PubMLST.org
@pubmlst.org
Public databases for molecular typing and microbial genome diversity. https://pubmlst.org
Reposted by PubMLST.org
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...
Release notes at github.com/kjolley/BIGS...
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...
github.com
November 25, 2025 at 1:19 PM
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...
Release notes at github.com/kjolley/BIGS...
Reposted by PubMLST.org
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!
Course: GenEpi-BioTrain - Virtual training 21 - Bacterial Strain Taxonomy for Genomic Surveillance
learning.ecdc.europa.eu
October 24, 2025 at 6:42 AM
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!
Reposted by PubMLST.org
New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...
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.
www.ndph.ox.ac.uk
October 17, 2025 at 7:24 PM
New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...
www.ndph.ox.ac.uk/news/new-stu...
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
August 27, 2025 at 7:33 AM
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 v1.51.4 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.
July 18, 2025 at 2:14 PM
#Kaptive analysis for surface polysaccharide typing is now available within the @pubmlst.org Acinetobacter database. 👇
Reposted by PubMLST.org
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
July 14, 2025 at 8:51 AM
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.
May 19, 2025 at 8:56 AM
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
March 13, 2025 at 8:17 AM
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 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
February 10, 2025 at 8:43 AM
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...
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.
January 21, 2025 at 1:13 PM
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.
rest.pubmlst.org
January 17, 2025 at 7:48 AM
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.
Reposted by PubMLST.org
BIGSdb v1.50.1 has been released. This adds support for Neighbour-Joining trees in GrapeTree. Full release notes at github.com/kjolley/BIGS...
January 8, 2025 at 10:38 AM
BIGSdb v1.50.1 has been released. This adds support for Neighbour-Joining trees in GrapeTree. Full release notes at github.com/kjolley/BIGS...
Reposted by PubMLST.org
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)
December 30, 2024 at 5:16 PM
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)
Reposted by 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 🧵
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
December 30, 2024 at 5:16 PM
🚨 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 🧵
Link: journals.asm.org/doi/full/10....
#Microbiology #MicroSky #AMR
Reposted by PubMLST.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.
www.cell.com
December 19, 2024 at 9:06 AM
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. 👇
December 2, 2024 at 11:42 AM
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
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...
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
November 26, 2024 at 11:23 AM
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...
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.
November 28, 2024 at 1:24 PM
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.