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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)
Noninvasive integrative approach applied to children in the context of recent air pollution exposure demonstrates association between fractional exhaled nitric oxide (FeNO) and urinary CC16., Nauwelaerts, S., Van Goethem Nina, De Cremer Koen, Bustos Sierra Natalia, Vercauteren Jordy, Stroobants Christophe, Bernard Alfred, Nawrot Tim, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Environ Res, 2022 Sep 30, Volume 216, Issue Pt 1, (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)
Urinary CC16, a potential indicator of lung integrity and inflammation, increases in children after short-term exposure to PM/PM and is driven by the CC16 38GG genotype., Nauwelaerts, S., Van Goethem Nina, Ureña Berta Tenas, De Cremer Koen, Bernard Alfred, Saenen Nelly D., Nawrot Tim S., Roosens Nancy, and De Keersmaecker Sigrid C. J. , Environ Res, 2022 09, Volume 212, Issue Pt B, (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)
Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products., D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Foods, 2021 Oct 30, Volume 10, Issue 11, (2021)
Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020., Van Goethem, Nina, Van den Bossche An, Ceyssens Pieter-Jan, Lajot Adrien, Coucke Wim, Vernelen Kris, Roosens Nancy, De Keersmaecker Sigrid C. J., Van Cauteren Dieter, and Mattheus Wesley , PLoS One, 2021, Volume 16, Issue 8, (2021)
Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants, Gand, Mathieu, Vanneste Kevin, Thomas Isabelle, Van Gucht Steven, Capron Arnaud, Herman Philippe, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Genes, Jan-04-2021, Volume 12, Issue 4, (2021)
Development of a multiplex mass spectrometry method for simultaneous quantification of urinary proteins related to respiratory health, Nauwelaerts, S., Roosens Nancy, Bernard Alfred, De Keersmaecker Sigrid C. J., and De Cremer Koen , Scientific Reports, Jan-12-2021, Volume 11, Issue 1, (2021)
Epidemiology of the Staphylococcus aureus CA-MRSA USA300 in Belgium, Argudín, Maria A., Deplano Ariane, Nonhoff Claire, Yin Nicolas, Michel Charlotte, Martiny Delphine, De Keersmaecker Sigrid C. J., and Hallin Marie , Eur J Clin Microbiol Infect Dis, 2021 Nov, Volume 40, Issue 11, (2021)
Evaluation of the added value of viral genomic information for predicting severity of influenza infection, Van Goethem, Nina, Robert Annie, Bossuyt Nathalie, Van Poelvoorde Laura, Quoilin Sophie, De Keersmaecker Sigrid C. J., Devleesschauwer Brecht, Thomas Isabelle, Vanneste Kevin, Roosens Nancy, et al. , BMC Infectious Diseases, Jan-12-2021, Volume 21, Issue 1, (2021)
Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations., Bogaerts, Bert, Winand Raf, Van Braekel Julien, Hoffman Stefan, Roosens Nancy, De Keersmaecker Sigrid C. J., Marchal Kathleen, and Vanneste Kevin , Microb Genom, 2021 11, Volume 7, Issue 11, (2021)
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., Yehouenou, Carine, Bogaerts Bert, Vanneste Kevin, Roosens Nancy, De Keersmaecker Sigrid C. J., Marchal Kathleen, Dissou Affolabi, Soleimani Reza, Rodriguez-Villalobos Hector, Van Bambeke Françoise, et al. , Ann Clin Microbiol Antimicrob, 2021 Jan 06, Volume 20, Issue 1, (2021)
Key considerations for the implementation of high throughput sequencing based metagenomics (mNGS) in diagnostic clinical, food and veterinary labs : a no-nonsense pointer. the Metastava consortium, Van Borm, Steven, Vandenbussche Frank, De Clercq Kris, Haegeman Andy, De Keersmaecker Sigrid C. J., Vanneste Kevin, Peeters Michael, Van Gucht Steven, Blanchard Yannick, Pavio Nicole, et al. , 2021, (2021)

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