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Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
the STEC strain from the endogenous E.coli strains while an Illumina MiSeq run takes 48 hours. Moreover, the lower-cost Flongle flow cell showed the same results after 24 hours of sequencing when using ...
Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019.
of gDNA directly from the submitted MGIT tubes, without preceding subculturing. All samples are then sequenced on an Illumina MiSeq sequencer and analyzed using an in-house developed and validated ...
Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination.
view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
study evaluated eight commercial DNA preparation kits for their potential influence on: (i) DNA quality for Nextera XT library preparation; (ii) MiSeq sequencing (data quality, read mapping against ...
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.
amplified and sequenced using the Illumina MiSeq, and analyzed with Mothur. Correct classification was variable, depending on the region amplified. Using a majority vote over all regions, most false positives ...
Use of next‐generation sequencing in microbial risk assessment
assessment MinION MiSeq nanopore sequencing next generation sequencing Abstract: Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm‐to‐fork chain, ...
Complete Genome Sequence of an Avian Metapneumovirus Subtype A Strain Isolated from Chicken () in Brazil.
metapneumovirus (aMPV) isolated from a tracheal tissue sample of a commercial layer flock. The complete genome sequence of aMPV-A/chicken/Brazil- SP /669/2003 was obtained using MiSeq (Illumina, Inc.) sequencing. ...
Development and implementation of a transversal NGS & bioinformatics platform at the Belgian Institute of Public Health
knowledge of genomics into public health policy. The platform has built up the capacity to both generate and analyze NGS data through an in-house Miseq and advanced bioinformatics pipelines and databases. ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.
Nextera XT library preparation; (ii) MiSeq sequencing (data quality, read mapping against plasmid and chromosome references); and (iii) WGS data analysis, i.e. isolate characterization (serotyping, ...
Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance.
A(H3N2) positive clinical specimens from the 2016-2017 Belgian season underwent WGS using the Illumina MiSeq system. HA-based classification according to WHO / ECDC guidelines did not allow classification ...