Philip Bejon

New analysis from Kevin Chau @modmedmicro.bsky.social for the SinkBug Consortium (a collaboration with teams across 29 UK hospitals, NITCAR, UKHSA): Pathogen and AMR gene burden in 287 hospital sink-trap metagenomes and factors associated with high burdens.

I work in the NHS: the government cannot accept doctors’ pay demands Junior doctor careers have been turned from a competition into a lottery with too few tickets

I don't find a lot in the Spectator that I like to read, but found this thought provoking and moving: www.spectator.co.uk/article/i-wo...

A new study by KEMRI Wellcome, @isglobal.org and the Manhiça Health Research Centre has highlighted that alongside bed nets, ivermectin reduced #malaria infection by 26% in children. Their findings show that it's a valuable tool for tackling the spread of malaria 🦟💊

Read more 👉 buff.ly/0OU6UhJ

Fewer papers = someone has to decide which papers don't see the light of day; i.e. which papers become "secret".

Job advert to come and work with me on tuberculosis closes tomorrow (Friday) at noon!

Part of #OxCOD4TB

bit.ly/4ndKOhF

@ndm.ox.ac.uk @modmedmicro.bsky.social
@oxfordbrc.bsky.social

Come and work with us!

Senior Biostatistical Researcher bit.ly/4kRfZxI
Senior Bioinformatic Engineer bit.ly/4ecl0hF
both Grade 8 or 7, closing noon Tue 8 Jul

Computational Mycobacteriologist
Grade 7, closing noon Fri 4 Jul bit.ly/4ndKOhF

@medsci.ox.ac.uk
@oxfordbrc.bsky.social
@ndm.ox.ac.uk

Nice data. To me the coolest, tho also most alarming, is slope of antibiotic resistance declining over time - gradient is shallow!

So that means if UTIs recur frequently, you can see how you burn through antibiotic options quickly!

#UTISky #IDSky #ClinMicro #AMR
academic.oup.com/jac/advance-...

Come and work with me and use the 53,897 samples of M. tuberculosis we have collated to help tackle this important disease!

We are part of the OxCoD4TB consortium that is developing new therapeutics for tuberculosis.

Grade 7, funding until 28 Feb 2028, deadline noon Fri 4 July

bit.ly/4ndKOhF

Job Opportunity at LSHTM: Research Assistant The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...

Come & work with me @benvyle.bsky.social @lshtm.bsky.social & @thelovetankcic.bsky.social Research Assistant with funded PhD within multidisciplinary project on Syphilis & STI control in the UK. Working with us to understand stakeholder & community perspectives on novel STI control strategies

The relaunch of crypticproject.info at #ESMyco by @philipwfowler.bsky.social

53,897 clinical tuberculosis samples with genetics and drug susceptibility testing data!

@vbrunner.bsky.social doing her pitch for her poster at #ESMyco!

@modmedmicro.bsky.social

Come and help us develop and validate genetic pipelines for processing pathogens in collaboration with
@eitoxford.bsky.social

Senior Bioinformatic Engineer
bit.ly/4ecl0hF

Senior Biostatistical Researcher
bit.ly/4kRfZxI

Grade 8 or 7, depending on experience
closing date: noon Wednesday 2 July

Just like buses, here is a third role we are advertising for!

Come and help @philipwfowler.bsky.social use the large TB datasets we hold to help the OxCoD4TB consortium develop new therapeutics for tuberculosis.

Grade 7, funding until 28 Feb 2028, deadline noon Fri 4 July

bit.ly/4ndKOhF

Come and help us develop and validate genetic pipelines for processing pathogens in collaboration with
@eitoxford.bsky.social

Senior Bioinformatic Engineer
bit.ly/4ecl0hF

Senior Biostatistical Researcher
bit.ly/4kRfZxI

Grade 8 or 7, depending on experience
closing date: noon Wednesday 2 July

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

What happens when humanitarian aid is cut or delayed? Humanitarian aid systems are under mounting pressure, with key donors like the US and UK cutting funding despite growing needs. New research in one of the world’s largest refugee camps shows that aid ...

🆕What happens when humanitarian aid is cut or delayed?

A 20% aid cut in one of the world's largest refugee camp didn’t just reduce what and how much refugees eat; it also triggered a cascade of effects across households and markets. voxdev.org/topic/instit...

with Vittorio Bruni and @wfp.org

UZH: Postdoctoral researcher in microbiology The Department of Quantitative Biomedicine is an interdisciplinary biomedical research unit that combines basic science with biotechnological and medical research, using both experimental and computat...

We are looking for a highly motivated postdoc to work on pathogen interactions. Please send in your application via

jobs.uzh.ch/job-vacancie...

Vaccination to prevent antimicrobial resistance: new evidence, future priorities and policy implications | Reports | Wellcome This report explores how vaccines can help reduce antimicrobial resistance (AMR), summarising new evidence from 11 Wellcome-funded projects and outlining what’s needed to strengthen policy decisions w...

Vaccines are powerful. But we’re missing a chance to use them to tackle antimicrobial resistance (AMR).

Our latest report examines how they can reduce AMR and where more evidence is needed to guide policy.

Read the report: wellcome.org/reports/vacc...

Fantastic game. I especially enjoyed seeing software development demonstrating fixing bugs on the spot to deal with new hardware. Then a period with an MVP and development version in parallel. Then a hack fix, but developers locked in to finding an elegant solution while the game continued.

Come and play our dance mat game named after me! Outside John Lewis in the Westgate as part of the @oxfordbrc.bsky.social showcase!

Come and find @modmedmicro.bsky.social at the Westgate in Oxford as part of the @oxfordbrc.bsky.social showcase!

Lots of bugs at the @oxfordbrc.bsky.social showcase in the Westgate!

Looping out bacteria (well couscous) is harder than it looks!

@oxfordbrc.bsky.social @modmedmicro.bsky.social

PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches

Excited to share 9 fully funded PhD projects with NIHR HPRU Public Health genomics at UKHSA and University of Birmingham. Deadline 31 July www.birmingham.ac.uk/research/cen...
Ranging from methods development, microbiome, metagenomics and species specific (TB, Strep pneumo, measles) projects

Ceftazidime retains in vivo efficacy against strains of Stenotrophomonas maltophilia for which traditional testing predicts resistance | mSphere Breakpoint interpretation criteria for ceftazidime against S. maltophilia were recently removed by CLSI and the FDA. It was noted that clinical data were insufficient to validate the current breakpoin...

🆕🌟Super interesting!
The study challenges IDSA guidance which recommend against the use of CAZ for treatment of S.maltophilia
Ceftazidime retains in vivo efficacy against strains of Stenotrophomonas maltophilia for which traditional testing predicts resistance #idsky
journals.asm.org/doi/10.1128/...

What is terrifying is how 10 years got squeezed in between 1 April 2022 to 31 March 2023.

It seems to me that if there is an interaction by site then by definition there is no "overall true effect estimate" in the sense that the effect by definition varies by site. I think to even state the effect size one has to specify which site this would apply to.

I think if there is an interaction then yes it is a problem, but that would be true also of most regular RCTs - and an interaction by site leads to massive problems with generalizability unless it can be well understood from a biological viewpoint.

Evolution of T cell responses in the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones. T cells contribute to immune protection and pathogenesis in tuberculosis, but measurements of polyclonal responses have failed to resolve correlates of outcome. We report the first temporal…

Interested in T cell immunity in TB? Check out our new pre-print on antigen-agnostic identification of generalisable human in vivo Mtb-reactive T cell responses: www.biorxiv.org/content/10.1...
with @qimmuno.bsky.social & @innate2adaptive.bsky.social

Opinion | Science Suffers With Trump’s Funding Freeze America’s scientific enterprise demands reliable stewardship, not destabilizing political intervention.

My father-in-law, Jack Strominger, and I wrote a letter to the @wsj.com editor about the current threats to science due to Trump's funding freeze. Please repost! www.wsj.com/opinion/scie...