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Version 1.41.3
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@kjolley kjolley released this 06 Mar 13:44
· 760 commits to develop since this release
v_1.41.3
827e686

Version 1.41.3 adds a plugin to run Kleborate (https://github.com/katholt/Kleborate) to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:

  • MLST sequence type
  • species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
  • ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
  • virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
  • antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
  • K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

kleborate4

The output is a table in HTML, tab-delimited text, and Excel formats.

kleborate5

In addition, if the analysis is run with the --all option then the results are stored as an arbitrary analysis within the isolate database linked to the isolate record (this is the same way that we store the rMLST species identification in the screenshot below). A formatted display of these results is available in the isolate information page.

Kleborate_isolate_info

The analysis can also be run using a standalone script - update_kleborate.pl - found in the scripts/maintenance directory. This will run the analysis against all isolates in a database and populate the arbitrary analysis table for display.

Arbitrary analysis results are stored within the isolate database as a JSON object and can be displayed within isolate information pages using a template file stored in /etc/bigsdb/templates. Currently, this information is not searchable within the BIGSdb search interface, but the plan is to develop this so that specific fields can be registered for searching.

Kleborate needs to be installed on the system and the path to the executable file specifed in the BIGSdb global configuration file (/etc/bigsdb/bigsdb.conf), e.g.

kleborate_path=/usr/local/bin/kleborate

The plugin is not enabled by default, even on databases with all_plugins="yes" set in the config.xml file, as it is only appropriate for use against Klebsiella assemblies. To enable the plugin, set the following attribute within the config.xml <system> section for the database.

Kleborate="yes"

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