E. coli genotyping plugin version 1.2 available

We are pleased to announce the latest update of our E. coli genotyping plugin: version 1.2. This version entails a major update of the plugin’s Knowledge Base (KB) to align it with the latest databases published by the Center for Genomic Epidemiology and some general improvements.

General improvements:

  • The user now has the option to revert to the default settings for each type of analysis.
  • The report now contains extra information related to version tracking of the analyses. For each analysis, time of analysis, version of the plugin used for the analysis and parameter settings used for the analysis are now reported.
  • Report assembly times have been further reduced.
  • The ‘search for gene fragments’ has been further optimized, allowing more reliable detection of genes fragmented across multiple contigs.

Following major changes to the antibiotic resistance prediction tool were performed:

  • The KB is now aligned with the resFinder database published November 28, 2018.
  • The KB now contains all currently known colistin resistance genes (mcr-1 to mcr-8).
  • Genes encoding for bla-NDM, bla-VIM, bla-KPC, bla-IMP, bla-TEM, bla-SHV, bla-CTX-M, bla-CMY, bla-ACC and bla-DHA were revised and new genes were added to the KB.
  • New genes encoding for fosfomycin, quinolone, macrolide, oxazolidinone, phenicol and sulphonamide resistance were added to the KB.

Following major changes to the virulence prediction tool were performed:

  • The KB is now aligned with the virulenceFinder database published October 12, 2018.

Following major changes to the plasmid detection tool were performed:

  • The KB is now aligned with the plasmidFinder database published November 20, 2018.

Following major changes to the serotype detection tool were performed:

  • The KB is now aligned with the serotypeFinder database published August 3, 2018.
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