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
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
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
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.
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.
#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...
![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)
November 19, 2025 at 3:43 PM
#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...
Huge thanks to the 82 (!) coauthors involved in this study, including study teams for BARNARDS, MBIRA, NeoBAC, Baby GERMS-SA, NeoOBS India, NIMBI, GBS-COP and the teams at MLW, CHRF and Aga Khan University Laboratory Network.
Most are not on bluesky (yet!)…
Most are not on bluesky (yet!)…
July 1, 2025 at 9:56 AM
Huge thanks to the 82 (!) coauthors involved in this study, including study teams for BARNARDS, MBIRA, NeoBAC, Baby GERMS-SA, NeoOBS India, NIMBI, GBS-COP and the teams at MLW, CHRF and Aga Khan University Laboratory Network.
Most are not on bluesky (yet!)…
Most are not on bluesky (yet!)…
All the data in the paper is available to explore interactively in an online app, developed by the wonderful @tomstantonmicro.bsky.social klebsiella.shinyapps.io/neonatal/
July 1, 2025 at 9:54 AM
All the data in the paper is available to explore interactively in an online app, developed by the wonderful @tomstantonmicro.bsky.social klebsiella.shinyapps.io/neonatal/
We did also look at O type distribution… there are far fewer types, and the top 5 account for 86% of neonatal sepsis, but it’s unclear how well O-based vaccines can protect against infection.
July 1, 2025 at 9:53 AM
We did also look at O type distribution… there are far fewer types, and the top 5 account for 86% of neonatal sepsis, but it’s unclear how well O-based vaccines can protect against infection.
A lot of sepsis cases are caused by bacterial outbreaks in neonatal units, which can hugely skew the estimated antigen prevalence. So we adjust for localised clustering at each site, to reduce this bias in our prevalence estimates. Turns out this makes a big difference to estimates for some K types.
July 1, 2025 at 9:50 AM
A lot of sepsis cases are caused by bacterial outbreaks in neonatal units, which can hugely skew the estimated antigen prevalence. So we adjust for localised clustering at each site, to reduce this bias in our prevalence estimates. Turns out this makes a big difference to estimates for some K types.
By choosing the top K types in each region, we get a set of 20 antigens that could in principle cover 70% of cases in all our target regions (South Asia and Eastern, Southern, and Western Africa).
Yes this is a lot of antigens! But it has been done for Streptococcus pneumoniae.
Yes this is a lot of antigens! But it has been done for Streptococcus pneumoniae.
July 1, 2025 at 9:50 AM
By choosing the top K types in each region, we get a set of 20 antigens that could in principle cover 70% of cases in all our target regions (South Asia and Eastern, Southern, and Western Africa).
Yes this is a lot of antigens! But it has been done for Streptococcus pneumoniae.
Yes this is a lot of antigens! But it has been done for Streptococcus pneumoniae.
Long story short, we estimate the top 5 K types alone would cover almost 50% of neonatal sepsis cases, but K types vary regionally and so coverage would vary regionally too.
July 1, 2025 at 9:49 AM
Long story short, we estimate the top 5 K types alone would cover almost 50% of neonatal sepsis cases, but K types vary regionally and so coverage would vary regionally too.
We brought together teams from 13 neonatal sepsis surveillance studies, conducted across 35 sites in South Asia and Africa, to pool data and estimate prevalence of capsule and O types amongst #Klebsiella pneumoniae causing sepsis in newborns, using Bayesian modelling.
July 1, 2025 at 9:47 AM
We brought together teams from 13 neonatal sepsis surveillance studies, conducted across 35 sites in South Asia and Africa, to pool data and estimate prevalence of capsule and O types amongst #Klebsiella pneumoniae causing sepsis in newborns, using Bayesian modelling.
The ESGEM-AMR subgroups have been busy encoding AMRrules for lots of pathogens - the beta release has core gene rules for all the ESKAPEE pathogens, plus Salmonella & Yersinia.
May 22, 2025 at 9:38 AM
The ESGEM-AMR subgroups have been busy encoding AMRrules for lots of pathogens - the beta release has core gene rules for all the ESKAPEE pathogens, plus Salmonella & Yersinia.
AMRrules tells us how to interpret these, and our Python package can apply the rules to annotate your AMRfinderplus output with these interpretations.
May 22, 2025 at 9:37 AM
AMRrules tells us how to interpret these, and our Python package can apply the rules to annotate your AMRfinderplus output with these interpretations.
The AMRrules beta release focuses on core genes. These are reported by AMRfinderplus and other tools, but don’t all confer clinical resistance.
May 22, 2025 at 9:37 AM
The AMRrules beta release focuses on core genes. These are reported by AMRfinderplus and other tools, but don’t all confer clinical resistance.
AMRrules encode organism-specific rules for interpreting AMR genotype calls: if I find this gene/mutation in this organism, what does it mean for clinical resistance?
May 22, 2025 at 9:36 AM
AMRrules encode organism-specific rules for interpreting AMR genotype calls: if I find this gene/mutation in this organism, what does it mean for clinical resistance?
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 9:35 AM
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
Super talk from @efosternyarko.bsky.social @lshtmamrcentre.bsky.social on nanopore based sequencing of cholera across Africa, with PulseNet Africa partners
#ABPHM25
www.biorxiv.org/content/10.1...
#ABPHM25
www.biorxiv.org/content/10.1...
May 21, 2025 at 2:03 PM
Super talk from @efosternyarko.bsky.social @lshtmamrcentre.bsky.social on nanopore based sequencing of cholera across Africa, with PulseNet Africa partners
#ABPHM25
www.biorxiv.org/content/10.1...
#ABPHM25
www.biorxiv.org/content/10.1...
First rose to bloom in our garden this spring, inspired the 4yo to draw this at nursery 🥰
May 17, 2025 at 7:14 PM
First rose to bloom in our garden this spring, inspired the 4yo to draw this at nursery 🥰
In case you’re not Australian, and therefore have no idea wtf a Bin Chicken is 😂
November 26, 2024 at 9:26 PM
In case you’re not Australian, and therefore have no idea wtf a Bin Chicken is 😂
Kleborate v3 is also out now, it calls Kaptive v3 for rapid serotype prediction, plus speciation, MLST, AMR and virulence genotyping. (V3 is also now available via Pathogenwatch and Bactopia) - so get Kleborating! #KLEBS24
November 20, 2024 at 6:12 PM
Kleborate v3 is also out now, it calls Kaptive v3 for rapid serotype prediction, plus speciation, MLST, AMR and virulence genotyping. (V3 is also now available via Pathogenwatch and Bactopia) - so get Kleborating! #KLEBS24
Kaptive v3 is out! It’s much faster than the old version, with improved typeability of K and O loci from low quality draft genomes. Go see Tom’s poster at #KLEBS24!
November 20, 2024 at 5:06 PM
Kaptive v3 is out! It’s much faster than the old version, with improved typeability of K and O loci from low quality draft genomes. Go see Tom’s poster at #KLEBS24!
In 2016, Anna Sheppard and Amy Mathers published this iconic paper on KPC plasmids in a Virginia hospital: “Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC”
pubmed.ncbi.nlm.nih.gov/27067320/
pubmed.ncbi.nlm.nih.gov/27067320/
November 20, 2024 at 1:05 PM
In 2016, Anna Sheppard and Amy Mathers published this iconic paper on KPC plasmids in a Virginia hospital: “Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC”
pubmed.ncbi.nlm.nih.gov/27067320/
pubmed.ncbi.nlm.nih.gov/27067320/
In 2015, we published this paper looking at genomic diversity across 300 global Kpn strains from human and animal sources
pubmed.ncbi.nlm.nih.gov/26100894/
pubmed.ncbi.nlm.nih.gov/26100894/
November 20, 2024 at 1:05 PM
In 2015, we published this paper looking at genomic diversity across 300 global Kpn strains from human and animal sources
pubmed.ncbi.nlm.nih.gov/26100894/
pubmed.ncbi.nlm.nih.gov/26100894/