Kat Holt

#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...

It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

They stole the internet’s knowledge and all the work that went into it and they want to sell it back to us for a fee. What a business model.

Thrilled to announce that the Department of Microbiology at the University of Washington, School of Medicine is hiring at the Assistant Professor level (tenure-track)! The Pacific Northwest is an awesome place to live and do science 🧪🦠. Join us! apply.interfolio.com/185622 Applications due 8/1.

Just a shout-out to the folks over at @pathoplexus.org and, importantly, all the scientists sharing genomic data with such amazing speed. It's great to see the field having moved to a new platform, with non-transparent platforms being a thing of the past. Fantastic.

⏰ Registration closing soon! Join us in Manchester for a 1-day meeting on Therapeutics & Antimicrobial Resistance (AMR). Talks, panels, ECR sessions, speed networking & a WAAW sandpit. Don’t miss out 👉 https://microb.io/TherAMR26

New preprint! The first first-author work of my postdoc at the Baker! So, babies' airways are colonised from birth, and our group has shown that early colonisers shape respiratory health. 1/7 www.biorxiv.org/content/10.6...

A new study led by Harry Veillard, MSc student @lshtm.bsky.social, found that nurse and pharmacist prescribing could improve access to care, reduce treatment delays, and ease pressure on primary care. The study also highlights the need for training and support. Read more 👉 bit.ly/4tERrvi

Having just finished my MCSA Fellowship with him, I would really encourage those looking to do a postdoc in microbial adaptation to check out Alex Couces lab in Madrid. Alex is a gifted researcher, and Madrid is a wonderful city to live in :) Details in link below: evoldir.net/brian/evoldi...

Being a PI is an intricate juggling act that requires tough decisions – intellectual, financial, strategic. Yet we are expected to navigate these dangerous waters with very little support. The solo PI model is deeply problematic. My latest blog post #AcademicSky occamstypewriter.org/mindthegap/2...

Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics

🚨🧪 Our UK Public Health Rapid Support Team has deployed a fully functioning mobile laboratory to one of the world’s most remote locations to support the hantavirus outbreak response. Read our blog post for the full story 🔗 https://bit.ly/4wxnlwo

Yes! Now do it for other pre-print servers, grant applications, social media posts and wedding speeches.

Finally, some good news for once. ArXiV will no longer tolerate hallucinated content in submitted works, with real, enforceable consequences.

@katholt.bsky.social gives the keynote @target-amr.bsky.social speech on interpretive standards for AMR genotypes #TARGetAMR26

Wake up! The House of Commons Education Committee says fifty - yes fifty - Higher Education Institutions are at risk of insolvency within the next three years. Wake up! committees.parliament.uk/work/9012/hi...

Since launching support for the Andes virus species of hantavirus two days ago, we have already received submissions from four countries' sequencing teams. This is a testament to the rapid response of researchers, sharing real-time data. Read more in our news post: pathoplexus.org/news/2026-05...

How much do you want to bet that the second Meta agrees to pay Elsevier, all the complaints about integrity and intellectual property will vanish? Bet number 2: of all the money Meta will pay Elsevier, exactly 0% will go to the authors of the papers.

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

If your brain is struggling due to anxiety,sadness,the way others have behaved,ADHD, autism,burnout,chronic illness &/or because the world’s too full of grimness then hi,me too. Research shows my photo’ll provide relief for your thoughts-pause & zoom into the details-& keep going, you’re not alone 🌿

I've spent yesterday and today talking to researchers across the globe trying to understand the hantavirus outbreak aboard the cruise ship MV Hondius. My story in @science.org is here (and some threaded thoughts coming): www.science.org/content/arti... 🧪 #IDsky

You can make a long, LONG list of technologies that were supposed to make stupid brick and mortar institutions of higher education obsolete. Printed books. Radio. Television. Personal computers. CD-ROMs. The Internet. MOOCs. Write the story once, and you can re-use it every five years!

😱 Take-home message: hospital sinks are perfectly safe if you don’t run the taps! #IDSky

An interesting essay by educationalist Will Ellis - raising serious concerns about AI, with studies showing that cognitive engagement shrinks in direct proportion to the degree of AI assistance - with adolescent brains particularly vulnerable: reclaimchildhoodmedia.substack.com/p/the-cost-o...

For no particular reason this week… If you want to know how close we came to having the human genome sequence behind a paywall, & the very concept of using gene sequences to benefit health (e.g. as diagnostic or drug targets) locked up behind patents, read this: www.worldofbooks.com/en-gb/produc...

Nice summary of MTB surveillance in the United States and detection/response to large outbreaks. The US sees almost 10k domestic cases each year, and a number of large outbreaks or clusters. AMD Platform is the bioinformatic engine that drives this genomic surveillance. www.cdc.gov/mmwr/volumes...

Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...

Join us! @wellcometrust.bsky.social postdoc position using experimental evolution to understand real-world resistance dynamics. See preprint for the 🤯 strain collection we will be working with www.biorxiv.org/content/10.6... Closing 15 May. Apply: www.jobs.manchester.ac.uk/Job/JobDetai... #mevosky

Howdy! Happy to announce that Bactopia v4 is finally out! 🥳 This release supports the latest from @seqera.io Nextflow v26 (strict syntax, static types, and records! oh my!) It also open's the doors to start doing some fun things with Bactopia. To learn more, check out: bactopia.io/blog/bactopi...

🎉 New in @plosbiology.org: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵 journals.plos.org/plosbiology/...

When life imitates art

Excited to finally share our new preprint on bioRxiv describing Verticall (github.com/rrwick/Verti...), a robust & efficient tool for building recombination-free bacterial phylogenies. Huge thanks to @rrwick.bsky.social & @katholt.bsky.social for this incredible work! www.biorxiv.org/content/10.6...

📢Extended deadline, now 27 April 2026. Got thoughts on artificial intelligence (AI) in microbiology—good, bad or undecided? We want to hear from you! Take part in the survey; you can find the link in the bio. #AI #artificialintelligence

I wrote a friendly rant about the use of causal language in AI. www.linkedin.com/posts/ewan-b...

A must-read for anyone interested in #Klebsiella or metal acquisition!

How’s your Friday going? We’re wrapping up the week by welcoming new leadership at our AMR Centre😍 Excited for what’s ahead in the fight against antimicrobial resistance 👇 www.lshtm.ac.uk/research/cen... @rebeccaglover.bsky.social, @ayodejimatuluko.bsky.social, @lshtm.bsky.social

New rapid, colorimetric #carbapenemase diagnostic method that's cheap and smart. 1) Take potential CPE and incubate with imipenem disk 2) Take disk and incubate with known carb sensitive isolate 3) Add resazurin as a live/dead indicator #AMR #IDSky journals.asm.org/doi/10.1128/...

@reecedinsdale.bsky.social Good morning Reece. Here is a timely reminder for all -

@yekwah.bsky.social launches FlexIt: the S. flexneri genotyping scheme at @shigellameeting.bsky.social 🎉

My super department @warwicklifesci.bsky.social is hiring 6 assistant profs in the wake of recent retirements. We're looking for people in microbiology/infection, cellular disease / immunity; environmental biology; and plant/crop science. #MicroSky warwick-careers.tal.net/vx/lang-en-G...

We are recruiting a PI in biomedical data science at @bakerresearchau.bsky.social in Melbourne! A fantastic opportunity and do get in touch if any q's! www.seek.com.au/job/91619982...