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Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products
feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and ...
An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.
Biology Feces Genome, Viral High-Throughput Nucleotide Sequencing Laboratory Proficiency Testing Metagenome Metagenomics RNA Viruses RNA, Viral Swine Swine Diseases Abstract: UNLABELLED: Metagenomic shotgun ...
Real-time cluster detection of Listeria to enhance outbreak investigation in Belgium
Next-Generation sequencing. The obtained data are analysed using an in-house Listeria pipeline (v1.2) in Galaxy, which amongst other analyses performs cgMLST (core genome MultiLocus Sequence Typing) based on the ...
Antimicrobial resistance in ESBL and indicator E. coli, Campylobacter spp.,Salmonella spp., methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecalis and faecium isolated from food and food-producing animals (primary production) in 2023
resistance levels are lower in C. jejuni than in C. coli. In 2023, Salmonella spp. recovered from food matrices have been analysed by whole genome sequencing (WGS). The highest levels of predicted ...
Lumpy Skin Disease Virus Genome Sequence Analysis: Putative Spatio-Temporal Epidemiology, Single Gene versus Whole Genome Phylogeny and Genomic Evolution.
a whole-genome-sequence (WGS)-based phylogeny and compared it with single-gene-based phylogenies. To study population and spatiotemporal patterns in greater detail, we reconstructed networks. We determined that there are ...
Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
have always been analyzed and characterized after isolation. Since the advent of second generation sequencing, it has been possible to characterize the complete genome of these isolates to the SNP level. ...
Introduction of WGS in food microbiology: advantages and challenges
Keywords: antimicrobial resistance (AMR) Food Safety foodborne outbreak investigation Monitoring SciCom Whole genome sequencing (WGS) Abstract: In October 2021 the Scientific Committee of the Federal Agency ...
Population Analysis of O26 Shiga Toxin-Producing Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing.
accessory genomic fraction. A novel O26 STEC clone belonging to Sequence Type (ST) 29 and harboring, and plasmid-borne genes has emerged and spread in Europe since the mid-1990s, while another ST29 clone ...
Listeria monocytogenes isolates from Cornu aspersum snails: Whole genome-based characterization and host-pathogen interactions in a snail infection model.
sequencing Abstract: Even though Listeria monocytogenes is an extensive-studied foodborne pathogen, genome analysis of isolates from snails that may represent a reservoir of L. monocytogenes are still scarce. ...
Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.
genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read ...