Keith Jolley
@kjolley.bsky.social
Bioinformatician in the Department of Biology, University of Oxford.
Working on microbial genomics | Developer of @PubMLST.org and BIGSdb | https://orcid.org/0000-0002-0751-0287
Working on microbial genomics | Developer of @PubMLST.org and BIGSdb | https://orcid.org/0000-0002-0751-0287
Reposted by Keith Jolley
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 Keith Jolley
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
October 21, 2025 at 1:47 PM
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...
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...
Reposted by Keith Jolley
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
September 25, 2025 at 11:22 AM
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
Reposted by Keith Jolley
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 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
September 6, 2025 at 7:32 PM
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 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
Reposted by Keith Jolley
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/.
Reposted by Keith Jolley
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.
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.
July 21, 2025 at 11:47 PM
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.
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.
July 18, 2025 at 7:57 AM
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...
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...
Reposted by Keith Jolley
@kjolley.bsky.social presenting challenges of maintaining genomic epidemiology platforms for public health surveillance of pathogens @pasteur.fr #BIGSdb
June 25, 2025 at 10:08 AM
@kjolley.bsky.social presenting challenges of maintaining genomic epidemiology platforms for public health surveillance of pathogens @pasteur.fr #BIGSdb
Reposted by Keith Jolley
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
Project manager: Genomic taxonomy of bacterial strains, epidemiological surveillance and antimicrobial resistance - Research
We are looking for a project manager to develop our activities around the genomic taxonomy of bacterial strains and the corresponding platform at https://bigsdb.pasteur.fr/. The project manager’s main...
research.pasteur.fr
June 12, 2025 at 2:46 PM
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
Reposted by Keith Jolley
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
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
KlebNET-GSP
klebnet.org
May 21, 2025 at 12:40 PM
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
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...
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system
Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that d...
www.biorxiv.org
May 7, 2025 at 7:03 AM
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...
Reposted by Keith Jolley
Very happy to see the second paper of my PhD now published in PLOS Pathogens!
dx.plos.org/10.1371/jour...
dx.plos.org/10.1371/jour...
Origin, evolution, and success of pbla, the gonococcal beta-lactamase plasmid, and implications for public health
Author summary Neisseria gonorrhoeae is a threat to sexual and reproductive health. With no available vaccine against gonococcal disease, control of infection depends on having effective antimicrobial...
dx.plos.org
May 7, 2025 at 6:27 AM
Very happy to see the second paper of my PhD now published in PLOS Pathogens!
dx.plos.org/10.1371/jour...
dx.plos.org/10.1371/jour...
Reposted by Keith Jolley
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.
May 2, 2025 at 5:05 PM
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.
Reposted by Keith Jolley
Very pleased to have been awarded this grant to collaborate with researchers at the University of Oslo!
The Oxford AMR Network and the IOI have awarded 10 Knowledge Exchange grants to early career researchers across the University of Oxford.
The grants will allow researchers to enhance collaborations and expertise in AMR.
Learn about their projects here: www.ineosoxford.ox.ac.uk/amr/news/10-...
The grants will allow researchers to enhance collaborations and expertise in AMR.
Learn about their projects here: www.ineosoxford.ox.ac.uk/amr/news/10-...
April 25, 2025 at 9:05 AM
Very pleased to have been awarded this grant to collaborate with researchers at the University of Oslo!
Reposted by Keith Jolley
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...
Very grateful for all the support I have received!!
www.ukri.org/news/9-milli...
£9 million investment fuels groundbreaking bioscience research
From unlocking the secrets of animal movement to tackling antimicrobial resistance, UK’s brightest bioscience minds are pushing the boundaries of innovation.
www.ukri.org
April 17, 2025 at 3:13 PM
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...
Very grateful for all the support I have received!!
www.ukri.org/news/9-milli...
Reposted by Keith Jolley
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...
Please apply and share this post:
www.jobs.ac.uk/job/DMP641/p...
Postdoctoral Research Associate at University of Oxford
Discover Postdoctoral Research Associate jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board.
www.jobs.ac.uk
April 7, 2025 at 10:15 AM
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...
Please apply and share this post:
www.jobs.ac.uk/job/DMP641/p...
Reposted by Keith Jolley
🚨 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
🗓️Save the date: 24th-25th September 2025
📝Register your interest on our website: campyuk.web.ox.ac.uk
Home
Why now? Campylobacter infections are on the rise globally, with increasing levels of antimicrobial resistance (AMR) making treatment more challenging. As the world’s most common bacterial cause of gastroenteritis, Campylobacter poses a growing public health threat, yet effective interventions remain limited. There is an urgent need for research into novel and sustainable strategies to mitigate its impact—spanning genomics, surveillance, food safety, and public health interventions.
campyuk.web.ox.ac.uk
February 22, 2025 at 7:31 PM
🚨 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
🗓️Save the date: 24th-25th September 2025
📝Register your interest on our website: campyuk.web.ox.ac.uk
Reposted by Keith Jolley
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...
Reposted by Keith Jolley
A hitchhiker’s guide to the gonococcal population: biorxiv.org/content/10.1...
The origin and evolution of the gonococcal beta-lactamase plasmid, and implications for public health
Neisseria gonorrhoeae is a leading cause of sexually transmitted infection (STI) and a priority AMR pathogen. Two narrow host range plasmids, p bla and pConj, have contributed to ending penicillin and...
biorxiv.org
January 8, 2025 at 9:55 AM
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...
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 Keith Jolley
Being treated to the most spectacular show to start the year
January 1, 2025 at 5:46 PM
Being treated to the most spectacular show to start the year
Reposted by Keith Jolley
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?"
VAL BENNETT - The Russians Are Coming [1968]
YouTube video by Bionic Dub
www.youtube.com
January 1, 2025 at 5:31 PM
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?"