Release Notes 2024
Pathogenwatch release notes for 2024
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
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
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
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.
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