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
Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics
https://doi.org/10.64898/2026.02.02.703236
https://doi.org/10.64898/2026.02.02.703236
February 12, 2026 at 12:34 PM
Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics
https://doi.org/10.64898/2026.02.02.703236
https://doi.org/10.64898/2026.02.02.703236
Reposted by Kat Holt
WHO Hub & Charité Center for Global Health have open 6 month Research Fellowships in Public Health Intelligence in Berlin.
Applications on pathogen genomics very welcome - more details below.
www.linkedin.com/posts/whopan...
Applications on pathogen genomics very welcome - more details below.
www.linkedin.com/posts/whopan...
https://www.linkedin.com/posts/whopandemichub_research-fellowship-in-public-health-in[…]m=member_desktop&rcm=ACoAAARSoLkBXZNxtmZ0HFAGh6r9MMGCoI0RVJg
February 12, 2026 at 12:59 PM
WHO Hub & Charité Center for Global Health have open 6 month Research Fellowships in Public Health Intelligence in Berlin.
Applications on pathogen genomics very welcome - more details below.
www.linkedin.com/posts/whopan...
Applications on pathogen genomics very welcome - more details below.
www.linkedin.com/posts/whopan...
Reposted by Kat Holt
It’s International Day of Women & Girls in Science 🤗
Today, we celebrate Regina Ami Banu, who is advancing awareness, mentorship, and community engagement on #AMR in Ghana 🇬🇭
Read more 👉 www.lshtm.ac.uk/research/cen...
Today, we celebrate Regina Ami Banu, who is advancing awareness, mentorship, and community engagement on #AMR in Ghana 🇬🇭
Read more 👉 www.lshtm.ac.uk/research/cen...
Leading the fight against Antimicrobial Resistance in Ghana | LSHTM
Leading the fight against Antimicrobial Resistance in Ghana | LSHTM
www.lshtm.ac.uk
February 11, 2026 at 12:02 PM
It’s International Day of Women & Girls in Science 🤗
Today, we celebrate Regina Ami Banu, who is advancing awareness, mentorship, and community engagement on #AMR in Ghana 🇬🇭
Read more 👉 www.lshtm.ac.uk/research/cen...
Today, we celebrate Regina Ami Banu, who is advancing awareness, mentorship, and community engagement on #AMR in Ghana 🇬🇭
Read more 👉 www.lshtm.ac.uk/research/cen...
Reposted by Kat Holt
📢 Now Live
🖥️ Catch last weeks webinar on our YouTube and Website!
🧬 The TyphiNET AMR surveillance dashboard: unlocking Salmonella Typhi genomics data to support public health
👉 Watch now: www.targetamr.org.uk/hdrevents/th...
🖥️ Catch last weeks webinar on our YouTube and Website!
🧬 The TyphiNET AMR surveillance dashboard: unlocking Salmonella Typhi genomics data to support public health
👉 Watch now: www.targetamr.org.uk/hdrevents/th...
February 10, 2026 at 4:25 PM
📢 Now Live
🖥️ Catch last weeks webinar on our YouTube and Website!
🧬 The TyphiNET AMR surveillance dashboard: unlocking Salmonella Typhi genomics data to support public health
👉 Watch now: www.targetamr.org.uk/hdrevents/th...
🖥️ Catch last weeks webinar on our YouTube and Website!
🧬 The TyphiNET AMR surveillance dashboard: unlocking Salmonella Typhi genomics data to support public health
👉 Watch now: www.targetamr.org.uk/hdrevents/th...
Reposted by Kat Holt
Announcing launch of the International Syphilis Symposium Webinar Series.
The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.
First meeting 26th March this year: Register below.
The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.
First meeting 26th March this year: Register below.
International Syphilis Symposium Webinar Series
events.zoom.us
February 10, 2026 at 6:26 PM
Announcing launch of the International Syphilis Symposium Webinar Series.
The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.
First meeting 26th March this year: Register below.
The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.
First meeting 26th March this year: Register below.
Reposted by Kat Holt
💻 Calling those in #PublicHealth interested in spatial analysis: Our @lshtm.bsky.social course teaches you to analyse spatial health data using R - no previous experience required #HealthData #geostatistics
Runs between June-July 2026
Apply by 2 May 🔽
www.lshtm.ac.uk/study/course...
Runs between June-July 2026
Apply by 2 May 🔽
www.lshtm.ac.uk/study/course...
February 10, 2026 at 9:33 AM
💻 Calling those in #PublicHealth interested in spatial analysis: Our @lshtm.bsky.social course teaches you to analyse spatial health data using R - no previous experience required #HealthData #geostatistics
Runs between June-July 2026
Apply by 2 May 🔽
www.lshtm.ac.uk/study/course...
Runs between June-July 2026
Apply by 2 May 🔽
www.lshtm.ac.uk/study/course...
Reposted by Kat Holt
The 2026 EMBO course in Computational and Experimental Microbiomics held in @uniofbath.bsky.social has been announced! Come and join us for this course to study host-microbe interactions and co-evolution.
⏰ When: 6-18 July 26
🚨 Registration: 11 May 26
🔗 meetings.embo.org/event/26-mic...
⏰ When: 6-18 July 26
🚨 Registration: 11 May 26
🔗 meetings.embo.org/event/26-mic...
February 9, 2026 at 8:58 AM
The 2026 EMBO course in Computational and Experimental Microbiomics held in @uniofbath.bsky.social has been announced! Come and join us for this course to study host-microbe interactions and co-evolution.
⏰ When: 6-18 July 26
🚨 Registration: 11 May 26
🔗 meetings.embo.org/event/26-mic...
⏰ When: 6-18 July 26
🚨 Registration: 11 May 26
🔗 meetings.embo.org/event/26-mic...
Reposted by Kat Holt
This is fascinating – normally meta-analyses are useful to work out whether a drug works, but this is an interesting assessment of something more subtle but probably equally valuable: whether the adverse effects are actually robust. Side effects can really put off target users, of course.
Almost all side effects on statin labels not caused by statins, finds major meta-analysis; authors call for labels to be updated.
Find out more 👉 spkl.io/63324AsjHO
Find out more 👉 spkl.io/63324AsjHO
February 8, 2026 at 1:46 PM
This is fascinating – normally meta-analyses are useful to work out whether a drug works, but this is an interesting assessment of something more subtle but probably equally valuable: whether the adverse effects are actually robust. Side effects can really put off target users, of course.
Reposted by Kat Holt
✨If you have a story you would like to share with the community, please submit an abstract by Feb 16. ✨
Kind reminder: There is one week left to apply for a talk for the Klebsiella Seminar Series!
Send your abstract by February 16th!
& Register for free in the link below:
forms.gle/LhJu11WQN6Yy...
#MicroSky #UTISky #AMRSky #Agenda
Send your abstract by February 16th!
& Register for free in the link below:
forms.gle/LhJu11WQN6Yy...
#MicroSky #UTISky #AMRSky #Agenda
The Klebsiella Seminar Series - 2026
Please use this form to register for the 2026 Klebsiella Seminar Series. To submit an abstract for consideration as a 15 minute research talk, please fill out the abstract submission portion at the en...
forms.gle
February 9, 2026 at 11:48 AM
✨If you have a story you would like to share with the community, please submit an abstract by Feb 16. ✨
Reposted by Kat Holt
No immigrant is safe in the USA.
Better not let this happen in the UK.
www.theguardian.com/us-news/2026...
Better not let this happen in the UK.
www.theguardian.com/us-news/2026...
Irish man with valid US work permit held in ICE detention for five months
Seamus Culleton, who has lived in US for two decades, faces deportation after being arrested on way home from work
www.theguardian.com
February 9, 2026 at 6:39 PM
No immigrant is safe in the USA.
Better not let this happen in the UK.
www.theguardian.com/us-news/2026...
Better not let this happen in the UK.
www.theguardian.com/us-news/2026...
Reposted by Kat Holt
⚠️ Burkholderia found in certain wipes.
Burkholderia are bacteria that rarely cause harm in healthy people but sometimes cause serious infections, particularly for those with certain medical conditions or managing IV lines at home:
https://bit.ly/3Hhq4W4
Burkholderia are bacteria that rarely cause harm in healthy people but sometimes cause serious infections, particularly for those with certain medical conditions or managing IV lines at home:
https://bit.ly/3Hhq4W4
February 6, 2026 at 11:09 AM
⚠️ Burkholderia found in certain wipes.
Burkholderia are bacteria that rarely cause harm in healthy people but sometimes cause serious infections, particularly for those with certain medical conditions or managing IV lines at home:
https://bit.ly/3Hhq4W4
Burkholderia are bacteria that rarely cause harm in healthy people but sometimes cause serious infections, particularly for those with certain medical conditions or managing IV lines at home:
https://bit.ly/3Hhq4W4
Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
February 6, 2026 at 8:05 AM
Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Kat Holt
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 5, 2026 at 3:38 AM
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
Reposted by Kat Holt
Why are there such big differences between the sexes when it comes to immune responses? This Essay looks at what further research is required to fully determine sex-differential mechanisms in #immunity.🧪 #immunosky
Knowledge gaps and research priorities to understand sex differences in immunity
Immunity differs profoundly according to biological sex, leading to sex differences in autoimmunity, infections, cancer and responses to immunotherapy and vaccines. This Essay explores the major…
plos.io
February 3, 2026 at 2:05 PM
Why are there such big differences between the sexes when it comes to immune responses? This Essay looks at what further research is required to fully determine sex-differential mechanisms in #immunity.🧪 #immunosky
Scratching my head over an invite to #SciFoo… held over a weekend in the middle of summer holidays…
WTF is this tech bro stuff & why is UK govt @aria-research.bsky.social supporting such non-inclusive BS?
Could you find any clearer way of signalling you are NOT interested in women attending?
WTF is this tech bro stuff & why is UK govt @aria-research.bsky.social supporting such non-inclusive BS?
Could you find any clearer way of signalling you are NOT interested in women attending?
February 3, 2026 at 9:20 PM
Scratching my head over an invite to #SciFoo… held over a weekend in the middle of summer holidays…
WTF is this tech bro stuff & why is UK govt @aria-research.bsky.social supporting such non-inclusive BS?
Could you find any clearer way of signalling you are NOT interested in women attending?
WTF is this tech bro stuff & why is UK govt @aria-research.bsky.social supporting such non-inclusive BS?
Could you find any clearer way of signalling you are NOT interested in women attending?
Reposted by Kat Holt
📢 Call for Abstracts!
📊 We're now accepting abstract submissions for Lightning Presentations at the TARGetAMR Conference 2026! 🧠
📅 Deadline: Friday 20th March, 5pm GMT
🔗 Submit yours here: www.targetamr.org.uk/now-open-cal...
#TARGetAMR26
📊 We're now accepting abstract submissions for Lightning Presentations at the TARGetAMR Conference 2026! 🧠
📅 Deadline: Friday 20th March, 5pm GMT
🔗 Submit yours here: www.targetamr.org.uk/now-open-cal...
#TARGetAMR26
February 3, 2026 at 11:33 AM
📢 Call for Abstracts!
📊 We're now accepting abstract submissions for Lightning Presentations at the TARGetAMR Conference 2026! 🧠
📅 Deadline: Friday 20th March, 5pm GMT
🔗 Submit yours here: www.targetamr.org.uk/now-open-cal...
#TARGetAMR26
📊 We're now accepting abstract submissions for Lightning Presentations at the TARGetAMR Conference 2026! 🧠
📅 Deadline: Friday 20th March, 5pm GMT
🔗 Submit yours here: www.targetamr.org.uk/now-open-cal...
#TARGetAMR26
Reposted by Kat Holt
The online ANI calculator (skani) that allows you to compare your genome data with reference sequences in GTDB saves so much time and faffing around. :)
GTDB - skani calculator
An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.
gtdb.ecogenomic.org
February 2, 2026 at 8:27 PM
The online ANI calculator (skani) that allows you to compare your genome data with reference sequences in GTDB saves so much time and faffing around. :)
Reposted by Kat Holt
Looking to build a foundational knowledge of #InfectiousDisease modelling?
Join our hybrid short course delivered by LSHTM and @ukhsa.bsky.social introducing key modelling tools and practical applications.
Runs from 15 - 26 June 2026
Apply by 15 May 2026👉 bit.ly/3bw2bWH
Join our hybrid short course delivered by LSHTM and @ukhsa.bsky.social introducing key modelling tools and practical applications.
Runs from 15 - 26 June 2026
Apply by 15 May 2026👉 bit.ly/3bw2bWH
February 2, 2026 at 11:09 AM
Looking to build a foundational knowledge of #InfectiousDisease modelling?
Join our hybrid short course delivered by LSHTM and @ukhsa.bsky.social introducing key modelling tools and practical applications.
Runs from 15 - 26 June 2026
Apply by 15 May 2026👉 bit.ly/3bw2bWH
Join our hybrid short course delivered by LSHTM and @ukhsa.bsky.social introducing key modelling tools and practical applications.
Runs from 15 - 26 June 2026
Apply by 15 May 2026👉 bit.ly/3bw2bWH
Reposted by Kat Holt
Only 2 more days to apply for this post as Research Fellow in the Health Protection Research Unit - Public Health Genomics at the University of Birmingham.
Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits
www.jobs.ac.uk/job/DQE112/r...
Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits
www.jobs.ac.uk/job/DQE112/r...
Research Fellow at University of Birmingham
Discover Research Fellow jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board.
www.jobs.ac.uk
February 2, 2026 at 4:08 PM
Only 2 more days to apply for this post as Research Fellow in the Health Protection Research Unit - Public Health Genomics at the University of Birmingham.
Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits
www.jobs.ac.uk/job/DQE112/r...
Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits
www.jobs.ac.uk/job/DQE112/r...
Reposted by Kat Holt
Harmonizing and integrating metadata across labs and systems can be difficult. In our new publication we describe an open source One Health data standard to support collaborative genomic surveillance of MPXV (Mpox virus).
www.microbiologyresearch.org/content/jour...
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
@microbiologysociety.org
The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance
A sudden increase in the number of Mpox virus (MPXV) cases worldwide prompted the WHO to declare a Public Health Emergency of International Concern in 2022 and again in 2024. Public health genomic sur...
www.microbiologyresearch.org
January 30, 2026 at 4:41 PM
Harmonizing and integrating metadata across labs and systems can be difficult. In our new publication we describe an open source One Health data standard to support collaborative genomic surveillance of MPXV (Mpox virus).
www.microbiologyresearch.org/content/jour...
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
@microbiologysociety.org
Reposted by Kat Holt
Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...
January 30, 2026 at 12:34 PM
Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...
Reposted by Kat Holt
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Research Group Leader
Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...
embl.wd103.myworkdayjobs.com
January 30, 2026 at 9:02 AM
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Reposted by Kat Holt
Lots of tools out there in the "AI for Science" space. I don't want something to slop-write my papers and "do my research" for me. But I have a ton of PDFs in Zotero, and I'd love an AI thing to help me understand what's in there. I found it today blog.stephenturner.us/p/zotero-con... 🧵 1/
January 29, 2026 at 9:52 PM
Lots of tools out there in the "AI for Science" space. I don't want something to slop-write my papers and "do my research" for me. But I have a ton of PDFs in Zotero, and I'd love an AI thing to help me understand what's in there. I found it today blog.stephenturner.us/p/zotero-con... 🧵 1/
Reposted by Kat Holt
I think I might take one of these "under 20 minutes" AI skills courses the UK Govt. seems very keen on everyone doing and live-post it here... Maybe we can all learn something together! The press release sends me to aiskillshub.org.uk/aiskillsboost/ - let's go and see!
AI Skills Boost - AI Skills Hub
aiskillshub.org.uk
January 28, 2026 at 12:07 PM
I think I might take one of these "under 20 minutes" AI skills courses the UK Govt. seems very keen on everyone doing and live-post it here... Maybe we can all learn something together! The press release sends me to aiskillshub.org.uk/aiskillsboost/ - let's go and see!
Reposted by Kat Holt
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
January 28, 2026 at 6:46 PM
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...