New personal view article
The role of microbial genomics in delivering the UK’s national action plan for confronting antimicrobial resistance 2024–29
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #AMR #OpenAccess #OA
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
The idea that humans sit atop an evolutionary hierarchy dates back to 1866, when a scientist drew the first tree of life with "Man" at the top. This inaccurate view still shapes how we think of the animal world, despite decades of genomic evidence proving evolution has no hierarchy.
buff.ly/055hdSo
More hope from mRNA vaccines. In this instance, individualized vaccines were given to women with triple negative breast cancer following surgery and adjuvant therapy. The results are quite remarkable. Despite cancer finding a ‘T cell-evading’ work-around in some patients.
#Science 🧪
Its a weird, head-spinning moment where, on one hand, we can create new software from scratch in minutes with Claude code and, on the other, we are entering html code manually to apply for NIH funding
Something very different and cool for my lab. Sequencing a 4.4mb TB genome using the Artic-style PCR amplicon method with >5128 primers in two reactions 🤯
Enables culture-free WGS for TB!
journals.asm.org/doi/10.1128/...
I wrote some words for this.weekinsecurity.com about how social media giants (aka: ad tech companies!) track you around the web, even if you don't have an account or use their apps. Follows from a brilliant column in the BBC about TikTok's use of website "pixels" to track people's browsing activity.
Thanks for the great summary!
Exposing Staph aureus to both low-dose antibiotics and a host drove rapid evolution of extreme virulence. Researchers passaged MRSA and MSSA through nematodes with sub-MIC oxacillin for 12 rounds, then tracked how virulence and resi...
https://www.biorxiv.org/content/10.1101/2024.08.31.610628
"We are deliberately walking away from the most advanced form of one of the most effective public health measures available to the human race, and instead we are investigated older technologies that happen to involve the administration’s friends"
Indeed.
www.science.org/content/blog...
Absolutely love this story! Turns out Staph aureus strains in the wild have developed some cool tricks to survive and thrive in the presence of other common bugs. Metal transport seems to be key! Great work from Sam 👏🏼👏🏼
Amongst other things, this again highlights the core point about due process. It’s bad enough to be in a “show me your papers” situation, but your precious citizen/non-citizen, “legal”/“illegal” distinctions are meaningless when you can’t prove anything to authorities because they don’t give a shit.
The State Dept is reviewing the online presence of all applicants for F,M,J,H1B visas. I warn clients all the time about the risks of international travel. Visa processing today is a minefield & it's key to weigh risks before going. This is one example of what we are seeing.
"in July 2023, 80% of Danes said they saw the US as a friend or ally. Now, fewer than 26% do".
www.theguardian.com/world/2026/f...
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
Wow. Journals like this should be immediately removed from the Clarivate database.
The HPV vaccine prevents cervical and other cancers.
This is a good thing and because of that reason RFK. Jr and his ACIP are going to go after this safe and effective vaccine to undermine its uptake.
Measles is back, Pertussis is back & if they have their way cervical cancer will not be eliminated.
William Foege has died. He was a central architect of smallpox eradication, pioneering surveillance-driven ring vaccination when vaccine supply was limited. That strategy helped eliminate the deadliest human pathogen we’ve ever known.
www.nytimes.com/2026/01/24/u...
www.findaphd.com/phds/project... interested in bacterial antagonism? PhD opportunity in our team, see below. Please repost!
‘We’ve invaded Iceland by mistake’
The first of some rather chunky papers coming out of Sam Fenn’s work here at @uccmicrobiology.bsky.social
Here we identify and characterise yet another way S. aureus survives life in the bloodstream, but remodelling a major part of its metabolism
Jan. 5, 2026 The rationale for the recent updates to the U.S. childhood immunization schedule is, at best, uncertain and sets a potentially dangerous precedent for public health. Whatever improvements may be needed to the process the U.S. Centers for Disease Control and Prevention (CDC) has followed in the past to update vaccine recommendations, it is unclear what scientific evidence led to these new guidelines. Protecting a country’s public health presents unique challenges that are specific to that country’s population. The prevalence of diseases in the U.S. is not the same as it is in other countries, and public health recommendations should be made based on the public health challenges faced by the American people. The changes by the CDC will reduce the number of recommended childhood vaccines from 17 to 11. This includes narrowing the recommendation for the flu, which has already contributed to the deaths of at least 9 children this season and a near record number of pediatric flu deaths last season. Vaccines are a safe and effective tool to prevent the spread of infectious disease and infection-related deaths, and they have saved and continue to save lives. While we concur with National Institutes of Health Director Jay Bhattacharya that “science demands continuous evaluation,” that must occur with full transparency and input from the scientific community. The schedule changes weaken vaccine recommendations at a particularly critical time. It is crucial that expert consultation and a review of scientific evidence be included in the decisions that impact the health and safety of the country.
The @asm.org statement in response to the changes in the childhood immunization schedule:
asm.org/press-releas...
The planned hepatitis B birth-dose trial in Guinea-Bissau raises serious ethical concerns. Withholding a proven, life-saving vaccine from newborns to answer speculative questions is an absence of equipoise with real downstream harms for trust in vaccines.
bktitanji.substack.com/p/how-unethi...
Our new Microbial Primer describes the mechanistic action and therapeutic potential of R-pyocins produced by P. aeruginosa. www.microbiologyresearch.org/content/jour...
Bronze plaque saying "A Letter to the Future. Ok is the first Icelandic glacier to lose its status as a glacier. In the next 200 years all our glaciers are expected to follow the same path. This monument is to acknowledge that we know what is happening and what needs to be done. Only you know if we did it. August 2019. 415ppm CO2"
TIL about a memorial ceremony in Iceland in 2019 to mark the end of a glacier, changing the place name from Okjökull to Ok (jökull = glacier). Uncompromising wording on the bronze plaque:
"This is to acknowledge that we know what is happening and what needs to be done. Only you know if we did it".
"There were car gods there: a powerful, serious-faced contingent, with blood on their black gloves and on their chrome teeth: recipients of human sacrifice on a scale undreamed-of since the Aztecs."
Ending road deaths will be one of the greatest public health wins.
www.nytimes.com/2025/12/02/o...
I can't stay quiet about what RFK jr is doing to the CDC and FDA:
stevensalzberg.substack.com/p/dont-trust...
Infographic with AI slop published in Nature Scientific Reports
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
