Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

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!

Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...

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

Ben Pascoe @benizao.bsky.social @sheppardlab.bsky.social shining a light on C. coli - although less common than C. jejuni, it has higher levels of AMR. His work in Peru highlights the importance of this pathogen in LMICs due constant exposure with backyard livestock and antibiotic use 🇵🇪 #CampyUK2025

Postdoc position (please re-post) A funded postdoctoral position, will open in 2026 to study aspects of Neisseria gonorrhoeae pathogenesis, antigenic variation, genetics, or physiology. If interested in more information, please contact Hank Seifert [email protected] #MicroSky

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/.

Woohoo Kaptive is now integrated within BIGSdb for #Klebsiella and #Acinetobacter. Thanks @kjolley.bsky.social! Also like to acknowledge that the Acineto dbs were developed and maintained by Johanna Kenyon and team at Griffith Uni.

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...

@kjolley.bsky.social presenting challenges of maintaining genomic epidemiology platforms for public health surveillance of pathogens @pasteur.fr #BIGSdb

The BIGSdb-Pasteur project, running under my supervision since 20 years, is looking for a project manager - great opportunity to contribute to this high-profile international resource in the field of reference strain taxonomies, genomic epidemiology and antimicrobial resistance surveillance

We are pleased to launch the KlebNET Genomic Epidemiology Consortium! We aim to build a public metadata repository; systematic risk framework for global genomic surveillance; and genomic epi reviews for high-impact #Klebsiella clones. Join us here: klebnet.org/klebnet-gsp-... #ABPHM25

New preprint describing a cgMLST scheme and LIN code system for Moraxella catarrhalis, with database hosted on @pubmlst.org. www.biorxiv.org/content/10.1...

Very happy to see the second paper of my PhD now published in PLOS Pathogens! dx.plos.org/10.1371/jour...

One of the many problems of the insane First Past The Post system this country uses for its elections, is that it completely breaks down when four or more parties are in with a shout, and the voter needs to decide what party to vote for to keep the swivel-eyed loons out.

Very pleased to have been awarded this grant to collaborate with researchers at the University of Oslo!

Super excited to have been awarded a 2024 BBSRC Fellowship to investigate antibiotic tolerance in staphylococci! ☺️🧫🦠💊 @ukri.org Very grateful for all the support I have received!! www.ukri.org/news/9-milli...

TWO postdoc positions in Computational Microbiology and/or biochemistry. Join our interdisciplinary group in the new Life and Mind Building @OxfordBiology, @UniofOxford, @IneosOxford Please apply and share this post: www.jobs.ac.uk/job/DMP641/p...

🚨 We're very happy to announce the #CampyUK2025 meeting in Oxford (@ox.ac.uk), which will focus on #AMR in collaboration with @ineosoxford.bsky.social 🗓️Save the date: 24th-25th September 2025 📝Register your interest on our website: campyuk.web.ox.ac.uk

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 hitchhiker’s guide to the gonococcal population: biorxiv.org/content/10.1...

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

Being treated to the most spectacular show to start the year

One of my favorites of the genre (though relatively late in the game) is Val Bennett's "The Russians Are Coming," (1968) which takes the Dave Brubeck Quartet's "Take Five" and says, "What would this sound like in 4-4 time *and* with a ska beat?"

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.

You guys remember TweetDeck? Bluesky has it, and it's free. Check out 🔗 deck.blue by @gildaswise.com for a multi-column interface. 2/10

Deadline for applications is midnight (GMT) today!

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).

I don’t think I’ve ever looked scarier. Video link to students in Xiamen.

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.

www.ineosoxford.ox.ac.uk/careers 👇

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...

PhD studentship alert!! Two projects available with me fully funded by BBSRC This one is a collaboration with Dr Michelle Buckner warwick.ac.uk/fac/cross_fa... And this one a collaboration with @overtonlab.bsky.social warwick.ac.uk/fac/cross_fa... Both will be lots of fun! Come & join us 😃

Time to say 'Au revoir Paris' after a fantastic #KLEBS2024. Great science and great people. So proud to have @tomstantonmicro.bsky.social @kalanip.bsky.social @bananabenana.bsky.social representing the lab, and congrats to Tom and Kalani for their poster prizes! 👏

#KLEBS2024 has just finished, big thanks to @chcrestani.bsky.social for her fantastic help in organizing

Thanks @sylvainbrisse.bsky.social for involving me in KlebNET-GSP as project manager 3y ago, it was a very enriching experience! Thanks to all the attendees of #KLEBS2024 for making this a great success, it was our best reward! And thanks to the @gatesfoundation.bsky.social for making it possible!

Quote post with a sunset pic you took yourself. Big Bay, Cape Town, South Africa

The UK’s democracy is far from satisfactory in many ways, but I have never once waited more than 2-3 minutes to vote at a polling station for a national or local election. Scenes like the below are a choice.

Having this experience shopping for a fire blanket today. 4,000 reviews. 4.8 stars. All the 5 star reviews are about how easy it is to install and how safe it makes them feel. The one star reviews are "the fire blanket caught on fire and covered me in fiberglass shards".

Was finally convinced to sign up. Hello, everyone ☁️🦋

Congratulations Georgia and Mathew! Two Dunn School PIs were recently awarded ERC starting grants: a big boost for antimicrobial resitant research in the department! Find out more: www.path.ox.ac.uk/news-article... (written by Isabella Maudlin)

For weeks (and arguably years) Trump and Trump supporters portrayed Harris as a barely verbal idiot. Then she thrashed him so badly he refused to debate her again. This says something about why diversity efforts matter and why the right opposes them www.theatlantic.com/ideas/archiv...

A cgMLST scheme for H. influenzae www.microbiologyresearch.org/content/jour...

MGen editors picks of the week! A cgMLST scheme for pneumococcus www.microbiologyresearch.org/content/jour...

🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...

The best day celebrating the end of an era at Birmingham!

BIGSdb v1.47.0 has been released and is now live on @PubMLST. This introduces an embargo system for isolate submissions. If enabled, submitters will now see an option to request an embargo when they submit isolates.