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...

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…

url.uk.m.mimecastprotect.com

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

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

Keith Jolley@kjolley.bsky.social · 3mo ago

BIGSdb v1.53.3 has been released. This brings a visual refresh to the user interface with new fonts, muted colours, and more consistency. Screenshots show side-by-side old and new versions. Release notes at github.com/kjolley/BIGS....

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.

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.

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.

Keith Jolley@kjolley.bsky.social · 5mo ago

BIGSdb v1.53.1 has been released. This version adds additional password complexity checks and an option to automatically register new accounts for all available databases. This is now live on @pubmlst.org. Release notes at github.com/kjolley/BIGS....

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.

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

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.

ndph.ox.ac.uk

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/.

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...

pubmlst.org

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

Keith Jolley@kjolley.bsky.social · last yr.

BIGSdb v1.51.4 has been released. This adds a new #Kaptive plugin for surface polysaccharide typing of Acinetobacter baumannii and Klebsiella. github.com/kjolley/BIGS... for details. Kaptive is developed by @tomstantonmicro.bsky.social, @kelwyres.bsky.social , @katholt.bsky.social and colleagues.

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...

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

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...

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...

pubmlst.org

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...

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...

pubmed.ncbi.nlm.nih.gov

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.

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

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)

🚨 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

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...

journals.asm.org

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.

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.

cell.com

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. 👇

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus - PubMed

<span><i>Haemophilus influenzae</i> exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key v...

pubmed.ncbi.nlm.nih.gov

Keith Jolley@kjolley.bsky.social · 2y ago

BIGSdb v1.50.0 has been released, introducing support for registering fields from the output of third-party analysis tools and then using these in queries and analyses (image shows querying hicap results in H. influenzae database).

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 - Public databases for molecular typing and microbial genome diversity

Public databases for molecular typing and microbial genome diversity

pubmlst.org

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.