Kat Holt
@katholt.bsky.social
Scientist… pathogen genomics & antimicrobial resistance, computational biology & infectious disease epidemiology.
Co-Director LSHTM AMR Centre @lshtmamrcentre.bsky.social
holtlab.net | klebnet.org | typhoidgenomics.org | amr.lshtm.ac.uk
Co-Director LSHTM AMR Centre @lshtmamrcentre.bsky.social
holtlab.net | klebnet.org | typhoidgenomics.org | amr.lshtm.ac.uk
Pinned
Kat Holt
@katholt.bsky.social
· Nov 19
![figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:q5nky4heg5sfix4get4zh2pw/bafkreibshmuvkuafxwd2uk3r42ss6ma2dhmaidbysgvufnbkbv5cn4guai@jpeg)
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Reposted by Kat Holt
Marco Rubio is reportedly saying Maduro will stand trial in US courts.
Which means it’s now the US administration’s position that US courts can hold foreign presidents, but not the US president, accountable for crimes.
Which means it’s now the US administration’s position that US courts can hold foreign presidents, but not the US president, accountable for crimes.
January 3, 2026 at 10:52 AM
Marco Rubio is reportedly saying Maduro will stand trial in US courts.
Which means it’s now the US administration’s position that US courts can hold foreign presidents, but not the US president, accountable for crimes.
Which means it’s now the US administration’s position that US courts can hold foreign presidents, but not the US president, accountable for crimes.
Reposted by Kat Holt
a big part of the issue surrounding the use of chatgpt/LLMs in academic research comes down to process vs. product. a lot of us know that the process of doing research matters because that's where intellectual work is done; but some "academics" and lots of techies only care about a fast product
December 21, 2025 at 2:49 PM
a big part of the issue surrounding the use of chatgpt/LLMs in academic research comes down to process vs. product. a lot of us know that the process of doing research matters because that's where intellectual work is done; but some "academics" and lots of techies only care about a fast product
Reposted by Kat Holt
Post-doc positions:
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
Call for Applications: Early Career Rescue Fellowship – Freiburg Institute for Advanced Studies
uni-freiburg.de
December 19, 2025 at 5:14 PM
Post-doc positions:
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
Reposted by Kat Holt
A last thought before taking off into your various breaks - Microbial Genomics is looking for editors! Scientific publishing is frustrating and so much money going to commercial publishers... be part of the change by supporting society publishing 😊 great opportunity to join a lovely community.
December 18, 2025 at 7:08 PM
A last thought before taking off into your various breaks - Microbial Genomics is looking for editors! Scientific publishing is frustrating and so much money going to commercial publishers... be part of the change by supporting society publishing 😊 great opportunity to join a lovely community.
Reposted by Kat Holt
One might think the Epstein files were due.
December 17, 2025 at 7:12 AM
One might think the Epstein files were due.
Reposted by Kat Holt
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
December 17, 2025 at 5:35 PM
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
In case anyone needed any more reasons NOT to engage with Frontiers 🤪
"Ask AI to summarize long sections, clarify jargon, or outline the structure. Always verify summaries against the original."
Frontiers guidance on AI in peer review for ECRs optimistically expects them to "verify summaries" of things they couldn't be bothered to read it in the first place.
Frontiers guidance on AI in peer review for ECRs optimistically expects them to "verify summaries" of things they couldn't be bothered to read it in the first place.
AI in peer review: what early-career researchers should know (and how to use it wisely)
For early-career researchers, AI has become part of everyday work, whether in drafting manuscripts, organizing ideas, or exploring literature. A survey of 1,645
www.frontiersin.org
December 17, 2025 at 8:22 PM
In case anyone needed any more reasons NOT to engage with Frontiers 🤪
Reposted by Kat Holt
Symposium & workshop on inequalities in infectious disease dynamics at LSHTM in April 2026. We aim to will bring together leading researchers and practitioners to share ideas, discuss recent advances, and reflect on future directions. Details & application: iddconf.org/lshtm-sympos... Closing 21 Jan
Social Inequalities in Infectious Disease Dynamics: a Symposium and Workshop
iddconf.org
December 16, 2025 at 8:58 PM
Symposium & workshop on inequalities in infectious disease dynamics at LSHTM in April 2026. We aim to will bring together leading researchers and practitioners to share ideas, discuss recent advances, and reflect on future directions. Details & application: iddconf.org/lshtm-sympos... Closing 21 Jan
Reposted by Kat Holt
Yearly reminder that the world will not end if that new manuscript or revision sits on your desk for a couple more weeks, or you are realistic about decision times.
Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
a cartoon drawing of minnie mouse talking on a phone
Alt: a cartoon drawing of minnie mouse working intensely
media.tenor.com
December 17, 2025 at 1:02 PM
Yearly reminder that the world will not end if that new manuscript or revision sits on your desk for a couple more weeks, or you are realistic about decision times.
Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
Reposted by Kat Holt
The European Commission (@ec.europa.eu) has just designated a new EU reference laboratory (EURL) for respiratory viruses.
This marks a significant step in reinforcing the European Union’s capacity to respond to serious cross-border threats.
Read more: www.ecdc.europa.eu/en/news-even...
This marks a significant step in reinforcing the European Union’s capacity to respond to serious cross-border threats.
Read more: www.ecdc.europa.eu/en/news-even...
New EU reference laboratory for respiratory viruses designated
The European Commission has adopted an Implementing Regulation establishing a new EU reference laboratory (EURL) for public health for respiratory viruses. This marks a significant step in reinforcing...
www.ecdc.europa.eu
December 17, 2025 at 2:09 PM
The European Commission (@ec.europa.eu) has just designated a new EU reference laboratory (EURL) for respiratory viruses.
This marks a significant step in reinforcing the European Union’s capacity to respond to serious cross-border threats.
Read more: www.ecdc.europa.eu/en/news-even...
This marks a significant step in reinforcing the European Union’s capacity to respond to serious cross-border threats.
Read more: www.ecdc.europa.eu/en/news-even...
Reposted by Kat Holt
(1/7) Really pleased to have this published in @natcomms.nature.com
We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic.
www.nature.com/articles/s41...
#MicroSky #microbiology #IDSky #EpiSky 🧪
We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic.
www.nature.com/articles/s41...
#MicroSky #microbiology #IDSky #EpiSky 🧪
The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study - Nature Communications
Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...
www.nature.com
December 17, 2025 at 4:30 AM
(1/7) Really pleased to have this published in @natcomms.nature.com
We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic.
www.nature.com/articles/s41...
#MicroSky #microbiology #IDSky #EpiSky 🧪
We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic.
www.nature.com/articles/s41...
#MicroSky #microbiology #IDSky #EpiSky 🧪
Reposted by Kat Holt
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
December 16, 2025 at 5:00 PM
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
Reposted by Kat Holt
My amazing joint grad student (with Ami Bhatt) Danica Schmidtke, gave me a ceramic phage she made as a gift. It makes me very happy indeed.
December 16, 2025 at 1:28 AM
My amazing joint grad student (with Ami Bhatt) Danica Schmidtke, gave me a ceramic phage she made as a gift. It makes me very happy indeed.
Reposted by Kat Holt
🎉 Save your seat!
📅 The TARGetAMR Annual Conference 2026 is happening on 14–15 May 2026 at The Studio, Birmingham
✨ Theme: Building the Future of AMR Genomics
🦠 Join experts & researchers tackling antimicrobial resistance
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
📅 The TARGetAMR Annual Conference 2026 is happening on 14–15 May 2026 at The Studio, Birmingham
✨ Theme: Building the Future of AMR Genomics
🦠 Join experts & researchers tackling antimicrobial resistance
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
December 16, 2025 at 11:51 AM
🎉 Save your seat!
📅 The TARGetAMR Annual Conference 2026 is happening on 14–15 May 2026 at The Studio, Birmingham
✨ Theme: Building the Future of AMR Genomics
🦠 Join experts & researchers tackling antimicrobial resistance
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
📅 The TARGetAMR Annual Conference 2026 is happening on 14–15 May 2026 at The Studio, Birmingham
✨ Theme: Building the Future of AMR Genomics
🦠 Join experts & researchers tackling antimicrobial resistance
👉 Register now: www.targetamr.org.uk/hdrevents/ta...
Reposted by Kat Holt
Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2
December 15, 2025 at 5:25 PM
Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2
Reposted by Kat Holt
Absolutely stoked to have this published in @plosbiology.org
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
journals.plos.org
December 13, 2025 at 9:46 AM
Absolutely stoked to have this published in @plosbiology.org
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
Reposted by Kat Holt
🎉 Big news for the future of #RStats. The project
"Enabling the next generation of R contributors"
has received £500k over 2 years.
- mentoring expert contributors
- modernising infrastructure
- improving governance
- strengthen communication and outreach
www.software.ac.uk/rsmf-round-1...
"Enabling the next generation of R contributors"
has received £500k over 2 years.
- mentoring expert contributors
- modernising infrastructure
- improving governance
- strengthen communication and outreach
www.software.ac.uk/rsmf-round-1...
RSMF Round 1 Projects | Software Sustainability Institute
Round 1 of the Research Software Maintenance Fund awarded just under £3 million to 13 projects selected for their potential to deliver high impact, value for money, feasibility, and quality. The funde...
www.software.ac.uk
December 12, 2025 at 12:15 PM
🎉 Big news for the future of #RStats. The project
"Enabling the next generation of R contributors"
has received £500k over 2 years.
- mentoring expert contributors
- modernising infrastructure
- improving governance
- strengthen communication and outreach
www.software.ac.uk/rsmf-round-1...
"Enabling the next generation of R contributors"
has received £500k over 2 years.
- mentoring expert contributors
- modernising infrastructure
- improving governance
- strengthen communication and outreach
www.software.ac.uk/rsmf-round-1...
Reposted by Kat Holt
Very interesting analysis from @bananabenana.bsky.social et al. on blaIMP dissemination from >4.5k genomes from strains of 93 species isolated over 20 years.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study - Nature Communications
Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...
www.nature.com
December 12, 2025 at 5:49 PM
Very interesting analysis from @bananabenana.bsky.social et al. on blaIMP dissemination from >4.5k genomes from strains of 93 species isolated over 20 years.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Congrats @efosternyarko.bsky.social and team for this great work building capacity for public health genomics to investigate cholera and other enteric bacteria, across Africa 👏
www.lshtm.ac.uk/research/cen...
www.lshtm.ac.uk/research/cen...
December 11, 2025 at 7:54 AM
Congrats @efosternyarko.bsky.social and team for this great work building capacity for public health genomics to investigate cholera and other enteric bacteria, across Africa 👏
www.lshtm.ac.uk/research/cen...
www.lshtm.ac.uk/research/cen...
Reposted by Kat Holt
📢Persistent antibiotic resistance of cholera-causing bacteria in Africa revealed from a multinational workshop for strengthening disease surveillance, hosted by PulseNet Africa and @lshtmamrcentre.bsky.social.
Read more here: microb.io/4aDdPze%F0%9... #MGEN #AntimicrobialResistance #Microbiology
Read more here: microb.io/4aDdPze%F0%9... #MGEN #AntimicrobialResistance #Microbiology
December 10, 2025 at 3:02 PM
📢Persistent antibiotic resistance of cholera-causing bacteria in Africa revealed from a multinational workshop for strengthening disease surveillance, hosted by PulseNet Africa and @lshtmamrcentre.bsky.social.
Read more here: microb.io/4aDdPze%F0%9... #MGEN #AntimicrobialResistance #Microbiology
Read more here: microb.io/4aDdPze%F0%9... #MGEN #AntimicrobialResistance #Microbiology
Reposted by Kat Holt
Prospective characterisation of drug-resistant bloodstream infections in Africa and Asia (ACORN2): a surveillance network assessment - The Lancet Microbe www.thelancet.com/journals/lan...
Great work by a tremendous team of collaborators!
@wellcometrust.bsky.social @acorn-amr.bsky.social @who.int
Great work by a tremendous team of collaborators!
@wellcometrust.bsky.social @acorn-amr.bsky.social @who.int
Prospective characterisation of drug-resistant bloodstream infections in Africa and Asia (ACORN2): a surveillance network assessment
ACORN2 has shown practical implementation of collecting linked clinical-laboratory
AMR data in low-income and middle-income countries and identified a significant burden
of WHO GLASS BSI. Adoption of ...
www.thelancet.com
December 9, 2025 at 11:50 AM
Prospective characterisation of drug-resistant bloodstream infections in Africa and Asia (ACORN2): a surveillance network assessment - The Lancet Microbe www.thelancet.com/journals/lan...
Great work by a tremendous team of collaborators!
@wellcometrust.bsky.social @acorn-amr.bsky.social @who.int
Great work by a tremendous team of collaborators!
@wellcometrust.bsky.social @acorn-amr.bsky.social @who.int
Reposted by Kat Holt
Immigrants make the world a more interesting place.
December 7, 2025 at 10:31 AM
Immigrants make the world a more interesting place.
Reposted by Kat Holt
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
November 30, 2025 at 7:51 PM
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 👇
Reposted by Kat Holt
This article suggests the possibility of training AI on pre-existing proposals and their review reports, scores and related decisions. I.e. training them on a system which is known to preferentially award larger amounts of money to white men. What could possibly go wrong?
UKRI exploring use of AI in grant review - this will prompt debate but interested to know if people think it’d encourage novelty or the opposite? www.chemistryworld.com/news/ukri-op...
UKRI opens up grant proposal data to explore using AI to smooth peer review
Surging applications has led the UK's main funder to look at ways to reduce the burden on reviewers
www.chemistryworld.com
December 4, 2025 at 10:49 PM
This article suggests the possibility of training AI on pre-existing proposals and their review reports, scores and related decisions. I.e. training them on a system which is known to preferentially award larger amounts of money to white men. What could possibly go wrong?
Reposted by Kat Holt
Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)
Antibiotic Resistance Microbiology Dataset Mass General Brigham (ARMD-MGB) v1.0.0
ARMD-MGB contains detailed microbiology and clinical metadata for >225,000 patients and >970,000 cultures collected over 10 years
physionet.org
December 5, 2025 at 7:39 AM
Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)