New paper: how well can we predict AMR in tuberculosis samples? This paper just published in Microbial Genomics examines how well our software tool, gnomonicus, predicts to which antibiotics a clinical sample that has been whole-genome sequenced is resistant. To do so, it implements the second…

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

New preprint: Predicting pyrazinamide resistance in M. tuberculosis using a graph convolutional network In previous work we've used "traditional" machine-learning approaches, like XGBoost, to learn and therefore predict which mutations in PncA confer resistance to pyrazinamide, one of the four…

New paper: Evaluating 12 WGS analysis pipelines for MBTC Ruan Spies did a careful systematic analysis of the publicly-available pipelines that claimed to process raw genetics files from M. tuberculosis complex samples, including the pipeline available via EIT's GPAS which we have written. The…

Dylan’s bedaquline paper one of the most read in Microbial Genomics in September! Received a lovely email from Dr Peter Cotgreave who is the Chief Executive of the Microbiological Society to say Dylan's manuscript where he created a resistance catalogue for bedaquiline was one of the most viewed…

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

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 you want to know more…

New preprint: rapidly and reproducibly building resistant catalogues for M. tuberculosis The CRyPTIC project carried out many exciting research projects but it never quite got around to building a catalogue of resistance- and susceptible-associated genetic variants in M. tuberculosis, in part…

New paper: predicting rifampicin resistance via free energy simulation This work was carried out by Xibei Zhang, who is doing her PhD with Peter Coveney at UCL. It builds on earlier work I did using alchemical free energy methods to calculate whether individual mutations in the protein target of…

CRyPTIC datasets available through new website The CRyPTIC project ran from 2016 to 2022 and collected >20,000 clinical samples from patients with tuberculosis. Each sample underwent whole genome sequencing and also was inoculated onto a 96-well plate containing 13 different antibiotics at a range…

Third Dx4LMICs conference Most of us attended the third Diagnostics for Low- and Middle-Income Countries (Dx4LMICs) conference at Reuben College in Oxford over the last two days. I am a Fellow at Reuben College and helped our President, Professor Lord Lionel Tarassenko and several others,…

CRyPTIC datasets available through new website The CRyPTIC project ran from 2016 to 2022 and collected >20,000 clinical samples from patients with tuberculosis. Each sample underwent whole genome sequencing and also was inoculated onto a 96-well plate containing 13 different antibiotics at a range…

I’m hiring! Thanks to funding from the OxCoD4TB project, I am hiring a postdoctoral research associate. This consortium pulls together expertise from all over the University, including in diagnostics, data science, drug and vaccine design, preclinical testing and clinical testing and brings it to…

New paper: a deep learning model that reads MICs from images of 96 well plates Our paper describing how a convolutional neural network model can determine the minimum inhibitory concentrations (MICs) from a photograph of the 96-well plate after two weeks incubation has been published in the…

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

ESM Annual Congress 2025 Several of us attended the 45th Annual Congress of the European Society of Mycobacteriology in Lisbon, Portugal. This is probably my favourite scientific meeting -- small, friendly and with plenty of time to talk, including organised social events. Viki Brunner, Dylan…

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

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

Another busy day at #ESCMIDGlobal! 0906 @vbrunner.bsky.social “RIF and subpopulations in TB” 0918 Ruan Spies “comparing TB pipelines" both in Hall 5 1000 Nicole Stoesser “plasmids & 1Health” in H2 1509 Jane Wei in Hall 2 “CAP and EHR” P1405 - Valentina Pennetta P2242 - Junko Takada

📢 Our preprint on rifampicin resistant subpopulations in clinical samples of M. tuberculosis has just been uploaded. We show how detection of resistant subpopulations can significantly improve WGS-based resistance prediction, and how they can help identify the source of resistance.

New preprint: looking at rifampicin-resistant subpopulations in clinical samples Since clinical samples are usually grown in a MGIT tube for a while before some "crumbs" are harvested for DNA extraction, they are metagenomic in the sense that they can and do contain multiple colonies. This means…

New grant: Ox4TB Very pleased to announce that I am a co-investigator on the recently announced Oxford4TB project that has been funded by the Ineos Oxford Institute for antimicrobial research (IOI). The project will received £5 million over three years and the main aim is to develop new therapies…

Can medical microbiology become a big data science? Lessons from CRyPTIC The CRyPTIC project ran from 2017 to around 2022 and in that time collected over 20,000 clinical samples of M. tuberculosis. Each sample underwent whole genome sequencing and phenotypic drug susceptibility testing (pDST); the…

New preprint: a deep learning model that can read 96-well broth micro dilution plates The CRyPTIC project used bespoke 96-well broth microdilution plates to measure the minimum inhibitory concentrations (MICs) of 13 different antibiotics; to reduce the error in the measurements, photographs of…

New preprint: automatically building a better bedaquiline catalogue A catalogue recording whether individual mutations confer resistance or not to specified antibiotics is a necessary component of genetics-based clinical microbiology. Such catalogues need to be not only accurate but also meet a…

SARS-CoV-2 pipeline live on EIT Pathogena Back in the SARS-CoV-2 pandemic we worked closely with ORACLE Corp to build and deploy a bioinformatics pipeline in ORACLE Cloud that processes raw genetic files and infers what the consensus genome is and hence what lineage (e.g. BA.2) it belongs to. The…

Updated preprint: A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology fowlerlab.org/2025/01/23/u...