Modernising Medical Microbiology

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

🔬 New blog post!

Infections after joint replacement are serious, and identifying the bacteria quickly is crucial for patient care. We explain our research into metagenomic sequencing—reading all DNA in a sample to identify bacteria without needing lab growth.

👉 tinyurl.com/mrh8ukha

#AMR #Genomics

Associated software and data links:
bit.ly/3YtpMAe
bit.ly/3MJkPRh

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...

Our paper is out in Microbial Genomics! 🧬

We evaluate gnomonicus, an open-source AMR prediction tool, using 2,663 Mycobacterium tuberculosis genomes—showing how WGS can deliver faster, scalable TB resistance predictions.

Read the full paper here🔗 bit.ly/4iZepd1

#TB #AMR #Genomics

Description Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

📢Job Alert! Translational Research Collaboration Manager in Infectious Disease and Antimicrobial resistance. 🦠💊 Know anyone who would be good? Pass it on! www.imperial.ac.uk/jobs/search-...

Our team wore blue for World Antimicrobial Awareness Week 2025💙

Research into how resistance emerges, spreads and can be prevented is vital. Our group works to understand these processes and develop better tools to detect, monitor and combat antimicrobial resistance.

#WAAW @oxfordbrc.bsky.social

Modernising Medical Microbiology and Big Infection Diagnostics | NIHR Oxford Biomedical Research Centre

This World Antimicrobial Resistance Awareness Week #WAAW, we’re championing our microbiology and infection researchers whose work is benefiting patients and informing health care policy. Read: oxfordbrc.nihr.ac.uk/research-the...

@ox.ac.uk @ouhospitals.bsky.social @modmedmicro.bsky.social

An infographic stating that between now and 2050, 39.1 million people globally will die from infections attributed to antimicrobial resistance. This number is equivalent to over half the current UK population.

An infographic stating that taking your full course of antibiotics can help reduce antimicrobial resistance and save lives.

Why is antimicrobial awareness important?

Antimicrobial resistant infections are rising. In the next 25 years an estimated 39.1 million people globally will die from infections with antimicrobial resistance.

So what can you do to help? Something as simple as finishing your course of antibiotics!

These subpopulations also reveal whether resistance arose before or after infection. Our findings show why even small resistant groups matter—and how choosing the wrong antibiotic can help them take over. 💥

#TB #AMR #WAAW #WAAW2025 #AntibioticResistance @oxfordbrc.bsky.social

In our study, we investigated how often such resistant minority populations occur in clinical TB samples, focusing on rifampicin (RIF). Including these minorities in resistance profiles significantly improved detection sensitivity. 🧪🔍

Resistance testing often yields a single profile per infection. If most bacteria appear susceptible, the antibiotic is used. But this approach fails when a minority, even as little as 5%, are resistant. Those few can survive treatment and take over the infection. ⚔️

Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired AbstractObjectives. WGS has become a key tool for diagnosing Mycobacterium tuberculosis infections, but discrepancies between genotypic and phenotypic drug

For #WorldAntimicrobialAwarenessWeek, we introduce our recent paper on antibiotic-resistant subpopulations in TB.
TB may be one of humanity’s oldest diseases, yet it still kills over 1M people yearly. As resistance spreads, knowing each patient’s resistance profile before treatment is vital. 🧬💊

Antimicrobial resistance occurs when bacteria, viruses, fungi & parasites change over time - leading to medicines being less effective against them.
Here you see bacteria growing and antibiotics (the small discs) which kill the bacteria...unless they are resistant!
#WAAW #AMR @oxfordbrc.bsky.social

Bash The Bug (@BashTheBug) / X Bash The Bug (@BashTheBug) / X

Are you interested in infections, the micro-organisms that cause them and antimicrobial resistance? So are @bashthebug.net and they're looking for new members to join their patient & public group. More info: bashthebug.net/lay-represen... Deadline 27 Nov @ouhospitals.bsky.social @medsci.ox.ac.uk

New paper: What can subpopulations tell us about rifampicin resistance? Last Thursday this work which we'd previously preprinted looking at looking at rifampicin-resistant subpopulations in clinical M. tuberculosis samples was published in JAC-Antimicrobial Resistance. If...

New paper by @vbrunner.bsky.social looking at detecting rifampicin resistant subpopulations in M. tuberculosis infections using genetics and putting a lower limit on the proportion that arose due to secondary infections.

bit.ly/47rwf42

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

🔔🔔Post-doc in microbial genomics with @modmedmicro.bsky.social🧬 - deadline tomorrow! Big genomic and clinical datasets to play with, friendly and very multidisciplinary team!

my.corehr.com/pls/uoxrecru...

Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired AbstractObjectives. WGS has become a key tool for diagnosing Mycobacterium tuberculosis infections, but discrepancies between genotypic and phenotypic drug

Our recent paper on rifampicin resistant subpopulations in M. tuberculosis (M. tb) has been published at JAC-antimicrobial resistance.

I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇
doi.org/10.1093/jaca...

We have a fully funded PhD studentship available @modmedmicro.bsky.social in Oxford to work on a really cool project looking at population heterogeneity in bloodstream infections www.ndm.ox.ac.uk/study/dphil-... Please spread the word/get in touch if you'd like to chat.

Now published in @natcomms.nature.com 🎉

www.nature.com/articles/s41...

With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!

Photo of the Modernising Medical Microbiology Green Team wearing protective clothing, helmets, and safety goggles at the Ardley Energy Recovery Centre during their field trip to see first hand how Oxfordshire waste is burned, instead of ending up in landfill, to generate electricity.

🧪 ♻️ Want to make lab and computational research more sustainable? Check out our Oxford Climate Society blog post:
oxfordclimatesociety.com/blog/from-pi...
Shout out to Green Team colleagues @modmedmicro.bsky.social for helping! #LEAFAward #GreenDiSC #GreenImpact #SustainableScience

From Pipettes to Pipelines — Oxford Climate Society Dorottya Nagy writes about the experiences from the Modernising Medical Microbiology (MMM) Unit research group on engaging wet lab, computer lab, and office teams on the sustainability agenda.

From Pipettes to Pipelines: Greening a Multidisciplinary Research Lab.

@dotnagy.bsky.social writes about the experiences from the Modernising Medical Microbiology (MMM) research group on engaging wet lab, computer lab, and office teams on the #sustainability agenda.

#GreenLab #SustainableScience

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies ('Nanopore') long-read only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance...

Great new work from #DotNagy @modmedmicro.bsky.social - she tool 96 clinical isolates from the NEKSUS study and sequenced with both Illumina and Nanopore - question was, can we do away with hybrid sequencing for the rest of the study?
www.biorxiv.org/content/10.1...