Release Notes 2024

Pathogenwatch release notes for 2024

v23.1.0

13th November

Updated

• The following modifications were made to the Vibrio cholerae AMR library and applied to all genomes:

  • The dfrA_new references sequence was replaced with a corrected version. Please ignore previous results for this gene.

  • Added the Doxycycline resistance to tet(A) and tet(B).

  • The tet(A) reference gene was discovered to be incomplete and has been replaced. This should not significantly affect results.

  • A second allele was added for tet(A) namee as tet(A2).

  • A tetracycline resistance gene called tetY was added.

v23.0.2

5th November

Updated

• The link to the Kleborate documentation from the Genome Reports has been updated to point to documentation for Kleborate 3.

v23.0.1

28th October

Fixed

• A rendering error was causing K. pneumoniae collections not to load in the viewer. This has been fixed.

v23.0.0

25th October

Updated

• All MLST schemes have been updated and the new version made available. The MLST schemes were updated on the 4th September. All genomes have been updated to the latest assignments.

  • The Enterobase Yersinia MLST scheme is now applied to all Yersinia genomes and not just Y. enterolitica.

• Similarly all cgMLST schemes have been updated as well, with the schemes downloaded on the 4th of September.

  • We have switched to the Enterobase cgMLST scheme for C. difficile, replacing the previous scheme from Ridom.

New

• We have added one MLST scheme:

  • C. perfringens (Enterobase)

• We have also added 13 new cgMLST schemes:

  • B. anthracis (PubMLST)

  • B. cereus (PubMLST)

  • B. mallei (PubMLST)

  • Brucella (PubMLST)

  • C. perfringens (Enterobase)

  • C. trachamotis (PubMLST)

  • H. influenzae (PubMLST)

  • M. abscessus (PubMLST)

  • S. uberis (PubMLST)

  • Y. enterolitica (Pasteur)

  • Y. tuberculosis (Pasteur)

  • Other Yersinia (Enterobase)

v22.5.4

16th October

Updated

• Minor modifications to the Kleborate and Kaptive pipelines to fix a small percentage of failures.

Fixed

• Where the Kleborate or Kaptive analyses have failed CSV files will still generate correctly.

v22.5.0

9th October

Updated

• Kleborate has been updated to v3.1.0. It is now provided in 3 different modes, according to the species - K. pneumoniae species complex, K. oxytoca species complex, and other Klebsiella. All Klebsiella genomes have been updated to the new version: https://kleborate.readthedocs.io/en/latest/index.html.
• Kaptive has been updated to v3.0.0b5. Kaptive is now run directly on K. pneumoniae complex species and CSV file results are now available for download separately from the Kleborate download. All A. baumannii and K. pneumoniae complex genomes have been updated: https://kaptive.readthedocs.io/en/latest/.

v22.3.9

30th September

This release should improve the performance and stability of the website for all users.

Removed

Sorting by "Country", "Type", and "Organism" has been disabled on the Genome view. Sorting by "Name" and "Date" is still available, which is now indicated by three horizontal lines in the column header.

v22.3.1 - v22.3.8

8-9th July

These releases represent a batch of updates mostly focused on improving the stability and robustness of the platform, especially when serving larger numbers of concurrent users.

Updated

• Database server, software and drivers for improved performance

Fixed

• A set of potentially slow database queries were identified and optimised

• A bug that prevented the building of trees for collections containing duplicate genomes in some cases.

v22.3.0

10th June

Updated

• S. pneumoniae GPSC strain assignments have been updated to the v8 scheme.

v22.2.0

17th May

Added

• MLST assignments using the PubMLST E. cloacae species complex scheme have been added for E. chengduensis, E. chuandaensis and E. pasteurii. The last of these species is not currently recognised by Speciator and is likely to be assigned to another member of the complex. However, MLST will should still be run for them.

v22.1.5

17th May

Updated

• Internal configuration update to ensure service stability.

v22.1.3

15th April

Updated

• The cgMLST profile single linkage clustering tool has been refactored to reduce memory and CPU use. There should be no impact on the results.

v22.1.0

20th January

Updated

• All cgMLST assignments have been updated to the latest version of the MLST code, with the schemes updated to 08/12/2023. This is includes several bug fixes, and we expect some significant improvements to the cgMLST profile-base clustering. Due to the complexity of the update, if you see any issues, please do get in touch.

v22.0.0

19th January

New

• PopPUNK cluster assignments for Vibrio cholerae, provided by our Vibriowatch collaboration. All V. cholerae genomes have been updated to include their cluster assignment.

Removed

• After further review, the previous Vista biotype assignments have been deemed unreliable. We would recommend that users do not rely on the previous results. A new version is under development by our collaborators at the Wellcome Sanger Institute.