Release Notes 2023

Pathogenwatch release notes for 2023

v21.4.3

21st December (final release of the year)

Fixed

  • A bug was causing the tree building process to fail for a small number of SARS-CoV-2 collections. The bug has been fixed and the collection trees created.

v21.4.2

14th December

Fixed

  • Streptococcus pneumoniae strain assignments from the Global Pneumococcal Sequencing Project (GPS) can now be viewed in the "Typing" table within the collection and cluster viewers.

v21.4.0

12th December

Updated

  • In collaboration with Enterobase and PubMLST we have modified our MLST tool to provide more robust assignment of ST profiles. We have also updated all the schemes as of 24th November, and applied the updates to all genomes. While in our testing we have not detected any regressions, please do contact us if you find your genome no longer has an ST code.

  • The NGSTAR scheme was also updated on the 8th December and all assignments for Neisseria gonorrhoeae have all been recalculated.

v21.3.0

6th November

Updated

  • The Pangolin tool has been updated to pangolin-data v1.23.1, along with all SARS-CoV-2 genomes.

v21.2.0

18th September

Updated

  • The Vibrio cholerae AMR database has been updated with 29 new genes and 2 new variants. All genomes have been updated to the latest version.

v21.1.0

11th September

Updated

  • The NG-STAR allele database was downloaded on 7th September and all N. gonorrhoeae genomes updated.

  • The Pangolin SARS-CoV-2 typing tool was updated to pangolin-data v1.22 and all genomes updated.

v21.0.0

10th August

New

  • We are please to announce the addition an AMR prediction library for Enterococcus faecium, provided and created by Francesc Coll I Cerezo and Theodore Gouliouris, and adapted for Pathogenwatch by Corin Yeats. A manuscript describing the curation and implementation as an Ariba pipeline (Github link) is under review, and a comparison of the sensitivity and specificity of the Ariba and Pathogenwatch implementations can be seen in the AMR documentation. The library is available in our OSS repository.

v20.5.5

12th July

Fixed

  • There were a small number of errors found in the V. cholerae AMR library, which have been fixed: (1) ARR-2 has been changed to Rifampicin from Chloramphenicol; (2) tet_new changed to Tetracycline and not antiseptic; (3) Sulfamethoxazole-resistance was removed from dfrA1 and added to sul1 & sul2.

v20.5.4

11th July

Updated

v20.5.1

4th July

Fixed

  • An issue was causing the "List genomes" button in the Clustering section of the Genome Reports to fail.

v20.5.0

30th June

Updated

  • The Pangolin SARS-CoV-2 lineage tool has been updated to pangolin-data v1.21. All genomes have been updated to the latest assignments.

v20.4.0

9th June

Updated

  • The Candida auris references have been renamed to include the name of the clade that they represent. E.g. B13916 is now B13916-Clade_I.

v20.3.0

5th June

Updated

  • Pangolin has been updated to pangolin v4.3 and pangolin-data v1.20. All SARS-CoV-2 genomes have been updated to the latest version.

v20.2.8

18th May

Fixed

  • Some samples have a "/" character in their name. This character is restricted on almost all file systems, causing issues when trying to download the FASTA. For these genomes, the "/" has been replaced with "|" when downloading the FASTA.

v20.2.4

10th May

Improved

  • cgMLST clustering has had some further performance optimisations applied, reducing both the run time and memory use.

Fixed

  • We identified a small bug in the cgMLST clustering code that slightly affects the distances of some comparisons. All public clusters have been recalculated. Users can submit their genomes for re-clustering via the genome report pages.

v20.2.0

26th April

Fixed

  • cgMLST and LIN code assignments no longer fail for Klebsiella quasivariicola.

Updated

  • cgMLST and LIN code assignments have been updated for all Klebsiella genomes.

  • The maximum file size limit for gzipped FASTQ files has been increased to 900MB in order to better support Candida auris assemblies.

v20.1.3

14th April

Improved

  • Clustering tasks now run 4-20 times faster.

Fixed

  • The website would erroneously report that a clustering task had failed while it was still pending in the task queue. This should no longer occur.

v20.1.0

11th April

Updated

  • Pangolin has been updated to pangolin-data v1.19 and all SARS-CoV-2 genomes updated.

v20.0.15

3rd April

Fixed

  • The last version of Vista failed to report some matches to ctXB as a virulence gene. This has now been fixed and all ctxB genes should be found. All V. cholerae genomes have been updated.

v20.0.14

27th March

Fixed

  • 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.

v20.0.9

15th March

Changed

  • 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.

v20.0.8

14th March

Updated

  • 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.

v20.0.0

7th March

New

  • 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.

v19.7.0

6th March

Fixed

  • 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.

v19.5.0

28th February

Updated

  • The Pangolin SARS-CoV-2 assignment tool has been updated to pangolin-data v1.18.1.1. All genomes have been updated to the latest assignments.

v19.14.0

20th February

Updated

v19.13.0

13th February

Updated

  • Kleborate has been updated to v2.3.1, and all Klebsiella and Raoulteolla genomes updated.

v19.12.0

7th February

Updated

v19.11.0

31st January

Removed

  • "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.

v19.10.0

25th January

Updated

  • Pangolin assignments for SARS-CoV-2 have been updated to pangolin v2.4 and pangolin-data v1.18.

v19.9.0

24th January

Updated

  • 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.

v19.8.0

12th January

Updated

  • Pangolin assignments for SARS-CoV-2 have been updated to pangolin v2.4 and pangolin-data v1.17.

v19.7.2

10th January

Fixed

  • 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.

v19.7.1

9th January

Updated

  • 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.

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