Modernising Medical Microbiology

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...

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1...

Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU.

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

Great new opportunity to work with #Liamshaw and @mutantbug.bsky.social as part of our HPRU collaboration (www.expmedndm.ox.ac.uk/research/hpr...) - sinks, phages, wastewater genomes, novel threat detection bit.ly/45Wcv6I - deadline 14th Sept 👀

Linking life expectancy to the bacteria in our gut: A final year undergraduate project My name is Akika Altman-Chandler, and I just graduated from the University of Oxford with a degree in Human Sciences. For my undergraduate dissertation, I worked with Teresa Street at the Modernisi…

Updated blog link -> bashthebug.net/2025/08/28/l...

#Microbiology #Microbiome #HealthyAging #GutHealth #StudentResearch

Linking life expectancy to the bacteria in our gut: A final year undergraduate project My name is Akika Altman-Chandler, and I just graduated from the University of Oxford with a degree in Human Sciences. For my undergraduate dissertation, I worked with Teresa Street at the Modernisi…

'Linking life expectancy to the bacteria in our gut: A final year undergraduate project'.

Akika investigated how the gut microbiome influences longevity, with fieldwork in Nagano, Japan—home to the country’s longest-living population.

Read the blog post here ➡️
bashthebug.net/2025/08/22/l...

More evidence to support best practice "water-safe" care in healthcare facilities is urgently needed. If you're interested please tap into the @hisinfection.bsky.social Wastewater and AMR Special Interest Collaborative (SPARC) - see you there!

The Sinkbug Survey: Antibiotics, AMR, Chemicals and Plumbing In this episode of Infection Control Matters, Martin Kiernan speaks with Dr. Nicole Stoesser about a large-scale, multi-centre study exploring the role of hospital sink infrastructure in antimicrob…

More discussion about the JHI study with @emrsa15.bsky.social in the Infection Control Matters podcast series infectioncontrolmatters.com/2025/04/02/t...

Survey of healthcare-associated sink infrastructure, and sink trap antibiotic residues and biochemistry, in twenty-nine UK hospitals Hospital sinks are linked to healthcare-associated infections. Antibiotics and chemicals in sink traps can select for pathogens and antimicrobial resistance (AMR). Optimizing sink design and usage can...

This builds on the SinkBug group's earlier work in @thejhi.bsky.social www.journalofhospitalinfection.com/article/S019... where we showed that sink infrastructure in hospitals was common, highly varied, and that antibiotics were detected in a third of sink-traps.

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.

Wellcome Connecting Science hybrid conference Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies Conference dates: 23–25 March 2026 Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online Bursary deadline: 01 December 2025 Abstract deadline: 15 December 2025 Registration deadlines: In person: 24 February 2026 | Virtual: 17 March 2026

Participate at our global conference on Antimicrobial Resistance🧬

🗓️ 23-25 March 2026 #AMR2026

Join a community at the vanguard of #AMR genomics, to explore how big data and innovative technologies are driving solutions to tackle this health crisis.

📎Abstracts welcome: bit.ly/3SWzJUm
#MicroSky

Bit over 24 hours left to apply for these two posts to help us develop pipelines to process pathogens..!

Senior Bioinformatic Engineer
bit.ly/4ecl0hF

Senior Biostatistical Researcher
bit.ly/4kRfZxI

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

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

Three posts all closing next week!

Senior Biostatistical Researcher bit.ly/4kRfZxI
Senior Bioinformatic Engineer bit.ly/4ecl0hF
both Grade 8 or 7, closing noon Wed 2 Jul

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

@medsci.ox.ac.uk

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

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

@modmedmicro.bsky.social

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

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

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

poster of event

Come along to Oxford’s Westgate Centre on Thursday 29 May for our Health Research Showcase, held jointly with @oxhealthbrc.bsky.social. It's a fantastic and fun way to find out about the research taking place in Oxford. oxfordbrc.nihr.ac.uk/brc-event/he... @ouhospitals.bsky.social @medsci.ox.ac.uk

Kevin Yuan talking now at #ESCMIDGlobal in Hall 9!