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Phil Ashton

@flashton.bsky.social
733 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
🚨 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
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
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
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
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 · 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
This Steve Albini quote on goals vs process inspired me to create the goal-process ouroboros.
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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 · 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
Is there anything better in the world than a 3000 word exploration of how terrible Man U are? www.theguardian.com/football/202...
theguardian.com
Systems evangelist Amorim meets Slot’s simpler pragmatism at Anfield | Barney Ronay
Manchester United’s new manager is increasingly looking like an odd hire, especially when compared to the successful succession at their arch rivals
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Phil Ashton @flashton.bsky.social · 04/01/2025
Just watched Phantom Thread, what an interesting movie! Odd balls! I’d watch Daniel Day Lewis watching paint dry.
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Phil Ashton @flashton.bsky.social · 03/01/2025
Anyone know of a hospital that sequences all of their invasive carbapenem resistant Kleb pneumo?
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Phil Ashton @flashton.bsky.social · 03/01/2025
All the books I read in 2024 medium.com/@flashton/bo...
medium.com
Books of 2024
Summary
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Phil Ashton @flashton.bsky.social · 03/01/2025
Very thought provoking article on the Pelicot case www.lrb.co.uk/the-paper/v4...
lrb.co.uk
Sophie Smith · Sleeping Women: On the Pelicot trial
Gisèle Pelicot doesn’t conceive of her now ex-husband or the other men who raped her as ‘bad apples’, aberrations...
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Phil Ashton @flashton.bsky.social · 02/01/2025
2.2 million Nigerians were kidnapped in the last year! allafrica.com/stories/2024...
allafrica.com
Nigeria: 614,937 Nigerians Killed, 2.2m Abducted in 1yr - NBS
No fewer than 614,937 Nigerians were killed and 2,235,954 others kidnapped across the country between May 2023 and April 2024, the National Bureau of Statistics (NBS) has revealed.
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Phil Ashton @flashton.bsky.social · 30/12/2024
I want a podcast that does for classical music what Great Art Explained does for artists. youtube.com/@greatartexp...
youtube.com
Great Art Explained
I'm James Payne, a curator, gallerist, and a passionate art lover. I am on a mission to demystify the art world and discover the stories behind the world’s greatest paintings and sculptures. Each epis...
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Phil Ashton @flashton.bsky.social · 30/12/2024
Step 1: Tell authors you have a "come as you are" submissions policy. Step 2: Return manuscript to authors so they can re-arrange information under your preferred headers 1/2
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Phil Ashton @flashton.bsky.social · 24/12/2024
Nothing like waking up to 18 messages from work telling me to prioritise self care! 🤣
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Kyle Wilson @kyle-wilson.bsky.social · 21/12/2024
Malarial retinopathy remains the most sensitive point-of-care test for CM in comatose parasitaemic children in malaria-endemic areas. See the complete results of the Blantyre Autopsy Study here: medrxiv.org/cgi/content/...
medrxiv.org
Re-evaluating malarial retinopathy to improve its diagnostic accuracy in cerebral malaria
Background Previous work has identified that malarial retinopathy (MR) has diagnostic value in cerebral malaria (CM). To improve our understanding of MR as a predictor of cerebral parasite sequestrati...
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Phil Ashton @flashton.bsky.social · 20/12/2024
Urban waste piles would be a great band name. www.sciencedirect.com/science/arti...
sciencedirect.com
Urban waste piles are reservoirs for human pathogenic bacteria with high levels of multidrug resistance against last resort antibiotics: A comprehensive temporal and geographic field analysis
Inadequate waste management and poor sanitation practices in Low- and Middle-Income Countries (LMICs) leads to waste accumulation in urban and peri-ur…
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Oded Rechavi @odedrechavi.bsky.social · 19/12/2024
Bummer that you can't escape politics on this platform, just give me science and jokes
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Kate Baker @ksbakes.bsky.social · 19/12/2024
Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2 1/n
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Phil Ashton @flashton.bsky.social · 12/12/2024
Does anyone know how PEPFAR distribute cotrimoxazole to high HIV burden countries? Just via normal wholesale channels, or via some special mechanism?
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 09/12/2024
If you missed my recent #MVIF talk on our precision nutrition work, you can catch it here youtu.be/L1VutD02lu8?... Thanks to the organizers for providing these virtual events for free to the microbiome community! 🎉 @microbiomevif.bsky.social
youtu.be
Sean Gibbons - My Digital Gut: a tool set for microbiome-mediated precision nutrition | S04 MVIF34
YouTube video by Microbiome Virtual International Forum
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Conor (Conchúr) Meehan @conmeehan.bsky.social · 09/12/2024
The Wellcome Connecting Science Learning and Training team are aiming to develop a course focusing on capacity building and strengthening in genomics and are conducting a needs assessment survey and would love your input! www.surveymonkey.com/r/GenomicsCa...
surveymonkey.com
Survey in genomics capacity development
Take this survey powered by surveymonkey.com. Create your own surveys for free.
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Phil Ashton @flashton.bsky.social · 07/12/2024
Lightning just struck our house and I got a fairly major shock because I had my hand on a tap! Ouch!
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Phil Ashton @flashton.bsky.social · 06/12/2024
Maybe I’m getting old but there are some things where innovation is unnecessary - hand brakes, infant clothing fasteners, and hotel shower controls.
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Phil Ashton @flashton.bsky.social · 05/12/2024
📢 Thrilled to share our latest research! Certain gut bacteria may protect against typhoid fever by producing short-chain fatty acids www.medrxiv.org/content/10.1...
medrxiv.org
Interplay Between the Gut Microbiome and Typhoid Fever: Insights from Endemic Countries and a Controlled Human Infection Model
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 contaminated food and...
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Phil Ashton @flashton.bsky.social · 03/12/2024
Is plagiarism from a cc-by article a copyright violation?
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Phil Ashton @flashton.bsky.social · 29/11/2024
Was in my first meeting when someone just sent an AI transcription service to attend for them today. Thoughts?
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Phil Ashton @flashton.bsky.social · 29/11/2024
In 2024, why would you not let me submit author details by uploading an Excel - I've got 32 authors to input 5 compulsory fields for?!
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