Release Notes 2023
Pathogenwatch release notes for 2023
- S. pneumoniae genomes that are missing a phenotype assignment inferred from the PBP genes (i.e. due to a missing PBP gene) were causing the Genome Reports to crash. This should no longer happen.
- The default maximum collection size is now 2000 for all species, except SARS-CoV-2 and Candida auris which are both limited to 1000 genomes.
- We have updated the Klebsiella cgMLST assignments and LIN codes as (downloaded on 7th March 2023). As part of a project to improve data sharing within the Klebsiella community, we provided all our public genomes without a defined ST for classification by the maintainers of the PubMLST scheme at the Pasteur Institute. As a result, the latest update now means all Pathogenwatch public Klebsiella genomes now have a fully defined cgMLST profile and LIN code.
- We have released our in-house core for building trees of our first fungal pathogen, Candida auris. For more details on the composition of the core see the linked documentation.
- As part of the release, along with the 5 complete reference genomes we have used to represent each lineage, we have also included 9 complete genomes and 1009 assembled genomes that all have location and sample date metadata in the ENA. These can be used to place query genomes into their genomic neighbourhood by viewing the reference-linked trees within collections. Simply create a collection of query genomes, and Pathogenwatch will create the relevant contexts.
- We have also created an AMR library for C. auris which is searched for every genome. For the full list of genes, SNPs and tested antimicrobials the database can be found in our Github repository: https://github.com/pathogenwatch/amr-libraries/blob/main/498019.toml.
- This scheme has been developed by Corin Yeats, Silvia Argimon, and Johanna Rhodes.
- The "List Genomes" button in the clustering section of the genome report should now work reliably. Please let us know if you still experience issues.
- The Pangolin SARS-CoV-2 assignment tool has been updated to pangolin-data v18.104.22.168. All genomes have been updated to the latest assignments.
- Kaptive K/O locus assignments for Acinetobacter baumanii have been updated to version v2.0.5: https://github.com/katholt/Kaptive/releases/tag/v2.0.5.
- The Vista genotyping and virulence factor detection tool for V. cholerae has been updated with new virulence factors. See the full list here: https://github.com/pathogenwatch-oss/vista/blob/main/data/metadata.toml#L19.
- The V. cholerae AMR library has also been updated with new genes, variants and antimicrobials. We identified and remove a few errors and imprecise annotations. The current AMR library can be seen here: https://github.com/pathogenwatch-oss/amr-libraries/blob/main/666.toml.
- "Sub-trees" are no longer generated for Salmonella Typhi in order to allow the growth of the public genome database. In order to generate a context for your uploaded genomes we recommend using the cgMLST-based clustering accessible via individual Genome Reports.
- Pangolin assignments for SARS-CoV-2 have been updated to pangolin v2.4 and pangolin-data v1.18.
- The version of the plasmidfinder database incorporated into Inctyper has been updated to the version 18th January 2023, and some corrections made to the species-library bindings. Notably, Acinetonacter baumanii has been moved from Gram positive to Gram negative. Note that the assignments are still being updated in the database and may not be complete until the 25th. However we don't expect many changes to the results beyond A. baumanii, since there have only been a few changes to the plasmidfinder database since the last update.
- Pangolin assignments for SARS-CoV-2 have been updated to pangolin v2.4 and pangolin-data v1.17.
- Klebsiella genomes without Kleborate annotations (i.e. due to Kleborate or the task runner failing) were causing the Collection Viewer to crash when interacting with the AMR tables. This has been fixed, and the pages should now be stable.
- The MLST and cgMLST schemes have been updated (downloaded on the 14th December 2022) for all currently supported species. All public and user genomes have been updated to reflect the latest assignments.
- Public genomes have all been re-clustered based on the latest cgMLST assignments. Previously uploaded genomes can be re-clustered via the Genome Report. Running a single genome will update the clustering for all uploaded genomes of that species.