Ghent University Academic Bibliography

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

Alexander Van Uffelen (UGent) , Andres Posadas Yabar (UGent) , Nancy H. C. Roosens, Kathleen Marchal (UGent) , Sigrid C. J. De Keersmaecker and Kevin Vanneste

(2024) SCIENTIFIC DATA. 11(1).
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Whole-genome sequencing of foodborne Bacillus cereus isolates indicates no clear association between their genomic diversity and food matrix types

Bram Jacobs (UGent) , Bert Bogaerts, Marie Verhaegen, Tom Van Nieuwenhuysen, Kevin Vanneste, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Jacques Mahillon, Andreja Rajkovic (UGent) and Koenraad Van Hoorde

(2024) 28th International ICFMH Conference (FoodMicro24), Abstract book. p.30-31
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Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Bram Bloemen (UGent) , Mathieu Gand, Kevin Vanneste (UGent) , Kathleen Marchal (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker

(2023) SCIENTIFIC REPORTS. 13(1).
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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

Johannes Berbers (UGent) , Kevin Vanneste, Nancy H. C. J. Roosens, Kathleen Marchal (UGent) , Pieter-Jan Ceyssens and Sigrid C. J. De Keersmaecker

(2023) MICROBIAL GENOMICS. 9(1).
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Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B2 products sold on the Belgian market using whole-genome sequencing

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

(2023) FRONTIERS IN MICROBIOLOGY. 14.
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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

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

(2023) 9th Applied Bioinformatics and Public Health Microbiology, Abstracts.
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Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

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

(2023) FRONTIERS IN MICROBIOLOGY. 14.
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Whole-genome sequence approach and phylogenomic stratification improve the association analysis of mutations with patient data in influenza surveillance

Laura Van Poelvoorde (UGent) , Kevin Vanneste, Sigrid C. J. De Keersmaecker, Isabelle Thomas, Nina Van Goethem, Steven Van Gucht, Xavier Saelens (UGent) and Nancy H. C. Roosens

(2022) FRONTIERS IN MICROBIOLOGY. 13.
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Metagenomics to detect and characterize viruses in food samples at genome level? Lessons learnt from a norovirus study

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

(2022) FOODS. 11(21).
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A general approach to identify low-frequency variants within influenza samples collected during routine surveillance

Laura Van Poelvoorde (UGent) , Thomas Delcourt, Marnik Vuylsteke (UGent) , Sigrid C. J. De Keersmaecker, Isabelle Thomas, Steven Van Gucht, Xavier Saelens (UGent) , Nancy Roosens and Kevin Vanneste

(2022) MICROBIAL GENOMICS. 8(9).

Academic Bibliography

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

Whole-genome sequencing of foodborne Bacillus cereus isolates indicates no clear association between their genomic diversity and food matrix types

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

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

Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B2 products sold on the Belgian market using whole-genome sequencing

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

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

Whole-genome sequence approach and phylogenomic stratification improve the association analysis of mutations with patient data in influenza surveillance

Metagenomics to detect and characterize viruses in food samples at genome level? Lessons learnt from a norovirus study

A general approach to identify low-frequency variants within influenza samples collected during routine surveillance

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