WHAT'S CHANGED?
 

• Sequence analysis pipeline:

  • List of bacterial species has been extended with Citrobacter freundii

  • Integrated plasmid functionality to detect plasmid contigs in the genome

  • Serotyping and pathotyping performed on samples identified as Escherichia coli / Shigella

  • MLST and Spa typing databases: allele nomenclature refreshed

  • Resistome database: growing content while further improving the curation* (details in the updated online help)

  • Virulome database: growing content and screening now available for most species* (details in the updated online help)

  • Upload and processing of FASTA gzip files

* As the nomenclature of some markers is evolving and this evolution is integrated in the databases, please compare results obtained with different versions of EPISEQ® CS with caution.​ Please note that previously analyzed sample are not reprocessed with the new pipeline and database.

• General:

  • Google Chrome added as supported browser

  • Internet Explorer removed as supported browser

  • Dashboard on the home page with information about the underlying credit plan, wet lab performance, time analysis of uploads and resistance genes occurrence

  • New button to select all (filtered) samples

  • Download button made more visible in all panels

• Sample results:

  • Resistome sample window:

    • Filtering lists available for Resistance mechanism categories, Drug and Drug families

    • Extra column displaying the type of mutation

    • Extra column reporting the plasmid accession in case the marker is found on a plasmid contig

  • Virulome sample window:

    • Extra information available for every marker hit (Reference locus, Citation, ecNumber, uniprot, pfam, …)   

    • Extra column reporting the plasmid accession in case the marker is found on a plasmid contig

  • QC sample window:

    • Parameter is displayed that caused a sample to fail

• Epidemiological analysis:

  • Metadata panel:

    • Color metadata columns based on field content

    • Configuration of the metadata columns is saved in user settings

    • Creation of a panel based on any sample selection

  • Resistome and Virulome panels:

    • Indication when marker is located on a plasmid contig

    • Equivalent hits are excluded from counted hits

    • Mutations at different positions on the same gene, each responsible for a certain resistance, are split over different columns

  • Minimum spanning tree:

    • Samples with distance 0 are grouped inside the same node

    • Node size reflects the number of samples contained in a node

    • Metadata fields can be picked as node identifier

    • New button to stretch/shrink the tree in the available space

• Bug fixes:

  • Cluster colors displayed on a dendrogram match those in the Report when the cluster cut-off value is changed

  • Calculated MLST column content is displayed if enabled

  • Clearing the collection date of a sample now results in a blank field

  • Branches in a Minimum spanning tree are scaled according to allele differences

  • Resistome data for Pseudomonas aeruginosa is displayed in the Sample resistome window