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.

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.

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

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...

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!

New study confirms genetic lineages of common bacterium Oxford Population Health study confirms two genetic lineages of M. catarrhalis and unveils a global tool to track strains and resistance.

New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...

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...

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/.

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

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...

This problem has now been resolved.

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

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...

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...

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...

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...

Updates have been completed successfully.

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.

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.

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

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

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).

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)

Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter isolates from infants and poultry in the Peruvian Amazon | mBio Antimicrobial resistance in Campylobacter is a growing public health concern, driven by the rapid evolution and zoonotic transmission of resistant strains. This study focuses on mutations in the cmeAB...

🚨 A twixmas surprise, our final paper of 2024:
Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in #Campylobacter 🧵

Link: journals.asm.org/doi/full/10....

#Microbiology #MicroSky #AMR

A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex Hepner et al. develop a 639-loci core genome multi-locus sequence typing (cgMLST) scheme for Borrelia burgdorferi sensu lato that extends the traditional 8-loci MLST to a genomic scale. The cgMLST scheme gains higher reliability, robustness, and resolution, enabling improved insights into the evolutionary history of the species complex.

Just published - A new cgMLST scheme for Borrelia burgdorferi, the causative agent of Lyme disease. www.cell.com/cell-reports.... Scheme is available on @pubmlst.org.

BIGSdb v1.50.0 is now live on PubMLST. This allows the results of hicap (pubmed.ncbi.nlm.nih.gov/30944197/) to be searchable within the H. influenzae database. 👇

PubMLST - Public databases for molecular typing and microbial genome diversity Public databases for molecular typing and microbial genome diversity

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 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.