Works by Vanneste, Kevin

Results: 60

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

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.

Published in:

Microorganisms, 2020, v. 8, n. 8, p. 1191, doi. 10.3390/microorganisms8081191

By:

Buytaers, Florence E.;
Saltykova, Assia;
Denayer, Sarah;
Verhaegen, Bavo;
Vanneste, Kevin;
Roosens, Nancy H. C.;
Piérard, Denis;
Marchal, Kathleen;
De Keersmaecker, Sigrid C. J.

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

Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms.

Published in:

Foods, 2023, v. 12, n. 3, p. 455, doi. 10.3390/foods12030455

By:

Fraiture, Marie-Alice;
D'aes, Jolien;
Guiderdoni, Emmanuel;
Meunier, Anne-Cécile;
Delcourt, Thomas;
Hoffman, Stefan;
Vandermassen, Els;
De Keersmaecker, Sigrid C. J.;
Vanneste, Kevin;
Roosens, Nancy H. C.

Publication type:

Article

Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study.

Published in:

Foods, 2022, v. 11, n. 21, p. 3348, doi. 10.3390/foods11213348

By:

Buytaers, Florence E.;
Verhaegen, Bavo;
Gand, Mathieu;
D'aes, Jolien;
Vanneste, Kevin;
Roosens, Nancy H. C.;
Marchal, Kathleen;
Denayer, Sarah;
De Keersmaecker, Sigrid C. J.

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

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.

Published in:

Genes, 2021, v. 12, n. 5, p. 644, doi. 10.3390/genes12050644

By:

Deneke, Carlus;
Brendebach, Holger;
Uelze, Laura;
Borowiak, Maria;
Malorny, Burkhard;
Tausch, Simon H.;
Vanneste, Kevin

Publication type:

Article

Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants.

Published in:

Genes, 2021, v. 12, n. 4, p. 565, doi. 10.3390/genes12040565

By:

Gand, Mathieu;
Vanneste, Kevin;
Thomas, Isabelle;
Van Gucht, Steven;
Capron, Arnaud;
Herman, Philippe;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation.

Published in:

Genes, 2021, v. 12, n. 2, p. 275, doi. 10.3390/genes12020275

By:

Barretto, Caroline;
Rincón, Cristian;
Portmann, Anne-Catherine;
Ngom-Bru, Catherine;
Vanneste, Kevin

Publication type:

Article

Autoimmunity and Genetic Syndromes: A Focus on Down Syndrome.

Published in:

Genes, 2021, v. 12, n. 2, p. 268, doi. 10.3390/genes12020268

By:

Ferrari, Marta;
Stagi, Stefano;
Vanneste, Kevin

Publication type:

Article

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.

Published in:

Nature Genetics, 2015, v. 47, n. 3, p. 304, doi. 10.1038/ng0315-304a

By:

Cai, Jing;
Liu, Xin;
Vanneste, Kevin;
Proost, Sebastian;
Tsai, Wen-Chieh;
Liu, Ke-Wei;
Chen, Li-Jun;
He, Ying;
Xu, Qing;
Bian, Chao;
Zheng, Zhijun;
Sun, Fengming;
Liu, Weiqing;
Hsiao, Yu-Yun;
Pan, Zhao-Jun;
Hsu, Chia-Chi;
Yang, Ya-Ping;
Hsu, Yi-Chin;
Chuang, Yu-Chen;
Dievart, Anne

Publication type:

Article

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.

Published in:

Nature Genetics, 2015, v. 47, n. 2, p. 186, doi. 10.1038/ng0215-186

By:

Vanneste, Kevin;
Tsai, Wen-Chieh;
Bian, Chao;
Liu, Weiqing;
Hsu, Chia-Chi;
Zhao, Xue-Min;
Xie, Gao-Chang;
Liu, Guo-Hui;
Huang, Lai-Qiang;
Luo, Yi-Bo;
Cai, Jing;
Liu, Xin;
Yang, Ya-Ping;
Hsu, Yi-Chin;
Dievart, Anne;
Dufayard, Jean-Francois;
Xiao, Xin-Ju;
Li, Li-Qiang;
Liu, Zhong-Jian;
Proost, Sebastian

Publication type:

Article

The genome sequence of the orchid Phalaenopsis equestris.

Published in:

Nature Genetics, 2015, v. 47, n. 1, p. 65, doi. 10.1038/ng.3149

By:

Cai, Jing;
Liu, Ke-Wei;
Su, Yong-Yu;
Huang, Lai-Qiang;
Chen, Hong-Hwa;
Van de Peer, Yves;
Liu, Zhong-Jian;
Liu, Xin;
Bian, Chao;
Zheng, Zhijun;
Sun, Fengming;
Liu, Weiqing;
Xu, Xun;
Wang, Jun-Yi;
Wang, Jun;
Vanneste, Kevin;
Proost, Sebastian;
He, Ying;
Tsai, Wen-Chieh;
Chen, Li-Jun

Publication type:

Article

Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.

Published in:

Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1336532

By:

Gand, Mathieu;
Navickaite, Indre;
Bartsch, Lee-Julia;
Grützke, Josephine;
Overballe-Petersen, Søren;
Rasmussen, Astrid;
Otani, Saria;
Michelacci, Valeria;
Rodríguez Matamoros, Bosco;
González-Zorn, Bruno;
Brouwer, Michael S. M.;
Di Marcantonio, Lisa;
Bloemen, Bram;
Vanneste, Kevin;
Roosens, Nancy H. C. J.;
AbuOun, Manal;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.

Published in:

Frontiers in Microbiology, 2024, p. 01, doi. 10.3389/fmicb.2024.1330814

By:

Buytaers, Florence E.;
Verhaegen, Bavo;
Van Nieuwenhuysen, Tom;
Roosens, Nancy H. C.;
Vanneste, Kevin;
Marchal, Kathleen;
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

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

Published in:

PLoS Biology, 2012, v. 10, n. 12, p. 1, doi. 10.1371/journal.pbio.1001446

By:

Voordeckers, Karin;
Brown, Chris A.;
Vanneste, Kevin;
van der Zande, Elisa;
Voet, Arnout;
Maere, Steven;
Verstrepen, Kevin J.

Publication type:

Article

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination.

Published in:

Antibiotics (2079-6382), 2020, v. 9, n. 8, p. 503, doi. 10.3390/antibiotics9080503

By:

Berbers, Bas;
Ceyssens, Pieter-Jan;
Bogaerts, Pierre;
Vanneste, Kevin;
Roosens, Nancy H. C.;
Marchal, Kathleen;
De Keersmaecker, Sigrid C. J.

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

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 15, p. 5585, doi. 10.3390/ijms21155585

By:

Gand, Mathieu;
Vanneste, Kevin;
Thomas, Isabelle;
Van Gucht, Steven;
Capron, Arnaud;
Herman, Philippe;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

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

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1532788

By:

Van Laere, Yari;
Fraiture, Marie-Alice;
Gobbo, Andrea;
De Keersmaecker, Sigrid C. J.;
Marchal, Kathleen;
Roosens, Nancy H. C.;
Vanneste, Kevin

Publication type:

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

Isolation of Burkholderia pseudomallei from a Pet Green Iguana, Belgium.

Published in:

2018

By:

Hellebuyck, Tom;
Wattiau, Pierre;
Boyen, Filip;
Moeremans, Ilse;
Roosens, Nancy H.;
Vanneste, Kevin;
Garmyn, An;
Saey, Veronique;
Pasmans, Frank;
Haesebrouck, Freddy

Publication type:

journal article

NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program.

Published in:

Cancers, 2020, v. 12, n. 11, p. 3180, doi. 10.3390/cancers12113180

By:

Delcourt, Thomas;
Vanneste, Kevin;
Soumali, Mohamed Rida;
Coucke, Wim;
Ghislain, Vanessa;
Hebrant, Aline;
Van Valckenborgh, Els;
De Keersmaecker, Sigrid C. J.;
Roosens, Nancy H.;
Van De Walle, Philippe;
Van Den Bulcke, Marc;
Antoniou, Aline

Publication type:

Article

Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market.

Published in:

2022

By:

Deckers, Marie;
Braekel, Julien Van;
Vanneste, Kevin;
Deforce, Dieter;
Fraiture, Marie-Alice;
Roosens, Nancy H C

Publication type:

Correction Notice

Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab060

By:

Deckers, Marie;
Braeckel, Julien Van;
Vanneste, Kevin;
Deforce, Dieter;
Fraiture, Marie-Alice;
Roosens, Nancy h.c

Publication type:

Article

Inference of Genome Duplications from Age Distributions Revisited.

Published in:

Molecular Biology & Evolution, 2013, v. 30, n. 1, p. 177, doi. 10.1093/molbev/mss214

By:

Vanneste, Kevin;
Van de Peer, Yves;
Maere, Steven

Publication type:

Article

Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification.

Published in:

Molecular Biology & Evolution, 2012, v. 29, n. 12, p. 3793, doi. 10.1093/molbev/mss183

By:

Vekemans, Dries;
Proost, Sebastian;
Vanneste, Kevin;
Coenen, Heleen;
Viaene, Tom;
Ruelens, Philip;
Maere, Steven;
Van de Peer, Yves;
Geuten, Koen

Publication type:

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

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-61158-0

By:

Berbers, Bas;
Saltykova, Assia;
Garcia-Graells, Cristina;
Philipp, Patrick;
Arella, Fabrice;
Marchal, Kathleen;
Winand, Raf;
Vanneste, Kevin;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

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

Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09537-5

By:

Gand, Mathieu;
Bloemen, Bram;
Vanneste, Kevin;
Roosens, Nancy H. C.;
De Keersmaecker, Sigrid C. J.

Publication type:

Article

Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea.

Published in:

Virus Genes, 2020, v. 56, n. 6, p. 696, doi. 10.1007/s11262-020-01791-z

By:

Van Borm, Steven;
Vanneste, Kevin;
Fu, Qiang;
Maes, Dominiek;
Schoos, Alexandra;
Vallaey, Eline;
Vandenbussche, Frank

Publication type:

Article

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03672-8

By:

Van Uffelen, Alexander;
Posadas, Andrés;
Roosens, Nancy H. C.;
Marchal, Kathleen;
De Keersmaecker, Sigrid C. J.;
Vanneste, Kevin

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

Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies.

Published in:

Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.738284

By:

Buytaers, Florence E.;
Saltykova, Assia;
Denayer, Sarah;
Verhaegen, Bavo;
Vanneste, Kevin;
Roosens, Nancy H. C.;
Piérard, Denis;
Marchal, Kathleen;
De Keersmaecker, Sigrid C. J.

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