![]() The WGS analysis confirmed the link between food and human isolates for each of the outbreaks and clearly discriminated between the two outbreaks occurring in a same time period, thereby suggesting a non-common source of contamination. Results: To all collected human and food outbreak isolates, classical microbiological investigation assigned phage type PT4 (variant phage type PT4a for one human isolate) and MLVA profile 3-10-5-4-1, both of which are common for human isolates in Belgium. Analysis of the WGS data was performed with currently available, user-friendly software and tools, namely CLC Genomics Workbench, the tools available on the server of the Center for Genomic Epidemiology and BLAST Ring Image Generator (BRIG). Retrospectively, WGS of six outbreak isolates was done on an Illumina HiSeq. Methods: The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Both the suspected food and human isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective whole genome sequencing (WGS) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise. Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Send an email to *protected email* to get information about IP address.Introduction: In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp.If you setup a custom folder location or Workspace, you will likely need to reestablish that path to access your data. Also note, when Paul Greer upgraded the client on my workstation, he was not prompted to upgrade the existing client, so the new version was installed as a new package.In that case, you will have to right click on the CLC Workbench icon and use the “Run as Administration” option to install plugins. On Windows installations, you may find the option to upgrade plugins grayed out. Once you have established a connection, you will need to install the necessary plugins required for your work.When the installer completes, the CLC Workbench will start and prompt for license information (see below). ![]() Run the installer and follow the instructions on the screen.Download the CLC Workbench client for your operating system, Windows, MAC or Linux, 64 or 32 bit.When you open the existing CLC Workbench client on your computer, you are prompted to upgrade the software with the latest version, and provided a download link.They have not changed, but you will need to manually enter them when you upgrade your CLC Workbench client software. Before you upgrade your existing client, please take note of the existing license server setting (see below).Please make sure you download v8.01 of the software and install any required plugins that you may need.Support all the major next-gen sequencing platforms, such as SOLiD, Ion Torrent, Complete Genomics, 454, Illumina Genome Analyzer and also Sanger. Acquired in collaboration with the Institute for Plant Genomics and Biotechnology. Comprehensive suite of tools for analysis of next-gen sequencing data including resequencing data, workflow management, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, and trio analysis.
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