 77 (1), 49-57, 2022 | 38 | 2022 |
| Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively … B Bogaerts, S Nouws, B Verhaegen, S Denayer, J Van Braekel, R Winand, ... Microbial genomics 7 (3), 000531, 2021 | 33 | 2021 |
| The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a national reference laboratory in a smaller country S Nouws, B Bogaerts, B Verhaegen, S Denayer, F Crombé, K De Rauw, ... Foods 9 (8), 1030, 2020 | 32 | 2020 |
| Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens B Bogaerts, A Van den Bossche, B Verhaegen, L Delbrassinne, ... Journal of Clinical Microbiology 62 (5), e01576-23, 2024 | 27 | 2024 |
| A bioinformatics whole-genome sequencing workflow for clinical mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively … B Bogaerts, T Delcourt, K Soetaert, S Boarbi, PJ Ceyssens, R Winand, ... Journal of Clinical Microbiology 59 (6), 10.1128/jcm. 00202-21, 2021 | 27 | 2021 |
| Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations B Bogaerts, R Winand, J Van Braekel, S Hoffman, NHC Roosens, ... Microbial Genomics 7 (11), 000699, 2021 | 17 | 2021 |
| Whole-genome-based phylogenomic analysis of the Belgian 2016–2017 influenza A (H3N2) outbreak season allows improved surveillance LAE Van Poelvoorde, B Bogaerts, Q Fu, SCJ De Keersmaecker, I Thomas, ... Microbial Genomics 7 (9), 000643, 2021 | 15 | 2021 |
| Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing MA Fraiture, B Bogaerts, R Winand, M Deckers, N Papazova, K Vanneste, ... Scientific Reports 10 (1), 7094, 2020 | 14 | 2020 |
| Whole genome sequencing provides an added value to the investigation of staphylococcal food poisoning outbreaks S Nouws, B Bogaerts, B Verhaegen, S Denayer, L Laeremans, K Marchal, ... Frontiers in Microbiology 12, 750278, 2021 | 13 | 2021 |
| Shifting national surveillance of Shigella infections toward geno‐serotyping by the development of a tailored Luminex assay and NGS workflow E Ventola, B Bogaerts, SCJ De Keersmaecker, K Vanneste, ... Microbiologyopen 8 (8), e00807, 2019 | 11 | 2019 |
| Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products J D’aes, MA Fraiture, B Bogaerts, SCJ De Keersmaecker, NHCJ Roosens, ... Life 12 (12), 1971, 2022 | 9 | 2022 |
| Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019 K Soetaert, PJ Ceyssens, S Boarbi, B Bogaerts, T Delcourt, K Vanneste, ... Acta Clinica Belgica 77 (5), 853-860, 2022 | 9 | 2022 |
| Whole-genome sequencing-based antimicrobial resistance characterization and phylogenomic investigation of 19 multidrug-resistant and extended-spectrum beta-lactamase-positive … CL Yehouenou, B Bogaerts, SCJ De Keersmaecker, NHC Roosens, ... Frontiers in microbiology 12, 752883, 2021 | 9 | 2021 |
| First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated … C Yehouenou, B Bogaerts, K Vanneste, NHC Roosens, ... Annals of clinical microbiology and antimicrobials 20, 1-7, 2021 | 8 | 2021 |
| Population Analysis of O26 Shiga Toxin-Producing Escherichia coli Causing Hemolytic Uremic Syndrome in Italy, 1989–2020, Through Whole Genome Sequencing V Michelacci, M Montalbano Di Filippo, F Gigliucci, S Arancia, P Chiani, ... Frontiers in Cellular and Infection Microbiology 12, 842508, 2022 | 7 | 2022 |
| Characterization of genetically modified microorganisms using short-and long-read whole-genome sequencing reveals contaminations of related origin in multiple commercial food … J D’aes, MA Fraiture, B Bogaerts, SCJ De Keersmaecker, NHC Roosens, ... Foods 10 (11), 2637, 2021 | 7 | 2021 |