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2023
Strain-level characterization without culture enrichment? Easing and accelerating 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. , BSFM, 2023-10-13, Brussels, Belgium, (2023)
Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms, Fraiture, Marie-Alice, D'aes Jolien, Guiderdoni Emmanuel, Meunier Anne-Cécile, Delcourt Thomas, Hoffman Stefan, Vandermassen Els, De Keersmaecker Sigrid C. J., Vanneste Kevin, and Roosens Nancy , Foods, Jan-02-2023, Volume 12, Issue 3, (2023)
Transforming Shiga toxin-producing surveillance through whole genome sequencing in food safety practices., Nouws, Stéphanie, Verhaegen Bavo, Denayer Sarah, Crombé Florence, Piérard Denis, Bogaerts Bert, Vanneste Kevin, Marchal Kathleen, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Front Microbiol, 2023, Volume 14, (2023)
Using a combination of short and long read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum-beta-lactamases (ESBL) in clinical Shigella and Salmonella isolates in Belgium, Berbers, Bas, Vanneste Kevin, Roosens Nancy, Marchal K., Ceyssens Pieter-Jan, and De Keersmaecker Sigrid C. J. , Microbial Genomics, 23/01/2023, Volume 9:000925, Number 23, (2023)
Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium, Berbers, Bas, Vanneste Kevin, Roosens Nancy, Marchal Kathleen, Ceyssens Pieter-Jan, and De Keersmaecker Sigrid C. J. , Microbial Genomics, Nov-01-2024, Volume 9, Issue 1, (2023)
Whole-genome sequencing-based phylogenomic investigation of unexpected Bacillus cereus contaminations collected from commercial vitamin B2 food and feed additives sold on the Belgian market, Bogaerts, Bert, Fraiture Marie-Alice, Huwaert Astrid, Van Nieuwenhuysen Tom, Jacobs Bram, Van Hoorde Koenraad, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Applied Bioinformatics and Public Health Microbiology , 2023, Hinxton, OK, (2023)
Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin., Yehouenou, Laurence Carine, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kpangon Arsène A., Dissou Affolabi, Simon Anne, Dossou Francis Moise, and Dalleur Olivia , Microorganisms, 2023 Jul 31, Volume 11, Issue 8, (2023)
2022
Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database, Saltykova, Assia, Van Braekel Julien, Papazova N., Fraiture Marie-Alice, Deforce Dieter, Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , Food Chemistry: Molecular Sciences, Jan-07-2022, Volume 4, (2022)
A general approach to identify low-frequency variants within influenza samples collected during routine surveillance., Van Poelvoorde, Laura, Delcourt Thomas, Vuylsteke Marnik, De Keersmaecker Sigrid C. J., Thomas Isabelle, Van Gucht Steven, Saelens Xavier, Roosens Nancy, and Vanneste Kevin , Microb Genom, 2022 09, Volume 8, Issue 9, (2022)
The key role of WGS-based surveillance of Listeria monocytogenes in both human and food isolates in outbreak investigations, Van den Bossche, An, De Keersmaecker Sigrid C. J., Mattheus Wesley, Roosens Nancy, Bogaerts Bert, Vanneste Kevin, Van Hoorde Koenraad, and Verhaegen Bavo , 26th Conference on Food Microbiology, 13-14/10/2022, Issue BSFM, Brussels, Belgium, (2022)
Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products, D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Life, 25/11/2022, Volume 12, Issue 12, (2022)
Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study, Buytaers, Florence E., Verhaegen Bavo, Gand Mathieu, D'aes Jolien, Vanneste Kevin, Roosens Nancy, Marchal Kathleen, Denayer Sarah, and De Keersmaecker Sigrid C. J. , Foods, Jan-11-2022, Volume 11, Issue 21, (2022)
Optimised long-read sequence bioinformatics tool for the analysis of the resistome and microbial communities, AbuOun, Manal, Otani Saria, Navickaite Indre, Gand Mathieu, Bloemen Bram, Vanneste Kevin, Michelacci Valeria, Matamoros Bosco Rodríguez, Roosens Nancy, and De Keersmaecker Sigrid C. J. , 13/12/2022, Zenodo, p.12, (2022)
Population Analysis of O26 Shiga Toxin-Producing Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing., Michelacci, Valeria, Montalbano Di Filippo Margherita, Gigliucci Federica, Arancia Silvia, Chiani Paola, Minelli Fabio, Roosens Nancy, De Keersmaecker Sigrid C. J., Bogaerts Bert, Vanneste Kevin, et al. , Front Cell Infect Microbiol, 2022, Volume 12, (2022)
Report on an initial assessment of long-read sequencing for metagenome (community and AMR) analysis (defined community, spiked and real simple and complex matrices) and comparison to current short-read standard, De Keersmaecker, Sigrid C. J., Gand Mathieu, Navickaite Indre, Gruetzke Josephine, Bartsch Lee-Julia, Otani Saria, Garofolo Giuliano, Di Domenico Marco, Michelacci Valeria, Matamoros Bosco R., et al. , 13/12/2022, Zenodo, p.44, (2022)
Report on initial findings of on-site diagnostic tests and IT solutions for human clinical, veterinary and environmental samples for early warning of emerging resistant pathogens, AbuOun, Manal, Navickaite Indre, Wilkes Thomas I., Di Domenico Marco, Garofolo Giuliano, Bloemen Bram, Gand Mathieu, Roosens Nancy, Vanneste Kevin, De Keersmaecker Sigrid C. J., et al. , 13/12/2022, Zenodo, p.12, (2022)
Report on the feasibility of using Hi-C sequencing for metagenomics to define the context of AMR genes, De Keersmaecker, Sigrid C. J., Grützke Josephine, Deneke Carlus, Fischer Jennie, Bartsch Lee Julia, Bloemen Bram, Vanneste Kevin, D'aes Jolien, Roosens Nancy, and AbuOun Manal , 13/12/2022, Zenodo, p.10, (2022)
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. , ONE Conference 2022, 21/06/2022, Issue EFSA, (2022)
Shotgun metagenomics as a ONE Health tool for better protecting human health, Gand, Mathieu, Buytaers Florence E., Bloemen Bram, Saltykova Assia, Denayer Sarah, Verhaegen Bavo, Mattheus Wesley, Piérard Denis, Bogaerts Bert, Marchal Kathleen, et al. , EFSA One, 21/06/2022, Issue EFSA, (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., and Roosens Nancy , Front Microbiol, 2022, 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., Thomas Isabelle, Van Goethem Nina, Van Gucht Steven, Saelens Xavier, and Roosens Nancy , Frontiers in Microbiology, Jul-04-2023, 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)

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