BIGSdb v1.53.4 has been released. This adds a Sunburst visualisation to the LINvis tool. This uses a series of concentric circles with each ring representing a different LIN threshold with each prefix value at that threshold sized proportionally to its frequency. github.com/kjolley/BIGS...

Really happy to share this new pre print on the development of a cgMLST and LIN code for Streptococcus pyogenes, led by Yan Ryan at @ukhsa.bsky.social www.biorxiv.org/content/10.6...

High resolution Streptococcus pyogenes core genome MLST and LIN coding scheme for outbreak detection

Streptococcus pyogenes is a globally important pathogen responsible for at least 500,000 deaths a year, causing significant burden on healthcare systems. It is the causative agent for ailments such as...

biorxiv.org

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....

Like Artemis/ACT but wish it was easier to install and more modern? Try Seqhiker. 🧬 Native desktop app (no Java) for Windows/mac/linux 🖱️ Drag-n-drop FASTA/GenBank/GFF3/BAM/VCF files 🔍 Genome browsing and ACT-style comparison ✨ Themes (customisable) and a Vim mode Docs: seqhiker.readthedocs.io

New paper 🧪🧬🧫GeneScanner is our new tool to profile genetic variation in bacterial populations. Use via GitHub or @pubmlst.org. Thanks to Ko and Pri @sheppardlab.bsky.social @broncio.bsky.social @kjolley.bsky.social @microbiologysociety.org @imibirmingham.bsky.social @ineosoxford.bsky.social

GeneScanner: profiling genetic variation across bacterial populations

Rapid, low-cost genome sequencing has transformed microbiology, advancing efforts to link genetic and phenotypic variation across diverse bacterial systems. Laboratory functional screens now uncover c...

microbiologyresearch.org

It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

journals.plos.org

Immigration make Britain brilliant

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.

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....

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

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 v1.53.0 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.

Super exciting news 🚨 I am hiring a technician to join my brand new lab at the University of Birmingham! @imibirmingham.bsky.social Come and support my BBSRC-funded research on understanding how staphylococci survive antibiotics. Please share! 🧫🧪 www.jobs.ac.uk/job/DRH271/a...

Assistant Technical Specialist at University of Birmingham

Searching for an academic job? Explore this Assistant Technical Specialist opening on jobs.ac.uk! Click to view more details and browse other academic jobs.

jobs.ac.uk

PhD student Priyanshu Raikwar showcasing his research on origin and evolution of life at #Microbio26 ; Microbiology society annual conference 2026 ! Do find him to know about the application of genomics, proteomics, ML in evolutionary biology. @microbiologysociety.org @ineosoxford.bsky.social

If you want to hear about LIN codes and their application to meningococcal outbreaks, then please come along to my talk at 4:45pm today in the Transformative Tools session at @microbiologysociety.org #MicroBio26 #omics

Really pleased to see our work (LIN codes developed for high-resolution typing of meningococci) has been directly utilised in the @ukhsa.bsky.social meningococcal disease outbreak technical briefing

Invasive Meningococcal Disease outbreak 2026: technical briefing 1

gov.uk

I am excited to share a pre print for one of the main outputs from my current postdoc, that I have been working on for a couple of years. This LIN code system for N. meningitidis adds a layer of stability for high resolution typing of the meningococcal population.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5mo ago

A Life Identification Number Barcoding (LIN Code) System for Neisseria meningitidis: high resolution multi-level typing of meningococci. https://www.biorxiv.org/content/10.64898/2026.03.03.708563v1

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.

In Iquitos, Peru this week 🇵🇪 working on enteric pathogen genomics and surveillance in the Amazon. Science powered by collaboration, rain, food… and Inca kola!

Neisseria gonorrhoeae carries an unusually large number of restriction–modification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...

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 👇

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

doi.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...

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...

Bacterial strain Taxonomy for Genomic Surveillance - GenEpi-BioTrain Webinar - Research

This workshop aims to provide participants with a comprehensive understanding of bacterial classification and nomenclature approaches used in genomic surveillance. Participants will gain insight into ...

research.pasteur.fr

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

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 h-seifert@northwestern.edu #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/.

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

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.

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 v1.51.4 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