Phil Ashton @flashton.bsky.social · 13/03/2026South 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. 010
Phil Ashton @flashton.bsky.social · 13/03/2026It's also a reservoir for AMR determinants that could transfer to dominant invasive Salmonella lineages like Typhimurium. ⚠️ 101
Phil Ashton @flashton.bsky.social · 13/03/2026Nearly 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. 100
Phil Ashton @flashton.bsky.social · 13/03/2026In 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. 100
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.orgHospital and environmental transmission of XDR Salmonella Isangi revealed by genomic Surveillance in Malawi and South AfricaABSTRACT Background Salmonella Isangi is an under-characterised serovar repeatedly associated with antimicrobial resistant hospital infections. Outbreaks of extensively drug-resistant (XDR) Salmonella... 120
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.orgGenomic Analysis of Salmonella Typhi from a Typhoid Conjugate Vaccine TrialBackground 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... 021
Phil Ashton @flashton.bsky.social · 04/12/2025Delighted to (belatedly) announce that this work is now published in Microbiome! link.springer.com/article/10.1...link.springer.comInterplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model - MicrobiomeBackground 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... 030
Phil Ashton @flashton.bsky.social · 04/12/2025Would now be delighted to read a 3000 word exploration of how terrible Liverpool are. 000
Phil Ashton @flashton.bsky.social · 11/05/2025Here’s a work one I can share, about plasmids integrating into chromosomes. This is ChatGPT o3 chatgpt.com/share/681f03...chatgpt.comChatGPT - Plasmid Integration ExamplesShared via ChatGPT 010
Phil Ashton @flashton.bsky.social · 11/05/2025London was looking lovely in the sunshine yesterday! 000
Phil Ashton @flashton.bsky.social · 11/05/2025Must 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 000
Phil Ashton @flashton.bsky.social · 11/05/2025Helped 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 000
Phil Ashton @flashton.bsky.social · 11/05/2025Art 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. 000
Phil Ashton @flashton.bsky.social · 09/05/2025I'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? 000
Phil Ashton @flashton.bsky.social · 09/05/2025Great 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.newsWhat's new in biologyReturn of the screwworm, new DNA vaccines, gene editing at scale, and more 010
Reposted by Phil AshtonConor (Conchúr) Meehan @conmeehan.bsky.social · 26/03/2025Speakers 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? 062
Reposted by Phil AshtonConor (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.ukAntibiotic Resistance and Mechanisms (ARM) Workshop for Researchers 2025 - The British Society for Antimicrobial Chemotherapy 1108
Phil Ashton @flashton.bsky.social · 18/03/2025Chuffed 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! 190
Phil Ashton @flashton.bsky.social · 02/03/2025Is 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"? 040
Reposted by Phil AshtonPathogenwatch @pathogenwatch.bsky.social · 12/02/2025Hi 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.socialpathogen.watchPathogenwatchA global platform for genomic surveillance. 2164
Reposted by Phil AshtonM. Nolan Gray 🥑 @mnolangray.bsky.social · 12/02/2025Today 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.comThe prophet of parkingA eulogy for the great Donald Shoup 24213
Phil Ashton @flashton.bsky.social · 06/02/2025I'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.comMicrobiome science needs more microbiologists - Nature MicrobiologyMicrobiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts. 021
Reposted by Phil AshtonKrisandra Allen @genomicepi.com · 06/02/2025I've been maintaining a job board at www.genomicepi.com/jobs for a couple of years. I started this with several goals in mindgenomicepi.comGenomic Epi Jobs 132
Phil Ashton @flashton.bsky.social · 05/02/2025Interesting,. Would be better if could be done without request? Or at least, default when uploading to being requested? 000
Phil Ashton @flashton.bsky.social · 05/02/2025What kind of psycopath has Sunday as the first day of the week on their calendar? 100
Reposted by Phil AshtonNatacha Couto @natachacouto.bsky.social · 28/01/2025Registration 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.orgRegistration & InformationLearn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID). 0117
Phil Ashton @flashton.bsky.social · 28/01/2025It would be nice if Google Scholar gave citation metrics excluding self-citations. 020
Phil Ashton @flashton.bsky.social · 28/01/2025I'm seeing this box on biorxiv pre-prints. Anyone know how to post a community review? 100
Phil Ashton @flashton.bsky.social · 24/01/2025Haha, at least the right people will be on hand to investigate any outbreaks! 010
Phil Ashton @flashton.bsky.social · 24/01/2025Strong petting zoo vibes from National Institute of Communicable Diseases in Joburg! 120
Phil Ashton @flashton.bsky.social · 23/01/2025If 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! 000
Phil Ashton @flashton.bsky.social · 18/01/2025Thanks, 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 010
Phil Ashton @flashton.bsky.social · 18/01/2025Jfc. 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?” 000
Phil Ashton @flashton.bsky.social · 18/01/2025Gah, 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. 101
Phil Ashton @flashton.bsky.social · 17/01/2025The substack subscription process is such a pain in the ass. 010
Phil Ashton @flashton.bsky.social · 17/01/2025Came across the quote on Austin Kleon’s excellent substack 000
Phil Ashton @flashton.bsky.social · 17/01/2025This Steve Albini quote on goals vs process inspired me to create the goal-process ouroboros. 100
Phil Ashton @flashton.bsky.social · 16/01/2025Here’s the link to the crowd funder for them. www.crowdfunder.co.uk/p/save-groun...crowdfunder.co.ukSave groundbreaking technology after arson attackHelp rebuild unique cutting-edge technology after an arson attack - to create low-cost sustainable electricity for all. 022
Reposted by Phil AshtonJason Andrews @jasonandrews.bsky.social · 15/01/2025We 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... 12010
Phil Ashton @flashton.bsky.social · 16/01/2025Some 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. 030
Phil Ashton @flashton.bsky.social · 06/01/2025Need a website that shows me outfits menswear guy has assessed and lets me guess his opinion and then compares my judgement with his. 010
Phil Ashton @flashton.bsky.social · 04/01/2025Shocking tease that they make you click through to the full article for the “never fail” recipe. 000