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Phil Ashton

@flashton.bsky.social
735 followers 209 following 158 posts

Genomic epidemiologist at the Centre for Genomic Pathogen Surveillance at Oxford. How can microbial genomics improve health in high infectious disease settings?

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Phil Ashton @flashton.bsky.social · 13/03/2026
South Africa's surveillance infrastructure caught this. Malawi's didn't exist to. This gap is not just a technical problem, it's a global equity problem. We cannot fight AMR without investing in surveillance capacity in low-resource settings.
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Phil Ashton @flashton.bsky.social · 13/03/2026
It's also a reservoir for AMR determinants that could transfer to dominant invasive Salmonella lineages like Typhimurium. ⚠️
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Phil Ashton @flashton.bsky.social · 13/03/2026
Nearly 90% of ST335 isolates carried XDR genotypes. Some had also acquired carbapenem and macrolide resistance. This is a very nasty bug, especially in this setting where treatment options are constrained.
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Phil Ashton @flashton.bsky.social · 13/03/2026
In Malawi, genomically identical isolates were found in children's bloodstream infections, neonatal ward surfaces, AND urban rivers downstream of the hospital. In South Africa, national genomic surveillance revealed the same lineage spreading between hospitals.
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Phil Ashton @flashton.bsky.social · 13/03/2026
🚨 New preprint: We've characterised one of the most drug-resistant Salmonella lineages we've ever encountered; Salmonella Isangi ST335, causing healthcare-associated bloodstream infections across southern Africa. www.medrxiv.org/content/10.6...
medrxiv.org
Hospital and environmental transmission of XDR Salmonella Isangi revealed by genomic Surveillance in Malawi and South Africa
ABSTRACT Background Salmonella Isangi is an under-characterised serovar repeatedly associated with antimicrobial resistant hospital infections. Outbreaks of extensively drug-resistant (XDR) Salmonella...
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Phil Ashton @flashton.bsky.social · 12/01/2026
📣 New pre-print alert! 🦠 We sequenced S. Typhi from a vaccine trial in Malawi 🇲🇼 📊 No genomic differences between vaccine and control arms 💡 But with short follow-up, that’s exactly why ongoing genomic surveillance after vaccination is essential to detect escape. www.medrxiv.org/content/10.6...
medrxiv.org
Genomic Analysis of Salmonella Typhi from a Typhoid Conjugate Vaccine Trial
Background Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, continues to pose a major public health challenge in many low- and middle-income countries (LMICs). The W...
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Phil Ashton @flashton.bsky.social · 04/12/2025
Delighted to (belatedly) announce that this work is now published in Microbiome! link.springer.com/article/10.1...
link.springer.com
Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model - Microbiome
Background Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminate...
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Phil Ashton @flashton.bsky.social · 04/12/2025
Would now be delighted to read a 3000 word exploration of how terrible Liverpool are.
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Phil Ashton @flashton.bsky.social · 11/05/2025
Here’s a work one I can share, about plasmids integrating into chromosomes. This is ChatGPT o3 chatgpt.com/share/681f03...
chatgpt.com
ChatGPT - Plasmid Integration Examples
Shared via ChatGPT
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Phil Ashton @flashton.bsky.social · 11/05/2025
London was looking lovely in the sunshine yesterday!
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Phil Ashton @flashton.bsky.social · 11/05/2025
Must be a nice view from the top, and at least you don’t have to look at the building when you’re in it :-D
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Phil Ashton @flashton.bsky.social · 11/05/2025
Helped me think about and structure project aims and milestones. It’s basically like a management consultant that would cost £1000. In addition it’s also a top notch art critic, recipe maker, personal trainer, research assistant, bioinformatician, etc etc. Send your email and I’ll send some examples
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Phil Ashton @flashton.bsky.social · 11/05/2025
Art galleries should provide good signal/free WiFi so that we can ask AI about the art work, rather than seemingly deliberately blocking it to stop people dicking about on their phones.
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Phil Ashton @flashton.bsky.social · 10/05/2025
ChatGPT o3 is just mind blowing!
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Phil Ashton @flashton.bsky.social · 09/05/2025
I'm sure that being a medieval peasant and growing all your own food must have been satisfying in its own way, but they'll never know the satisfaction of having a fully charged battery pack will they?
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Phil Ashton @flashton.bsky.social · 09/05/2025
Great post from Works in Progress mag on recent scientific findings: "For over 50 years, the USDA has airdropped millions of sterilized male screwworm flies weekly along the Panama–Colombia border." www.worksinprogress.news/p/reporter-g...
worksinprogress.news
What's new in biology
Return of the screwworm, new DNA vaccines, gene editing at scale, and more
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Conor (Conchúr) Meehan @conmeehan.bsky.social · 26/03/2025
Speakers include @flashton.bsky.social @dralhubb.bsky.social @danybeste.bsky.social @jodywinter.bsky.social @dannagifford.bsky.social and more! Plus, lots of time to interact with other researchers and industry people in the field (including dinner!). Maybe see you there?
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Conor (Conchúr) Meehan @conmeehan.bsky.social · 26/03/2025
@friendlymicrobe.bsky.social and I invite you to the @bsacandjac.bsky.social antibiotic resistance and mechanisms conference Nov 27-28 in Birmingham! We have great talks on global AMR healthcare, mechanisms, vaccines/immunotherapy, antimicrobial interactions and outreach. bsac.org.uk/antibiotic-r...
bsac.org.uk
Antibiotic Resistance and Mechanisms (ARM) Workshop for Researchers 2025 - The British Society for Antimicrobial Chemotherapy
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Phil Ashton @flashton.bsky.social · 18/03/2025
Chuffed to announce that I've started a new job with @daanensen.bsky.social at the @thecgps.bsky.social, supporting the uptake of genomics for AMR in global health!
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Phil Ashton @flashton.bsky.social · 02/03/2025
Is it acceptable to respond to a reviewers comment by saying "yes, that's a lovely idea, but we already have 27 supplementary tables, so i'm not going to do it"?
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Pathogenwatch @pathogenwatch.bsky.social · 12/02/2025
Hi Bluesky! We’re looking forward to engaging with the community and our users on here. Follow this account for updates on the Pathogenwatch platform (pathogen.watch), as well as our sister tools @microreact.bsky.social and @amrwatch.bsky.social developed by @thecgps.bsky.social
pathogen.watch
Pathogenwatch
A global platform for genomic surveillance.
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M. Nolan Gray 🥑 @mnolangray.bsky.social · 12/02/2025
Today in @worksinprogress.bsky.social, I reflect on Donald Shoup's legacy. Perhaps the most interesting question: how did the most unlikely professor kick off an international parking reform movement? substack.com/home/post/p-...
substack.com
The prophet of parking
A eulogy for the great Donald Shoup
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Phil Ashton @flashton.bsky.social · 06/02/2025
I'm very interested in the idea to think about microbiome/metagenome datasets in terms of ecological guilds presented in this paper www.nature.com/articles/s41... Is there any ontology, or other organised database, of microbial ecological guilds, with example species?
nature.com
Microbiome science needs more microbiologists - Nature Microbiology
Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.
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Krisandra Allen @genomicepi.com · 06/02/2025
I've been maintaining a job board at www.genomicepi.com/jobs for a couple of years. I started this with several goals in mind
genomicepi.com
Genomic Epi Jobs
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Phil Ashton @flashton.bsky.social · 05/02/2025
Maundaymas?
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Phil Ashton @flashton.bsky.social · 05/02/2025
Interesting,. Would be better if could be done without request? Or at least, default when uploading to being requested?
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Phil Ashton @flashton.bsky.social · 05/02/2025
What kind of psycopath has Sunday as the first day of the week on their calendar?
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Natacha Couto @natachacouto.bsky.social · 28/01/2025
Registration for #IMMEM14 is now open! Don't forget it is limited to 350 participants so secure your spot. @escmid.bsky.social @esgem.bsky.social escmid.org/congress-eve...
escmid.org
Registration & Information
Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).
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Phil Ashton @flashton.bsky.social · 28/01/2025
It would be nice if Google Scholar gave citation metrics excluding self-citations.
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Phil Ashton @flashton.bsky.social · 28/01/2025
I'm seeing this box on biorxiv pre-prints. Anyone know how to post a community review?
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Phil Ashton @flashton.bsky.social · 24/01/2025
Haha, at least the right people will be on hand to investigate any outbreaks!
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Phil Ashton @flashton.bsky.social · 24/01/2025
Strong petting zoo vibes from National Institute of Communicable Diseases in Joburg!
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Phil Ashton @flashton.bsky.social · 23/01/2025
If your journal sets my postal address field as required information as part of reviewer sign up, you'd better be prepped for some expletive laden address info!
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Phil Ashton @flashton.bsky.social · 18/01/2025
Thanks, closer than I got, but not quite it. Was a table of occupations (scientist, sales, accountant, artist) and mental health (adhd, depression, etc) and the OR of each association
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Phil Ashton @flashton.bsky.social · 18/01/2025
Jfc. I’d love to have been a fly on the wall when they explained what they wanted to the techies. “You want us to close a website?”
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Phil Ashton @flashton.bsky.social · 18/01/2025
Gah, can anyone help me find the paper that showed the association between various professions and different mental health conditions that was circulating a while back? Google and chatgpt failing.
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Phil Ashton @flashton.bsky.social · 18/01/2025
Haha, wut?
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Phil Ashton @flashton.bsky.social · 17/01/2025
The substack subscription process is such a pain in the ass.
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Phil Ashton @flashton.bsky.social · 17/01/2025
Came across the quote on Austin Kleon’s excellent substack
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Phil Ashton @flashton.bsky.social · 17/01/2025
This Steve Albini quote on goals vs process inspired me to create the goal-process ouroboros.
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Phil Ashton @flashton.bsky.social · 16/01/2025
Here’s the link to the crowd funder for them. www.crowdfunder.co.uk/p/save-groun...
crowdfunder.co.uk
Save groundbreaking technology after arson attack
Help rebuild unique cutting-edge technology after an arson attack - to create low-cost sustainable electricity for all.
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Reposted by Phil Ashton
Jason Andrews @jasonandrews.bsky.social · 15/01/2025
We developed a simple, inexpensive, colorimetric assay based on detection of S. Typhi-specific phages, which are more abundant and easily detectable. Our latest preprint describes this assay & application in 4 countries. Happy to share reagents & make this accessible. www.medrxiv.org/content/10.1...
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Phil Ashton @flashton.bsky.social · 16/01/2025
Some days you wake up and the sun is shining and the birds are singing. Other days, you wake up and there’s no power, no water, and a decomposing rat in the garage.
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Phil Ashton @flashton.bsky.social · 10/01/2025
fingers crossed! Looking forward to reading it.
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Phil Ashton @flashton.bsky.social · 10/01/2025
Haha, no problem!
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Phil Ashton @flashton.bsky.social · 10/01/2025
Link is broken? Congrats though!
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Phil Ashton @flashton.bsky.social · 10/01/2025
@andrewjpage.bsky.social made a starter pack
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Phil Ashton @flashton.bsky.social · 06/01/2025
Need a website that shows me outfits menswear guy has assessed and lets me guess his opinion and then compares my judgement with his.
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Phil Ashton @flashton.bsky.social · 04/01/2025
Shocking tease that they make you click through to the full article for the “never fail” recipe.
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Phil Ashton @flashton.bsky.social · 04/01/2025
Hungry boy! More about food than clothes.
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