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
· Jul 1
Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage
Background: Klebsiella pneumoniae causes ~20% of sepsis in neonates, with ~40% crude mortality. A vaccine administered to pregnant women, protecting against 70% of K. pneumoniae infections, could aver...
doi.org
I'm super happy to share this preprint on ‘Distribution of capsule and O types in #Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage’
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Kat Holt
In almost suspiciously perfect timing of the #ASTMH #TropMed25 starting; hot off the press Allan Zuza's first author paper taking a deep dive into genome dynamics of #Klebsiella long-term lingering lineages, congratulations Allan! 🎉
#MicroSky #IDSky 💻🧬
www.medrxiv.org/content/10.1...
#MicroSky #IDSky 💻🧬
www.medrxiv.org/content/10.1...
Temporal genome dynamics of ST39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi
Background: Klebsiella pneumoniae (Kpn) is an important cause of healthcare-associated infections (HAI). In low and middle-income countries, HAI due to Kpn disproportionally affects neonates. In this ...
www.medrxiv.org
November 9, 2025 at 5:54 PM
In almost suspiciously perfect timing of the #ASTMH #TropMed25 starting; hot off the press Allan Zuza's first author paper taking a deep dive into genome dynamics of #Klebsiella long-term lingering lineages, congratulations Allan! 🎉
#MicroSky #IDSky 💻🧬
www.medrxiv.org/content/10.1...
#MicroSky #IDSky 💻🧬
www.medrxiv.org/content/10.1...
Reposted by Kat Holt
A white poppy is a symbol of peace that, when worn, commemorates all victims of war, including both soldiers and civilians. It is also a call to action, encouraging the pursuit of peaceful resolutions to conflict rather than war. I fail to see the problem either way.
November 9, 2025 at 12:25 PM
A white poppy is a symbol of peace that, when worn, commemorates all victims of war, including both soldiers and civilians. It is also a call to action, encouraging the pursuit of peaceful resolutions to conflict rather than war. I fail to see the problem either way.
Reposted by Kat Holt
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
November 8, 2025 at 1:58 PM
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
Reposted by Kat Holt
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Resistance to last-resort antibiotics in enterococci
Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The
academic.oup.com
November 8, 2025 at 5:41 PM
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Reposted by Kat Holt
Newly released Stockholm Declaration recommends the following reforms to publishing:
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
Reformation of science publishing: the Stockholm Declaration | Royal Society Open Science
Science relies on integrity and trustworthiness. But scientists under career pressure
are lured to purchase fake publications from ‘paper mills’ that use AI-generated data,
text and image fabrication....
royalsocietypublishing.org
November 5, 2025 at 7:07 PM
Newly released Stockholm Declaration recommends the following reforms to publishing:
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
Reposted by Kat Holt
Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply!
apply.interfolio.com/176402
apply.interfolio.com/176402
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 4, 2025 at 6:57 PM
Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply!
apply.interfolio.com/176402
apply.interfolio.com/176402
Apart from the AI junk part… the notion that one should not offer a potential mechanistic explanation for an observation, without first spending years & (unavailable) $$ trying to test possibilities before sharing the observation with others (who may be better equipped to investigate the mechanism)…
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 10:37 PM
Apart from the AI junk part… the notion that one should not offer a potential mechanistic explanation for an observation, without first spending years & (unavailable) $$ trying to test possibilities before sharing the observation with others (who may be better equipped to investigate the mechanism)…
Reposted by Kat Holt
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
November 3, 2025 at 2:35 PM
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
Reposted by Kat Holt
I cannot agree more! The cost of making all vaccines free will be completely offset by lives saved and all the morbidity & hospical costs averted
Why All Vaccines Should Be Free
@crof.bsky.social
thetyee.ca/Analysis/202...
Why All Vaccines Should Be Free
@crof.bsky.social
thetyee.ca/Analysis/202...
Why All Vaccines Should Be Free | The Tyee
COVID-19 normalized vaccination for adults, and we should go further to protect people from shingles and RSV.
thetyee.ca
November 3, 2025 at 1:59 AM
I cannot agree more! The cost of making all vaccines free will be completely offset by lives saved and all the morbidity & hospical costs averted
Why All Vaccines Should Be Free
@crof.bsky.social
thetyee.ca/Analysis/202...
Why All Vaccines Should Be Free
@crof.bsky.social
thetyee.ca/Analysis/202...
Reposted by Kat Holt
New online! Microbial genomics for antimicrobial resistance ecology and action
Microbial genomics for antimicrobial resistance ecology and action
Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.
www.nature.com
November 3, 2025 at 1:07 PM
New online! Microbial genomics for antimicrobial resistance ecology and action
Reposted by Kat Holt
“MARTi has its origins in software we developed for really rapid identification of #pathogens in preterm infants, but we’ve since adapted it to use in a wide range of settings...including in agriculture, and biosurveillance..."
A powerful new tool for real-time analysis of #nanopore #metagenomics 👇
A powerful new tool for real-time analysis of #nanopore #metagenomics 👇
New software tool MARTi fast-tracks identification and response to microbial threats.
Scientists at the Earlham Institute introduce MARTi, a powerful new tool for the real-time analysis of nanopore metagenomics.
buff.ly
November 3, 2025 at 10:00 AM
“MARTi has its origins in software we developed for really rapid identification of #pathogens in preterm infants, but we’ve since adapted it to use in a wide range of settings...including in agriculture, and biosurveillance..."
A powerful new tool for real-time analysis of #nanopore #metagenomics 👇
A powerful new tool for real-time analysis of #nanopore #metagenomics 👇
Reposted by Kat Holt
Good for PSF - they value a diverse and welcoming community, and they won’t be bullied into doing otherwise.
Python Foundation declines substantial grant
The Python Software Foundation (PSF) is withdrawing its application for a $1.5 million (€1.3 million) grant from the US National Science Foundation (NSF).
www.techzine.eu
October 30, 2025 at 1:53 AM
Good for PSF - they value a diverse and welcoming community, and they won’t be bullied into doing otherwise.
Reposted by Kat Holt
🌍 The ComBac-Africa website is now live!
GARDP is proud to be a partner in this consortium of 12 institutions across 7 countries working to tackle multidrug-resistant Gram-negative bacteria through diagnostics, antimicrobial stewardship and a One Health approach.
🔗 www.combac-africa.org
GARDP is proud to be a partner in this consortium of 12 institutions across 7 countries working to tackle multidrug-resistant Gram-negative bacteria through diagnostics, antimicrobial stewardship and a One Health approach.
🔗 www.combac-africa.org
ComBac-Africa | Fighting AMR in Sub-Saharan Africa
Advancing diagnostics and antimicrobial stewardship in Africa to combat drug-resistant bacteria and improve treatment access.
www.combac-africa.org
October 30, 2025 at 6:53 AM
🌍 The ComBac-Africa website is now live!
GARDP is proud to be a partner in this consortium of 12 institutions across 7 countries working to tackle multidrug-resistant Gram-negative bacteria through diagnostics, antimicrobial stewardship and a One Health approach.
🔗 www.combac-africa.org
GARDP is proud to be a partner in this consortium of 12 institutions across 7 countries working to tackle multidrug-resistant Gram-negative bacteria through diagnostics, antimicrobial stewardship and a One Health approach.
🔗 www.combac-africa.org
Reposted by Kat Holt
As a not-for-profit, the Microbiology Society has invested in research for 80 years. By publishing with us, you help ensure the continued success and development of the microbiology community. Publish with us - microb.io/Publishing-f...
October 30, 2025 at 1:04 PM
As a not-for-profit, the Microbiology Society has invested in research for 80 years. By publishing with us, you help ensure the continued success and development of the microbiology community. Publish with us - microb.io/Publishing-f...
Reposted by Kat Holt
"...the only long-term solution is for governments to invest in safe drinking water and sanitation."
www.theguardian.com/global-devel...
www.theguardian.com/global-devel...
Cholera is spreading fast, yet it can be stopped. Why haven’t we consigned it to history? | Hakainde Hichilema and Tedros Adhanom Ghebreyesus
Vaccine production must be expanded to combat this ancient disease, especially in Africa, but a lack of political will is holding us back
www.theguardian.com
October 27, 2025 at 12:22 PM
"...the only long-term solution is for governments to invest in safe drinking water and sanitation."
www.theguardian.com/global-devel...
www.theguardian.com/global-devel...
Reposted by Kat Holt
Celebrating the first wet-lab experiment in my group. Successfully carried out by Sophie, my first MRes student and research assistant in Liverpool @liverpooluni.bsky.social, and me. Thanks to colleagues in the APT group of ISMIB @livuni-ismib.bsky.social for sharing their experience. #nanopore
October 24, 2025 at 6:05 PM
Celebrating the first wet-lab experiment in my group. Successfully carried out by Sophie, my first MRes student and research assistant in Liverpool @liverpooluni.bsky.social, and me. Thanks to colleagues in the APT group of ISMIB @livuni-ismib.bsky.social for sharing their experience. #nanopore
Reposted by Kat Holt
How certain is certain enough? This is probably the last public London talk I'll be giving on Proof in 2025 – and it's free – so see you there at 5.30pm on 24th November if you're around!
www.lshtm.ac.uk/newsevents/e...
www.lshtm.ac.uk/newsevents/e...
How certain is certain enough? | LSHTM
When faced with a new health threat, there are three crucial questions we must consider. What is going on? What can we do about it? And how can we communicate these things effectively? This talk will
www.lshtm.ac.uk
October 24, 2025 at 6:28 PM
How certain is certain enough? This is probably the last public London talk I'll be giving on Proof in 2025 – and it's free – so see you there at 5.30pm on 24th November if you're around!
www.lshtm.ac.uk/newsevents/e...
www.lshtm.ac.uk/newsevents/e...
Reposted by Kat Holt
Agata Pacho and I published an article on self care and UTIs/AMR this week! In Sociology of Health and Illness:
onlinelibrary.wiley.com/doi/10.1111/.... @lshtmamrcentre.bsky.social
onlinelibrary.wiley.com/doi/10.1111/.... @lshtmamrcentre.bsky.social
onlinelibrary.wiley.com
October 24, 2025 at 2:19 PM
Agata Pacho and I published an article on self care and UTIs/AMR this week! In Sociology of Health and Illness:
onlinelibrary.wiley.com/doi/10.1111/.... @lshtmamrcentre.bsky.social
onlinelibrary.wiley.com/doi/10.1111/.... @lshtmamrcentre.bsky.social
Reposted by Kat Holt
Intrinsic resistance pathways & #ResistanceBreaking. Study shows that inhibiting efflux pumps & cell envelope biogenesis sensitizes #bacteria to #antibiotics, but rapid evolutionary recovery may limit long-term effectiveness of resistance-breaking strategies #AMR @plosbiology.org 🧪 plos.io/4huAtvo
October 23, 2025 at 4:27 PM
Intrinsic resistance pathways & #ResistanceBreaking. Study shows that inhibiting efflux pumps & cell envelope biogenesis sensitizes #bacteria to #antibiotics, but rapid evolutionary recovery may limit long-term effectiveness of resistance-breaking strategies #AMR @plosbiology.org 🧪 plos.io/4huAtvo
Reposted by Kat Holt
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Kat Holt
Always take sentences using “the Cloud” or “the Internet” and try replacing those phrases with “A shed in Virginia” to see how they hold up. “Our service is fully based in a shed in Virginia”; “All my files are in a shed in Virginia”; “A shed in Virginia was designed to survive a nuclear war”, etc.
October 20, 2025 at 5:39 PM
Always take sentences using “the Cloud” or “the Internet” and try replacing those phrases with “A shed in Virginia” to see how they hold up. “Our service is fully based in a shed in Virginia”; “All my files are in a shed in Virginia”; “A shed in Virginia was designed to survive a nuclear war”, etc.
Reposted by Kat Holt
#WHO report shows rising #antibiotic resistance in common bacteria
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
October 20, 2025 at 9:53 AM
#WHO report shows rising #antibiotic resistance in common bacteria
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
@katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics.
www.lshtm.ac.uk/newsevents/n...
Reposted by Kat Holt
🌍🧼 Today on #CleanHospitalDay we shine a spotlight on what’s often unseen: hospital cleanliness and the unsung heroes who keep it safe.
👉Surfaces matter.
💁♂️Cleaners matter.
🤝Patient safety matters.
Let’s make the invisible visible👍
Read more 👉 bit.ly/3L3ILhn
👉Surfaces matter.
💁♂️Cleaners matter.
🤝Patient safety matters.
Let’s make the invisible visible👍
Read more 👉 bit.ly/3L3ILhn
October 20, 2025 at 8:20 AM
🌍🧼 Today on #CleanHospitalDay we shine a spotlight on what’s often unseen: hospital cleanliness and the unsung heroes who keep it safe.
👉Surfaces matter.
💁♂️Cleaners matter.
🤝Patient safety matters.
Let’s make the invisible visible👍
Read more 👉 bit.ly/3L3ILhn
👉Surfaces matter.
💁♂️Cleaners matter.
🤝Patient safety matters.
Let’s make the invisible visible👍
Read more 👉 bit.ly/3L3ILhn
Reposted by Kat Holt
Interesting that there has been absolutely no communication with submitters/users of the system, and no statements from the scientific governance or compliance boards on what would seem to be a fairly significant change to GISAID data access policy and platform operations. gisaid.org/about-us/gov...
October 17, 2025 at 7:07 PM
Interesting that there has been absolutely no communication with submitters/users of the system, and no statements from the scientific governance or compliance boards on what would seem to be a fairly significant change to GISAID data access policy and platform operations. gisaid.org/about-us/gov...
Reposted by Kat Holt
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...