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.
It's also a reservoir for AMR determinants that could transfer to dominant invasive Salmonella lineages like Typhimurium. ⚠️
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.
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.
🚨 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...
📣 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...
Delighted to (belatedly) announce that this work is now published in Microbiome! link.springer.com/article/10.1...
Would now be delighted to read a 3000 word exploration of how terrible Liverpool are.
Here’s a work one I can share, about plasmids integrating into chromosomes. This is ChatGPT o3 chatgpt.com/share/681f03...
London was looking lovely in the sunshine yesterday!
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
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
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.
ChatGPT o3 is just mind blowing!
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?
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...
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?
@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...
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!
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"?
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
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-...
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?
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
Maundaymas?
Interesting,. Would be better if could be done without request? Or at least, default when uploading to being requested?
What kind of psycopath has Sunday as the first day of the week on their calendar?
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...
It would be nice if Google Scholar gave citation metrics excluding self-citations.
I'm seeing this box on biorxiv pre-prints. Anyone know how to post a community review?