Long-read sequencing of Mycobacterial tuberculosis is comparable to short-read sequencing for antimicrobial resistance prediction and epidemiological studies. www.biorxiv.org/content/10.64898/2026.04...

TB is preventable and treatable — but only if we can stay ahead of it.
#WorldTBDay #Tuberculosis

Together, these studies reinforce a clear message:
Faster, scalable, and accessible diagnostics are essential — not just to improve individual patient outcomes, but to limit the global spread of resistant TB.

Predicting pyrazinamide resistance in Mycobacterium tuberculosis using a graph convolutional network - BMC Microbiology BMC Microbiology - Pyrazinamide is an important first-line antibiotic for treating tuberculosis, with resistance primarily driven by mutations in the pncA gene. Traditional machine learning models...

Using graph neural networks and protein structural data, we’ve also shown how deep learning can improve prediction of pyrazinamide resistance — highlighting the potential of structure-aware models to tackle complex antimicrobial resistance challenges.
link.springer.com/article/10.1...

Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competiti...

We’ve explored compensatory mutations that can restore bacterial fitness in resistant strains, helping explain how resistant TB continues to spread — and reinforcing the urgency of better diagnostics and stewardship.
www.microbiologyresearch.org/content/jour...

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach Bedaquiline (BDQ) has only been approved for use for just over a decade and is a key drug for treating multidrug-resistant tuberculosis; however, rising levels of resistance threaten to reduce its eff...

Our work on bedaquiline resistance (catomatic) provides a reproducible way to construct catalogues of resistance-associated variants — critical for protecting one of the key drugs used to treat MDR-TB.
www.microbiologyresearch.org/content/jour...

Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 Mycobacterium tuberculosis samples Tuberculosis remains a global health problem. Making it easier and quicker to identify which antibiotics an infection is likely to be susceptible to will be a key part of the solution. Whilst whole-ge...

We’ve developed tools like gnomonicus, which translate genomic data into actionable resistance predictions using the WHO catalogue, achieving >95% sensitivity and specificity for two key first-line drugs.
www.microbiologyresearch.org/content/jour...

Our recent preprint shows that Oxford Nanopore sequencing, combined with improved DNA extraction and amplification, can deliver rapid and reliable genomic characterisation directly from clinical cultures — helping move toward real-time TB diagnostics.
Read more: www.biorxiv.org/content/10.6...

The CRyPTIC project has collected and collated over 53,000 TB samples linking genomics with drug susceptibility data — a powerful global resource to accelerate research and improve diagnostics.
Find out more: crypticproject.info

A major part of tackling TB — especially multidrug-resistant TB (MDR-TB) — is improving how quickly and accurately we can diagnose infections and identify effective treatments.
Over the last few years, our work has focused on exactly that:

On #WorldTBDay, it’s important to reflect on the scale of the challenge we’re facing.
In 2024 alone, tuberculosis (TB) caused 1.23 million deaths worldwide, remaining the leading cause of death from a single infectious agent, according to WHO

@ndm.ox.ac.uk

Rapid testing of tuberculosis is available & recommended. Early diagnosis is a gamechanger!

Rapid diagnosis of tuberculosis is available and recommended!
Early diagnosis is a gamechanger.

Ask your provider for access to WHO-recommended rapid tests for TB, including the latest near-point-of-care tests, to ensure a quick diagnosis and early treatment.

Open datasets such as these are key for tackling AMR in diseases such as tuberculosis.

#WorldTBDay

Since 2017 the CRyPTIC project collected and collated 53,897 clinical TB samples with genetics and drug susceptibility testing data.

You can download the datasets via crypticproject.info and v4.0.0 will appear later this year.

#WorldTBDay @modmedmicro.bsky.social

Bash the Bug at ATOM Festival: Dancing, Germs, and the Challenge of Antimicrobial Resistance!

We had a fantastic time this weekend at ATOM Festival in Abingdon, bringing microbiology to life with our Bash the Bug public engagement activities.

It was fantastic to see so many people getting involved, asking great questions, and learning about microbiology in the sunshine. Thanks to everyone who came to say hello, and to our brilliant team for all their enthusiasm!

#BashTheBug #Microbiology #PublicOutreach #ATOMFestival

We had a brilliant time this weekend at ATOM Festival in Abingdon! ☀️🦠

We brought along our favourite interactive activities to help people learn about antimicrobial resistance #AMR, including our dance mat game where you fight germs with antibiotics, and we tested everyone’s handwashing skills!

Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study Background Clinical metagenomics (CMg) offers high-throughput respiratory pathogen detection with a wider range than targeted, probe-dependent diagnostics. Sequencing cost and the challenges of high h...

1/4 Thrilled to get this metagenomic diagnostic study over the line. We have an in house method that targets RNA viruses in respiratory samples, and evaluated this against 344 prospective samples tested by multiplex PCR.

www.medrxiv.org/content/10.6...

Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study Background Clinical metagenomics (CMg) offers high-throughput respiratory pathogen detection with a wider range than targeted, probe-dependent diagnostics. Sequencing cost and the challenges of high h...

New preprint from us @modmedmicro.bsky.social where we validate the diagnostic accuracy of a metagenomic nanopore sequencing method for respiratory RNA viruses.

www.medrxiv.org/content/10.6...

Are you a post-doctoral microbiologist interested in characterising bacterial resistance evolution and want to apply your knowledge and expertise to developing new therapeutics for Klebsiella (and other Enterobacterales) infections? Then we need you! Apply now bit.ly/3MX39Ce close date March 13th 👀

Hoping to innovate community population-level AMR surveillance with the ALARUM team bmjopen.bmj.com/content/16/2.... Can we use metagenomics of pooled colonisation samples to predict clinical AMR burden & inform antimicrobial guidelines?

International Day of Women and Girls in Science 👩‍🔬

Proud to work alongside the scientists in our #microbiology lab whose work in antimicrobial resistance, public health and diagnostics has real-world impact!

#WomenInScience #AMR #PublicHealth @medsci.ox.ac.uk @ox.ac.uk @oxfordbrc.bsky.social

Biofilms on microplastic surfaces and their effect on pollutant adsorption in the aquatic environment - Journal of Material Cycles and Waste Management The extensive use of plastics has led to the widespread presence of a new type of pollutant called “microplastics (MPs)” in aquatic environments. MPs have large specific surface areas and strong hydro...

Image taken from doi.org/10.1007/s101...

UNIQplus projects | University of Oxford Projects available for entry in 2026As part of your UNIQplus Research Internship, you will be working on a project under the supervision of academic staff from our community of world-leading

In this project, you’ll use lab experiments and a microplastics library to explore how bacteria grow and develop antimicrobial resistance in a hospital-like environment. Hands-on microbiology meets a real-world health challenge!

www.ox.ac.uk/admissions/g...

Life and medical sciences > CLINICAL 04

MMM has an exciting UNIQ+ project running this summer -apply now!

Bacteria, microplastics & resistance — what’s the connection?

#Microplastics are everywhere, even in hospitals. But what happens when bacteria stick to them? Come and find out!

@afswinkels.bsky.social @nstoesser.bsky.social

Happy our preprint is out🦠:

"Evaluation of an Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT culture"

We developed and tested a workflow for long-read sequencing of #mycobacteria, including optimising DNA extraction and assessing how #ONT performs compared with #Illumina.

Our project "Sardinia’s Invisible Marine Microbiome" is one of six 2026 #PartArt4OW participatory art initiatives! Excited to do this with the brilliant @annadumitriu.bsky.social (image credit), Sardinian scientists, citizens of Alghero, and colleagues in @modmedmicro.bsky.social @bashthebug.net

Discovery of Novel Klebsiella Hits Through In-Depth Genomic Profiling, Fragment-Based Drug Design and Accumulation Assays Annette von Delft and collaborators Nicole Stoesser, Lizbe Koekemoer, Ed Griffen, Paul Brennan, Frank von Delft, Phil Fowler, and Thomas Lanyon-Hoggat of the University of Oxford in the United Kingdom...

Delighted to be involved in the Gram-Negative Antibiotic Discovery Innovator (Gr-ADI) consortium novonordiskfonden.dk/en/news/new-... as part of a project led by Annette von Delft gcgh.grandchallenges.org/grant/discov... @modmedmicro.bsky.social @samlipworth.bsky.social @philipwfowler.bsky.social

What is UNIQplus? | University of Oxford The UNIQplus programmeThe UNIQplus programme is aimed at supporting talented undergraduates from under-represented groups, who would find continuing into postgraduate study a challenge for reasons

Univ of Oxford UNIQ+ scheme applications open: 7-week research internship this Summer www.ox.ac.uk/admissions/g.... Lots of projects - one in our lab on microplastics & AMR & hospital environments at @modmedmicro.bsky.social led by Aram Swinkels www.ox.ac.uk/admissions/g... (Clin Med 04). Join us!

Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue Metagenomic approaches to the diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adapti...

Read the full paper here: tinyurl.com/2a5z6tt8