Cargando…

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

The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years,...

Descripción completa

Detalles Bibliográficos
Autores principales:	Buytaers, Florence E., Saltykova, Assia, Denayer, Sarah, Verhaegen, Bavo, Vanneste, Kevin, Roosens, Nancy H. C., Piérard, Denis, Marchal, Kathleen, De Keersmaecker, Sigrid C. J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2020
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463776/ https://www.ncbi.nlm.nih.gov/pubmed/32764329 http://dx.doi.org/10.3390/microorganisms8081191

Ejemplares similares

Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies
por: Buytaers, Florence E., et al.
Publicado: (2021)

Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study
por: Saltykova, Assia, et al.
Publicado: (2020)

Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
por: Buytaers, Florence E., et al.
Publicado: (2021)

The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country
por: Nouws, Stéphanie, et al.
Publicado: (2020)

Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study
por: Buytaers, Florence E., et al.
Publicado: (2022)

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices
por: Nouws, Stéphanie, et al.
Publicado: (2023)

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
por: Nouws, Stéphanie, et al.
Publicado: (2020)

Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks
por: Nouws, Stéphanie, et al.
Publicado: (2021)

Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
por: Bogaerts, Bert, et al.
Publicado: (2021)

A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products
por: Buytaers, Florence E., et al.
Publicado: (2021)

Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept
por: Saltykova, Assia, et al.
Publicado: (2019)

Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:-
por: Saltykova, Assia, et al.
Publicado: (2018)

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
por: Bloemen, Bram, et al.
Publicado: (2023)

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java
por: Gand, Mathieu, et al.
Publicado: (2019)

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
por: Berbers, Bas, et al.
Publicado: (2020)

Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory’s Viewpoint
por: Wuyts, Véronique, et al.
Publicado: (2015)

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO
por: Fraiture, Marie-Alice, et al.
Publicado: (2018)

Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database
por: Saltykova, Assia, et al.
Publicado: (2022)

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
por: Gand, Mathieu, et al.
Publicado: (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
por: Berbers, Bas, et al.
Publicado: (2023)

Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products
por: D’aes, Jolien, et al.
Publicado: (2022)

MinION sequencing technology to characterize unauthorized GM petunia plants circulating on the European Union market
por: Fraiture, Marie-Alice, et al.
Publicado: (2019)

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination
por: Berbers, Bas, et al.
Publicado: (2020)

Use of metagenomic microbial source tracking to investigate the source of a foodborne outbreak of cryptosporidiosis
por: Ahlinder, J., et al.
Publicado: (2021)

Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations
por: Bogaerts, Bert, et al.
Publicado: (2021)

Guidelines for Optimisation of a Multiplex Oligonucleotide Ligation-PCR for Characterisation of Microbial Pathogens in a Microsphere Suspension Array
por: Wuyts, Véronique, et al.
Publicado: (2015)

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation
por: Bogaerts, Bert, et al.
Publicado: (2021)

Detection and discrimination of five E. coli pathotypes using a combinatory SYBR® Green qPCR screening system
por: Barbau-Piednoir, Elodie, et al.
Publicado: (2018)

A general approach to identify low-frequency variants within influenza samples collected during routine surveillance
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2022)

A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium
por: Wuyts, Véronique, et al.
Publicado: (2015)

Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution
por: Van Poelvoorde, Laura A. E., et al.
Publicado: (2021)

Whole-genome sequencing of Listeria monocytogenes serotype 4b isolated from ready-to-eat lentil salad in Algiers, Algeria
por: Drali, R., et al.
Publicado: (2019)

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
por: Yehouenou, Carine Laurence, et al.
Publicado: (2021)

Whole-Genome Sequencing of Six Strains of Salmonella enterica Isolated from Imported Meat in Algeria
por: Deriet, A., et al.
Publicado: (2019)

Whole-Genome Sequencing of Multidrug-Resistant Escherichia coli Strains Harboring the mcr-1 Gene, Isolated from Seawater of the Algiers Coast in Algeria
por: Berrazeg, M., et al.
Publicado: (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: Neisseria meningitidis as a Proof-of-Concept
por: Bogaerts, Bert, et al.
Publicado: (2019)

Bacterial networking
por: Marchal, Kathleen, et al.
Publicado: (2008)

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
por: Yehouenou, Carine, et al.
Publicado: (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
por: Bogaerts, Bert, et al.
Publicado: (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
por: D’aes, Jolien, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_67smingsiqf77sk5in8kms1fi9