iiinova — where your digital self keeps evolving

Reposted by PubMLST.org

Charlene Rodrigues @cmcrodrigues.bsky.social · 22/07/2026

Delighted to share our paper-17 years of meningococcal genomic surveillance, looking at changes in diversity, distribution and demographics in Scotland. The positive impact of vaccines and what is now circulating following COVID-19/restrictions period url.uk.m.mimecastprotect.com/s/lJN8CM1Gzc...

url.uk.m.mimecastprotect.com

Genomic epidemiology of invasive meningococcal disease in Scotland before, during, and after the COVID-19 pandemic: a retrospective observational study

Invasive meningococcal disease (IMD) remains a major global health threat. Despite vaccination, meningococcal genetic diversity means disease, includi…

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PubMLST.org @pubmlst.org · 16/07/2026

PubMLST will be unavailable tomorrow, Friday 17 July, for up to 1 hour starting at 7.50am (UK time).

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PubMLST.org @pubmlst.org · 03/07/2026

The PubMLST user interface has been updated with the new release of BIGSdb. 👇

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 14/05/2026

You can also now search for a specific isolate within the LINvis display. Search can be performed either by isolate id or name. If present, all encompassing circles representing different LIN code thresholds will be highlighted by a dotted red border and the inner node will have a solid border.

LINvis visualisation with a specific node representing an isolate highlighted by a red border. Encompassing circles representing higher LIN thresholds have a dotted border.

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 14/05/2026

BIGSdb v1.53.2 has been released and is now live on @pubmlst.org. This adds functionality to the LINvis plugin. This includes annotation of nodes representing specific LIN prefixes entered as a list.

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PubMLST.org @pubmlst.org · 07/05/2026

It is now easier to setup new @pubmlst.org accounts and register these with all available databases. After account validation and initial password change, new accounts now automatically register for all public databases, removing a step that sometimes tripped users up.

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 01/05/2026

BIGSdb v1.53.0 has been released. This version addresses an issue that has been raised by PubMLST users seeking easier authenticated access to the @pubmlst.org API. We have now introduced personal API keys that can be used instead of OAuth authentication for ad-hoc scripts and pipelines.

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 02/03/2026

BIGSdb v1.52.1 has been released. This adds 2 new plugins for LIN code visualisation - LINtree (@giphy-ip.bsky.social) and LINvis. See github.com/kjolley/BIGS... for release notes. BIGSdb powers all the databases at @pubmlst.org and BIGSdb Pasteur.

Tree drawn within the iTOL interface generated by LINtree. The tree is annotated with LIN codes and clonal complexes in different colours.

LINvis displays datasets of LIN codes as a series of hierarchical packed circles.

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PubMLST.org @pubmlst.org · 21/01/2026

PubMLST will be unavailable for up to 1 hour from 10am on Friday 23 January while we perform server maintenance.

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 25/11/2025

BIGSdb v1.15.6 has been released. This contains 2 new plugins - GeneScanner and a wrapper for PlasmidFinder. Also added support for third party analysis fields for various plugins and performance improvements. Release notes at github.com/kjolley/BIGS...

github.com

Release Version 1.51.6 · kjolley/BIGSdb

This release adds two new analysis plugins and other improvements: New GeneScanner plugin New PlasmidFinder plugin Updates to various plugins to support analysis fields (third-party results stored...

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Reposted by PubMLST.org

sylvain Brisse @sylvainbrisse.bsky.social · 24/10/2025

The recordings of the 6-hour webinar on Bacterial Strain Taxonomy for Genomic Surveillance are now available through the @ecdc.europa.eu ECDC Learning portal: learning.ecdc.europa.eu/course/view.... - cgMLST, SNPs, K-mer based strain nomenclatures applications and more!

learning.ecdc.europa.eu

Course: GenEpi-BioTrain - Virtual training 21 - Bacterial Strain Taxonomy for Genomic Surveillance

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PubMLST.org @pubmlst.org · 27/08/2025

A new MLST scheme is now available for Actinobacillus spp. at pubmlst.org/organisms/ac.... The scheme was developed by Nick Vereecke and colleagues at Ghent University and PathoSense, Belgium. It is described in pubmed.ncbi.nlm.nih.gov/37020296/.

pubmlst.org

Actinobacillus spp.

The MLST scheme hosted in this database was developed by Nick Vereecke and colleagues at Ghent University and PathoSense, Belgium. It is described in Vereecke et al. 2023 Vet Res 54:33. Database curat...

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PubMLST.org @pubmlst.org · 18/07/2025

#Kaptive analysis for surface polysaccharide typing is now available within the @pubmlst.org Acinetobacter database. 👇

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 14/07/2025

BIGSdb v1.51.3 has been released. This provides performance improvements to distance matrix calculation in Genome Comparator, by rewriting the pairwise comparison in C. In addition, iTOL and Microreact trees can now be constructed from allelic profiles, not just sequences. github.com/kjolley/BIGS...

github.com

Release Version 1.51.3 · kjolley/BIGSdb

This version provides the following enhancements: Distance matrix calculation is now significantly quicker in Genome Comparator. Various optimisations were made to avoid redundant hash lookups and...

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PubMLST.org @pubmlst.org · 19/05/2025

We are currently experiencing an issue with OAuth authentication to the API following a move to a new server.

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PubMLST.org @pubmlst.org · 13/03/2025

A new MLST scheme is now available for Streptococcus parasuis, an emerging zoonotic pathogen. This has been developed by Han Zheng and colleagues at the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. pubmlst.org/organisms/st...

pubmlst.org

Streptococcus parasuis

This MLST scheme has been developed by Han Zheng and colleagues at the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Database c...

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PubMLST.org @pubmlst.org · 10/02/2025

A new database is now available on @PubMLST.org for Halobacteria MLST. This is our first scheme for Archaea. The scheme is based on MLSA loci described in Papke et al. 2011 (pubmed.ncbi.nlm.nih.gov/21296924/). Database is curated by Kayo Cesar Bianco Fernandes (FIOCRUZ). pubmlst.org/organisms/ha...

pubmed.ncbi.nlm.nih.gov

A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales - PubMed

Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integ...

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PubMLST.org @pubmlst.org · 21/01/2025

Please note that we will be performing a software update on the main PubMLST website on Thursday 23/1/2025 between 7-9am UK time. There will be short periods of disruption when the website will be unavailable during this window.

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PubMLST.org @pubmlst.org · 17/01/2025

HTTP requests have been disabled on the API. All requests to rest.pubmlst.org are now forwarded automatically to rest.pubmlst.org. In the future, unencrypted traffic (HTTP) will be blocked at the University firewall and these requests will fail, so please update any scripts to use HTTPS only.

rest.pubmlst.org

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 08/01/2025

BIGSdb v1.50.1 has been released. This adds support for Neighbour-Joining trees in GrapeTree. Full release notes at github.com/kjolley/BIGS...

Neighbour-joining phylogenetic tree with coloured nodes at the ends of branches representing clonal complexes.

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Reposted by PubMLST.org

Ben Pascoe @benizao.bsky.social · 30/12/2024

We find more examples of these high resistance in global datasets - particularly in LMICs, and predominantly in lineages associated with chicken production (credit to @pubmlst.org)

Global, source, sequence type, and time distribution of the high-resistance cmeB gene from Campylobacter strains in the PubMLST database. Percentage of Campylobacter strains from various countries around the world with the RE-cmeB high-resistance gene (minimum 40 genomes).

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · 26/11/2024

BIGSdb v1.49.1 has been released. This version improves the layout of user registration and admin pages, and provides the option to export LIN code prefixes of specified length in the Export plugin. BIGSdb powers the databases on pubmlst.org and bigsdb.pasteur.fr. github.com/kjolley/BIGS...

pubmlst.org

PubMLST - Public databases for molecular typing and microbial genome diversity

Public databases for molecular typing and microbial genome diversity

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PubMLST.org @pubmlst.org · 28/11/2024

PubMLST is now on Bluesky! This account will post service updates, general news about the site, and information related to organisms with databases that we host.

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