Kate Baker

Finally out!! It was a long time in the making, I hope you enjoy it!! #salmonella #iNTS #AMR

Really looking forward to the First #Shigella International Meeting to be held in Paris, France, April 2026! The meeting website is almost ready. Please follow @shigellameeting.bsky.social for more information and updates! #Microsky 🦠 🧫 🔬

Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...

A selfie of three people, all smiling, having lunch in front of a red-brick building

Had a great lunch today at @unibirmingham.bsky.social's Winterbourne Gardens with Rivie and Kev, the brilliant @target-amr.bsky.social admin team.

I am also terrible at making selfies.

Good luck with the grant Conor and regardless of how it goes down you get the award for best namer of cats 🐱

No brainstorming without resource*

and now formally tagging @fxweill.bsky.social‬ who recently joined bluesky! Welcome FX!

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

ASM National Meeting 2026 — Australian Society for Microbiology The annual meeting is the premier conference on microbiology, bringing together a diverse group of scientists, clinical researchers and other professionals to discuss the latest advances in microbiolo...

Am super excited about this ... www.theasm.org.au/asm-conferen...

Great work from PDU PDRAs this week supporting this summer school!

This was great team science and many thanks are also due to @danielleingle.bsky.social @ellarodwell.bsky.social @charlotteechong.bsky.social @malakades.bsky.social, @jayhinton.bsky.social and @neilhall.bsky.social of Salmonella10k, @mariechattaway.bsky.social Ben Howden, Deb Williamson and more!

Massive thanks to the phenomenal co-first authors @1caiseypulford and @blancaps.bsky.social‬ and especially to one of my favourite scientists to work with, co-corresponding author and fellow history fanatic @weill_xavier 10/n

So, welcome to your new genomic understanding of S. Panama and please go ahead and check out the data yourselves on the associated ‪@microreact.bsky.social‬ page! microreact.org/project/span... 9/n

As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social‬ for the ML classifier to do so) 8/n

Temporal analysis revealed that the four major clades all emerged in the late 1800s, coincident with European efforts to build the Panama canal (‘Panama Fever’ by ‪@matthewparker70.bsky.social‬ is recommended reading for those with an interest in the history here) 7/n

We also found multidrug resistance cassettes; fluoroquinolone resistance (bumping S. Panama onto the WHO AMR priority pathogens list); and a single extensively drug-resistant isolate 6/n

Although antimicrobial resistance (AMR) levels were low overall (14% of isolates), resistant isolates were predominately found in Clade 2 (European-associated) and Clade 4 (associated with Oceania and Asia) 5/n

Population structure analyses revealed the presence of four major Clades that had significant geographic associations 4/n

To better characterise S. Panama we sequenced a global collection of isolates (n=731) from public health surveillance datasets from @ukhsa.bsky.social‬ @thedohertyinst.bsky.social‬, historical collections from ‪@pasteur.fr‬ and publicly available data (n=105) from 1931 to 2019 3/n

S. Panama causes major disease concerns, including high rates of iNTS in French Guiana, large outbreaks in European pork, AMR in Asia, and outbreaks in American soldiers from where the first (extant) isolate from 1931 came from (More in our 2019 review: 10.1128/IAI.00273-19) 2/n

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

New research article

Global diversity and evolution of #Salmonella enterica serovar #Panama: a genomic epidemiology study

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #MicroSky #AMR #OpenAccess #OA

Very pleased to say we have an Assistant Professor job opening (tenure track) in the Department of Genetics at Trinity College Dublin! 😀
www.jobs.ac.uk/job/DOA399/a... - deadline is August 19th! Please repost!

Two PhD studentships available in real-time infectious disease modelling, jointly with LSHTM, Imperial and UKHSA. January 2026 start + 3.5 years of funding: www.lshtm.ac.uk/study/fees-a...

Aw, heartwarming stuff and lots of familiar faces - good luck with the Professorship, and see some of you next week! ✈️ 🍁 🦠

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

Not to be smug, but I inadvertently stopped doing this a couple of years ago - it wasn’t a DORA thing I just assumed we were aiming to best help people find the relevant reference and that PMIDs were more useful for this 🤷‍♀️

Faraday Discovery Fellowships Accelerated International Route | Royal Society The Faraday Discovery Fellowships Accelerated International Route provides a fast-track option for attracting mid-career researchers looking to relocate to the UK from overseas, providing up to £4m ov...

Our new Faraday Discovery Fellowships Accelerated International Route provides a fast-track option for international mid-career researchers looking to relocate to the UK, providing up to £4m over a five-year period. Find out more: #RSGrants royalsociety.org/grants/farad...

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs

⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco...
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!