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Optimised long-read sequence bioinformatics tool for the analysis of the resistome and microbial communities
https://doi.org/10.5281/zenodo.7433258 Keywords: Antimicrobial resistance bioinformatics Long read metagenomic sequencing Microbial community Resistome Health Topics: Antimicrobial resistance (AMR) Food consumption and food safety ...
ESCAIDE 2022 Oral presentation: International outbreak of Salmonella Typhimurium linked to a chocolate factory in 2022: Belgian findings
were analysed for Salmonella spp. using real-time PCR. Whole genome sequence (WGS) analysis of isolates of probable cases and positive food samples is still ongoing. Results We identified 62 probable ...
Population Analysis of O26 Shiga Toxin-Producing Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing.
Hemolytic-Uremic Syndrome Humans ITALY Multilocus Sequence Typing Shiga-Toxigenic Escherichia coli whole genome sequencing Abstract: Shiga toxin-producing (STEC) belonging to the O26 serogroup represent an important ...
Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance.
mainly focused on the hemagglutinin gene. Whole-genome sequencing (WGS) enables tracking mutations across all influenza segments allowing a better understanding of the epidemiological effects of intra- and ...
Development of a data-intensive centralized system for surveillance and outbreak investigation of bacterial pathogens using whole-genome sequencing
a limiting factor, as full runs on Illumina sequencers typically take several days to complete. Therefore, a real-time data analysis protocol for Illumina sequencing was implemented, enabling data analysis ...
Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing
consensus genome sequence of the most abundant strain is taken into consideration for analysis, but multiple variant strains are now circulating in the population. Consequently, in diagnostic samples, ...
Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.
segment B closely related to D3976 /1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT- PCR result. IBV sequence variation analysis ...
Epidemiology of the Staphylococcus aureus CA-MRSA USA300 in Belgium
Genotype Humans Infant Male Methicillin-Resistant Staphylococcus aureus middle aged Phylogeny Staphylococcal Infections Young adult Abstract: The methicillin-resistant Staphylococcus aureus (MRSA) sequence ...
Molecular and virological characterization of the first poultry outbreaks of Genotype VII.2 velogenic avian orthoavulavirus type 1 (NDV) in North-West Europe, BeNeLux, 2018.
polybasic sequence of the fusion gene cleavage site and the intracerebral pathotyping assay demonstrated the high pathogenicity of the strain. This paper represents the first notification of this specific ...
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
single nucleotide polymorphism VALIDATION whole genome sequencing Abstract: The use of whole genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. ...