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
![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
Our study of neonatal sepsis in a NICU in Botswana underscores the value of integrating colonization surveillance, environmental investigation, and genomics to uncover hidden reservoirs and strengthen infection prevention and control (IPC) practices in resource-limited settings.
In a study in Botswana, @ahmedmicrobes.bsky.social and co tracked an outbreak of Kpn ST1414 in the neonatal unit to contaminated IV fluid bags 🧬🕵️https://www.medrxiv.org/content/10.1101/2025.11.06.25339637v1
Using Genomic and Traditional Epidemiologic Approaches to Define Complex Transmission Pathways of Klebsiella pneumoniae Infection in a Neonatal Unit in Botswana, 2022–2023
Background Klebsiella pneumoniae ( Kpn ) is a major cause of infant mortality worldwide, with most transmission occurring among hospitalized neonates in low-and middle-income countries where infection...
www.medrxiv.org
November 25, 2025 at 7:36 PM
Our study of neonatal sepsis in a NICU in Botswana underscores the value of integrating colonization surveillance, environmental investigation, and genomics to uncover hidden reservoirs and strengthen infection prevention and control (IPC) practices in resource-limited settings.
Reposted by Kat Holt
We have an amazing opportunity for Early-Career Researchers to join our Board of Directors!
We're looking for someone with experience in leading #OpenScience projects to support and lead eLife in our mission to change research communication.
🔗 buff.ly/SZgtgVv
We're looking for someone with experience in leading #OpenScience projects to support and lead eLife in our mission to change research communication.
🔗 buff.ly/SZgtgVv
November 24, 2025 at 9:02 PM
We have an amazing opportunity for Early-Career Researchers to join our Board of Directors!
We're looking for someone with experience in leading #OpenScience projects to support and lead eLife in our mission to change research communication.
🔗 buff.ly/SZgtgVv
We're looking for someone with experience in leading #OpenScience projects to support and lead eLife in our mission to change research communication.
🔗 buff.ly/SZgtgVv
Reposted by Kat Holt
If you're about to push these last manuscripts before wrapping up 2025, remider that our MGen Eukaryotic collection @microbiologysociety.org is open & growing; #Protists #Parasites #Fungi; friend or foe; all welcome 😊
#MicroSky #IDSky #Protistsonsky 🧬💻
www.microbiologyresearch.org/content/micr...
#MicroSky #IDSky #Protistsonsky 🧬💻
www.microbiologyresearch.org/content/micr...
Microbial Genomics of Eukaryotes | Microbiology Society
With technological advances like single-cell sequencing and long-read sequence techniques continually improving, allowing the full resolution of increasingly complex highly repetitive genomes, and wit...
www.microbiologyresearch.org
November 24, 2025 at 6:54 AM
If you're about to push these last manuscripts before wrapping up 2025, remider that our MGen Eukaryotic collection @microbiologysociety.org is open & growing; #Protists #Parasites #Fungi; friend or foe; all welcome 😊
#MicroSky #IDSky #Protistsonsky 🧬💻
www.microbiologyresearch.org/content/micr...
#MicroSky #IDSky #Protistsonsky 🧬💻
www.microbiologyresearch.org/content/micr...
Reposted by Kat Holt
Join us on 26 Nov 2025 for the NeoNET AFRICA & KlebNET-GSP seminar on Klebsiella genomics and neonatal sepsis.
Our Co-Director @katholt.bsky.social will speak on serotype prevalence & vaccine coverage
⏰ 15:00–16:00 SAST
🔗 bit.ly/klebs_seminar
Our Co-Director @katholt.bsky.social will speak on serotype prevalence & vaccine coverage
⏰ 15:00–16:00 SAST
🔗 bit.ly/klebs_seminar
November 21, 2025 at 2:03 PM
Join us on 26 Nov 2025 for the NeoNET AFRICA & KlebNET-GSP seminar on Klebsiella genomics and neonatal sepsis.
Our Co-Director @katholt.bsky.social will speak on serotype prevalence & vaccine coverage
⏰ 15:00–16:00 SAST
🔗 bit.ly/klebs_seminar
Our Co-Director @katholt.bsky.social will speak on serotype prevalence & vaccine coverage
⏰ 15:00–16:00 SAST
🔗 bit.ly/klebs_seminar
Reposted by Kat Holt
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Kat Holt
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
November 20, 2025 at 5:32 PM
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
Reposted by Kat Holt
💉 Our annual lecture will be given by Prof Caroline Trotter, who will explore work estimating the #PublicHealth impact of vaccination of Gavi & discuss its implications for #vaccine policy
🗓️ Thursday 27 November, 17:30 GMT
📍 LSHTM | Online
Details ⬇️
www.lshtm.ac.uk/newsevents/e...
🗓️ Thursday 27 November, 17:30 GMT
📍 LSHTM | Online
Details ⬇️
www.lshtm.ac.uk/newsevents/e...
November 4, 2025 at 12:14 PM
💉 Our annual lecture will be given by Prof Caroline Trotter, who will explore work estimating the #PublicHealth impact of vaccination of Gavi & discuss its implications for #vaccine policy
🗓️ Thursday 27 November, 17:30 GMT
📍 LSHTM | Online
Details ⬇️
www.lshtm.ac.uk/newsevents/e...
🗓️ Thursday 27 November, 17:30 GMT
📍 LSHTM | Online
Details ⬇️
www.lshtm.ac.uk/newsevents/e...
Reposted by Kat Holt
Our sister journal has joined the Bluesky party!
Give them a follow if you are interested in clinical research and the open science space
Give them a follow if you are interested in clinical research and the open science space
We are thrilled to now be on BlueSky!
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
November 20, 2025 at 3:09 PM
Our sister journal has joined the Bluesky party!
Give them a follow if you are interested in clinical research and the open science space
Give them a follow if you are interested in clinical research and the open science space
Reposted by Kat Holt
We are thrilled to now be on BlueSky!
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
November 20, 2025 at 2:31 PM
We are thrilled to now be on BlueSky!
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
We prioritize studies addressing critical health challenges—from major diseases to health equity—that bridge scientific rigor with real-world impact, connecting researchers, clinicians, and policymakers to advance global health 🧬🧪
#OpenScience #MedSky
Reposted by Kat Holt
Don't forget to register for the #1st ever @shigellameeting.bsky.social at Pasteur next year! Apr 20 - 24 www.shigella2026.conferences-pasteur.org/home
Home - EMBO Workshop Shigella: from biology to prevention
EMBO Workshop Shigella: from biology to prevention
www.shigella2026.conferences-pasteur.org
November 20, 2025 at 3:37 PM
Don't forget to register for the #1st ever @shigellameeting.bsky.social at Pasteur next year! Apr 20 - 24 www.shigella2026.conferences-pasteur.org/home
Reposted by Kat Holt
KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family
https://doi.org/10.1093/nar/gkaf1122
https://doi.org/10.1093/nar/gkaf1122
November 20, 2025 at 4:30 PM
KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family
https://doi.org/10.1093/nar/gkaf1122
https://doi.org/10.1093/nar/gkaf1122
Reposted by Kat Holt
Another PhD!!
Are you, or someone you know, looking for a PhD, starting in Oct 2026?
Do you like phages, genomes & public health impact?🦠🧬🧩
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
Please apply or share by 6 Jan🗓️
#PhDposition #academicsky
Are you, or someone you know, looking for a PhD, starting in Oct 2026?
Do you like phages, genomes & public health impact?🦠🧬🧩
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
Please apply or share by 6 Jan🗓️
#PhDposition #academicsky
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
www.uea.ac.uk
November 20, 2025 at 3:47 PM
Another PhD!!
Are you, or someone you know, looking for a PhD, starting in Oct 2026?
Do you like phages, genomes & public health impact?🦠🧬🧩
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
Please apply or share by 6 Jan🗓️
#PhDposition #academicsky
Are you, or someone you know, looking for a PhD, starting in Oct 2026?
Do you like phages, genomes & public health impact?🦠🧬🧩
Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?
Please apply or share by 6 Jan🗓️
#PhDposition #academicsky
I don’t think we have enough evidence that presence of iuc, without iro+rmp, leads to an increase in severity and I would not call it hypervirulent. This is an area we urgently need to address with clin data.
Instead I agree with your earlier paper on this topic! www.thelancet.com/journals/lan...
Instead I agree with your earlier paper on this topic! www.thelancet.com/journals/lan...
November 20, 2025 at 5:58 PM
I don’t think we have enough evidence that presence of iuc, without iro+rmp, leads to an increase in severity and I would not call it hypervirulent. This is an area we urgently need to address with clin data.
Instead I agree with your earlier paper on this topic! www.thelancet.com/journals/lan...
Instead I agree with your earlier paper on this topic! www.thelancet.com/journals/lan...
To hear more, join us online next week (November 26) for a webinar on 🧬 Klebsiella pneumoniae Genomics to Support Neonatal Sepsis bit.ly/klebs_seminar
November 19, 2025 at 3:59 PM
To hear more, join us online next week (November 26) for a webinar on 🧬 Klebsiella pneumoniae Genomics to Support Neonatal Sepsis bit.ly/klebs_seminar
@neleshg.bsky.social and the Baby GERMS-South Africa team explored transmission clusters of ESKAPE pathogens across 6 South African hospitals, and identified large outbreaks of carbapenem-resistant #Klebsiella ST152 and Acinetobacter baumannii ST1 & ST2 www.medrxiv.org/content/10.1...
Enhanced detection of neonatal invasive infection clusters in South Africa using epidemiological and genomic surveillance data
Introduction Invasive bacterial infections, particularly those caused by the ESKAPE group, account for a substantial proportion of neonatal deaths in low- and middle-income countries, yet the contribu...
www.medrxiv.org
November 19, 2025 at 3:59 PM
@neleshg.bsky.social and the Baby GERMS-South Africa team explored transmission clusters of ESKAPE pathogens across 6 South African hospitals, and identified large outbreaks of carbapenem-resistant #Klebsiella ST152 and Acinetobacter baumannii ST1 & ST2 www.medrxiv.org/content/10.1...
In a neonatal unit Zambia, a massive outbreak of #Klebsiall ST307 affecting nearly 300 neonates was interrupted by an infection control intervention, only to be replaced later by unrelated strains of ST307 and other strains. www.medrxiv.org/content/10.1...
Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle
Background Klebsiella pneumoniae is a leading cause of neonatal sepsis in low-and middle-income countries, with antimicrobial resistance (AMR) significantly contributing to associated mortality. Infec...
www.medrxiv.org
November 19, 2025 at 3:55 PM
In a neonatal unit Zambia, a massive outbreak of #Klebsiall ST307 affecting nearly 300 neonates was interrupted by an infection control intervention, only to be replaced later by unrelated strains of ST307 and other strains. www.medrxiv.org/content/10.1...
In a study in Botswana, @ahmedmicrobes.bsky.social and co tracked an outbreak of Kpn ST1414 in the neonatal unit to contaminated IV fluid bags 🧬🕵️https://www.medrxiv.org/content/10.1101/2025.11.06.25339637v1
Using Genomic and Traditional Epidemiologic Approaches to Define Complex Transmission Pathways of Klebsiella pneumoniae Infection in a Neonatal Unit in Botswana, 2022–2023
Background Klebsiella pneumoniae ( Kpn ) is a major cause of infant mortality worldwide, with most transmission occurring among hospitalized neonates in low-and middle-income countries where infection...
www.medrxiv.org
November 19, 2025 at 3:55 PM
In a study in Botswana, @ahmedmicrobes.bsky.social and co tracked an outbreak of Kpn ST1414 in the neonatal unit to contaminated IV fluid bags 🧬🕵️https://www.medrxiv.org/content/10.1101/2025.11.06.25339637v1
One study from KWTRP in Kenya found 81% of neonatal sepsis cases in 2 large hospitals belonged to transmission clusters, with a case fatality rate of 32%.
Most strains carried ESBL genes, and the dominant clones were ST14 and ST17 www.medrxiv.org/content/10.1...
Most strains carried ESBL genes, and the dominant clones were ST14 and ST17 www.medrxiv.org/content/10.1...
Genomic epidemiology of Klebsiella pneumoniae neonatal and infant sepsis in Kenyan hospitals
Background Klebsiella pneumoniae ( Kpn ) is a leading cause of sepsis among hospitalised neonates and commonly causes outbreaks. Lack of surveillance data from low- and middle-income countries hampers...
www.medrxiv.org
November 19, 2025 at 3:54 PM
One study from KWTRP in Kenya found 81% of neonatal sepsis cases in 2 large hospitals belonged to transmission clusters, with a case fatality rate of 32%.
Most strains carried ESBL genes, and the dominant clones were ST14 and ST17 www.medrxiv.org/content/10.1...
Most strains carried ESBL genes, and the dominant clones were ST14 and ST17 www.medrxiv.org/content/10.1...
Excitingly, some of the collaborating studies have also posted preprints reporting detailed analyses of transmission in specific settings. 🧫🧬🕵️🏥
November 19, 2025 at 3:53 PM
Excitingly, some of the collaborating studies have also posted preprints reporting detailed analyses of transmission in specific settings. 🧫🧬🕵️🏥
The meta-analysis was led by @erkison.bsky.social, with 60 wonderful co-authors contributing data, ideas and interpretations, including @neleshg.bsky.social @[email protected] @ahmedmicrobes.bsky.social @evaheinz7.bsky.social @kelwyres.bsky.social and many others not on BlueSky
November 19, 2025 at 3:52 PM
The meta-analysis was led by @erkison.bsky.social, with 60 wonderful co-authors contributing data, ideas and interpretations, including @neleshg.bsky.social @[email protected] @ahmedmicrobes.bsky.social @evaheinz7.bsky.social @kelwyres.bsky.social and many others not on BlueSky
All the data and code from the paper is available at github.com/klebgenomics...
GitHub - klebgenomics/KlebNNS_transmission
Contribute to klebgenomics/KlebNNS_transmission development by creating an account on GitHub.
github.com
November 19, 2025 at 3:52 PM
All the data and code from the paper is available at github.com/klebgenomics...
In a logistic regression model, newly detected Kpn strains with ESBL or carbapenemase genes were more likely to be associated with onward transmission in the unit 🏥. #AMR
A few STs were also significantly associated with transmission (including ST14, ST17) but no K or O types.
A few STs were also significantly associated with transmission (including ST14, ST17) but no K or O types.
November 19, 2025 at 3:52 PM
In a logistic regression model, newly detected Kpn strains with ESBL or carbapenemase genes were more likely to be associated with onward transmission in the unit 🏥. #AMR
A few STs were also significantly associated with transmission (including ST14, ST17) but no K or O types.
A few STs were also significantly associated with transmission (including ST14, ST17) but no K or O types.
The fraction of cases attributed to transmission at each site ranged ~20-80%.
14 STs caused outbreak clusters in multiple sites, and accounted for 64% of all infections.
These include some of the usual suspects known to cause outbreaks in Europe, US etc including ST307, ST117, ST14, ST15, ST101.
14 STs caused outbreak clusters in multiple sites, and accounted for 64% of all infections.
These include some of the usual suspects known to cause outbreaks in Europe, US etc including ST307, ST117, ST14, ST15, ST101.
November 19, 2025 at 3:50 PM
The fraction of cases attributed to transmission at each site ranged ~20-80%.
14 STs caused outbreak clusters in multiple sites, and accounted for 64% of all infections.
These include some of the usual suspects known to cause outbreaks in Europe, US etc including ST307, ST117, ST14, ST15, ST101.
14 STs caused outbreak clusters in multiple sites, and accounted for 64% of all infections.
These include some of the usual suspects known to cause outbreaks in Europe, US etc including ST307, ST117, ST14, ST15, ST101.
This approach to clustering, sensitivity exploration, and data visualisation is implemented in a R Shiny app 💻 📊📈 developed by @erkison.bsky.social
klebsiella.shinyapps.io/transmission...
klebsiella.shinyapps.io/transmission...
klebsiella.shinyapps.io
November 19, 2025 at 3:49 PM
This approach to clustering, sensitivity exploration, and data visualisation is implemented in a R Shiny app 💻 📊📈 developed by @erkison.bsky.social
klebsiella.shinyapps.io/transmission...
klebsiella.shinyapps.io/transmission...
We identified clusters of cases isolated within 28 days from the same unit, with genetic distance ≤10 SNPs.
The choice of thresholds for 🧬 SNP distance and 📆 temporal distance had little impact on clustering.
The choice of thresholds for 🧬 SNP distance and 📆 temporal distance had little impact on clustering.
November 19, 2025 at 3:48 PM
We identified clusters of cases isolated within 28 days from the same unit, with genetic distance ≤10 SNPs.
The choice of thresholds for 🧬 SNP distance and 📆 temporal distance had little impact on clustering.
The choice of thresholds for 🧬 SNP distance and 📆 temporal distance had little impact on clustering.