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PubMLST.org @pubmlst.org · Aug 27

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

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PubMLST.org @pubmlst.org · Jul 18

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

Keith Jolley @kjolley.bsky.social · Jul 18

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.

Output from Kaptive analysis shown in a BIGSdb isolate record. Tabular results are shown followed by a graphical representation of the genes within the locus analysed.

Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · Jul 14

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...

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...

github.com

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PubMLST.org @pubmlst.org · May 19

This problem has now been resolved.

PubMLST.org @pubmlst.org · May 19

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 · Mar 13

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

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PubMLST.org @pubmlst.org · Feb 10

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

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PubMLST.org @pubmlst.org · Jan 23

Updates have been completed successfully.

PubMLST.org @pubmlst.org · Jan 21

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 · Jan 17

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

Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · Jan 8

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 · Dec 30

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

Ben Pascoe @benizao.bsky.social · Dec 30

🚨 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

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Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · Dec 19

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.

www.cell.com

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PubMLST.org @pubmlst.org · Dec 2

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. 👇

Reposted by PubMLST.org

Keith Jolley @kjolley.bsky.social · Nov 26

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

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PubMLST.org @pubmlst.org · Nov 28

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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