Kat Holt

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).

Good for PSF - they value a diverse and welcoming community, and they won’t be bullied into doing otherwise.

ComBac-Africa | Fighting AMR in Sub-Saharan Africa Advancing diagnostics and antimicrobial stewardship in Africa to combat drug-resistant bacteria and improve treatment access.

🌍 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

Advertising about the Microbiology Society's 80th Anniversary, inviting delegates to submit their microbiology papers to be published in our portfolio

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...

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

"...the only long-term solution is for governments to invest in safe drinking water and sanitation."

www.theguardian.com/global-devel...

Photo in my lab

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

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

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...

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

Genome-wide screen to identify Escherichia coli gene knockouts hypersensitive to trimethoprim and chloramphenicol. Top left: Schematic showing the screening strategy for identifying hypersensitive gene knockouts from the Keio mutant library. All mutants were cultured in LB and LB supplemented with trimethoprim (TMP) and chloramphenicol (CMP) at their respective IC50s. Top right: Distribution of drug-susceptibilities of Keio mutants grown in indicated growth media obtained after normalizing the growth of each mutant to wild type (set to 1). Mean ± S.D. derived after fitting each distribution to a Gaussian function are shown. Bottom left: Analysis of gene functional categories for hypersensitive mutants compared with the frequency of genes in each category encoded by E. coli K-12 MG1655. Percentage of the total in each case is provided above each bar. Bottom right: Comparison of hypersensitive mutants identified in the trimethoprim and chloramphenicol screens shown as a Venn diagram. Representative genes from each set are named and gene names are colored by functional categories.

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

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

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-...

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.

#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...

🌍🧼 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

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...

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.

New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...

An email appointing Kyle Walsh is director of the National Institute of Environmental Health Sciences

VERY TROUBLING NEWS REGARDING NIH INSTITUTE DIRECTORS

A new appointment for NIEHS

1/3

🚨 Funded PhD alert 🚨

We are recruiting for a PhD student to join the @langridgelab.bsky.social in October 2026 - please share!

If you like bacteria, genomics and puzzles, this could be the project for you 🦠🧬🧩

Apply by 2 Dec 🗓️

#PhDposition

Find out more ⬇️

www.uea.ac.uk/course/phd-d...

Reclaiming microbiology: scientists as community members and advocacy leaders Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefi...

To celebrate and support the great @blackinmicro.bsky.social initiative and what joining could mean for you, please take a look through the commentary in Microbial Genomics @microbiologysociety.org hot off the press today! #MicroSky #MicrobiomeSky 💻🧬🧪🦠 www.microbiologyresearch.org/content/jour...

After a short website glitch, the applications are now open again - three #PhD opportunities; featuring (in no particular order) #Klebsiella, #protists, #biofilms, #microscopy, #bioinformatics, #mosquitoes, #midges and #microbiomes, see below!
#MicroSky #MicrobiomeSky #ProtistsOnSky #evobio 💻🧬🧪🦠🦟🔬

My internet was down most of today. I guess in the new world order of AI supremacy that means all university functions cease, so we can have a day off… like an old fashioned snow day! ❄️ ⛄️

Seems especially awkward when Russia is clearly toying with our energy and internet systems but hey ho…

I am being asked to tell my department which pieces of lab equipment should be supported with backup power because they expect rolling blackouts and brownouts in 2026 due to increased energy demands from AI. In case you're wondering how my day is going.

Enhanced virulence and stress tolerance are signatures of epidemiologically successful Shigella sonnei
@sydneylmiles.bsky.social @katholt.bsky.social
🙏to transformative collaborative effort

www.nature.com/articles/s41...

The Art of Data Visualization with ggplot2 The TidyTuesday Cookbook

The Art of Data Visualization with ggplot2: A free online book by @nrennie.bsky.social that guides us through the entire process of creating plots, including why certain decisions were made, using real datasets that have been part of #TidyTuesday. Very excited to get stuck into this one. #rstats

Reminds me of how in Australia, it’s not uncommon for universities to badge internal groups as ‘the Australian centre for XYZ’ when there is nothing national or even multi-institutional about it.

convergence on ‘global’ comes from European platforms assuming those in other regions want to jump on board and upload their data.

Key Qs:
- Who owns data & analysis
- How does it fit with benefit sharing agreements being hashed out?
Some new ideas on this at PHA4GE/IPSN conference later this month

The world feels heavy with so much uncertainty. But standing here, working alongside incredible scientists & institutions like the WHO, I feel grateful, hopeful. Even in difficult times, people are working tirelessly to ensure children everywhere, including in 🇧🇩, have access to life-saving vaccines.

you can read about all the actions here: www.trumpactiontracker.info?
it's chilling and it's getting worse, but we won't stop chronicling what's happening.. looking away is not an option

Piss poor.

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠

Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:

www.biorxiv.org/content/10.1...

#microsky #microbiome

Oh come on. This is so weak. You made a mistake by admitting Musk as a Fellow in the first place. High time to reverse that mistake. Strip him of his Fellowship. He's dragging your reputation through the mud. The longer you dilly-dally, the worse it gets.

Stoopid, just stupid. He should have never been made a fellow, but now Melon needs to be booted out with force. With prejudice.

Cowardly behaviour from the society. Don't expect any support or understanding for this. You blundered and are refusing to make it right, just because you're scared.