New paper: predicting pyrazinamide using a graph convolutional network This paper is the start of us, as a group, using deep learning methods to predict antimicrobial resistance whilst taking into structural and chemical features. You can read a more detailed description in an earlier post and notably it is our first paper in a special issue for a while. Dylan Dissanayake did the research and was helped by Viki Brunner and Dylan Adlard, along with Joe Morrone from IBM Research.

New paper: predicting pyrazinamide using a graph convolutional network

This paper is the start of us, as a group, using deep learning methods to predict antimicrobial resistance whilst taking into structural and chemical features. You can read a more detailed description in an earlier post and…

Congratulations Dr Adlard! Dylan successfully defended his DPhil on Friday 6 March, well done. From what he said his examiners, Professor Sam Sheppard and Associate Professor Louis Grandjean gave his work a thorough examination. As luck would have it we received the reviews from the last manuscript to come out of his thesis the day before..

Congratulations Dr Adlard!

Dylan successfully defended his DPhil on Friday 6 March, well done. From what he said his examiners, Professor Sam Sheppard and Associate Professor Louis Grandjean gave his work a thorough examination. As luck would have it we received the reviews from the last…

New preprint: comparing long- and short-read sequencing of Mycobacteria

In this preprint, we compare the differences when Mycobacterial samples are sequenced with either long- or short-read sequencing and show that long-read sequencing (as exemplified by Oxford Nanopore Technologies) is now…

New paper: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny Zam Iqbal, at the University of Bath, led this epic study published today in Nature Methods where we assembled all SARS-CoV-2 genomes deposited in the European Nucleotide Archive before 2 March 2023. In total a staggering 4,395,655 samples were processed. Since SARS-CoV-2 was almost always sequenced using tiled amplicons (e.g. ARTICv3), he and his team wrote viridian which is a variant caller that identifies the amplicon scheme used and then uses that information to avoid making spurious calls.

New paper: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Zam Iqbal, at the University of Bath, led this epic study published today in Nature Methods where we assembled all SARS-CoV-2 genomes deposited in the European Nucleotide Archive before 2 March 2023. In total a…

Gr-ADI consortium announced

Pleased and excited to be a small part of the Gram-Negative Antibiotic Discovery Innovator (Gr-ADI) consortium which was announced today. Gr-ADI is a join initiative between the Gates Foundation, Novo Nordisk Foundation, and Wellcome. Our project is headed by Dr Annette…

Congratulations Dr Brunner! Viki successfully defended her DPhil thesis on Tuesday 9 December 2025 - well done! I always tell everyone they will enjoy the viva after half an hour or so and I hope she did. Her examiners were Professor Tim Walker and Associate Professor Conor Meehan.

Congratulations Dr Brunner!

Viki successfully defended her DPhil thesis on Tuesday 9 December 2025 - well done! I always tell everyone they will enjoy the viva after half an hour or so and I hope she did. Her examiners were Professor Tim Walker and Associate Professor Conor Meehan.

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 edition of the WHO catalogue of resistance-associated mutations (WHOv2) which in turn we had to, in effect, translate from the original Excel and PDF report.

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 first-line antibiotics used to treat tuberculosis. A key limitation is that because the data are presented in a tabular form, one in effect learns mutation-by-mutation rather than allele-by-allele. We can get away with this in…

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: 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

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 please read the blog post we wrote when it was preprinted. A nice touch, however, was that this was just in time for Viki Brunner to include in her thesis as she submitted it the following day!

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 because near the end of the project we donated our entire dataset to the Seq&Treat project who used it to build the first edition of the WHO catalogue of mutations in…

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 an antibiotic reduce how well the drug can bind, thereby conferring resistance. The method was first shown to work on…

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 of concentrations. We also collated some existing datasets and the project continued to collect data following the original data freeze in April 2020.

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, including Dylan Adlard, organise the conference. It was the biggest conference the college has held to date with about 110-120 attendees and we had to close registration a few weeks before and had a waiting list.

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 of concentrations. We also collated some existing datasets and the project continued to collect data following the original data freeze in April 2020.

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 Computational and Structural Biology Journal. You can get the model, which is called TMAS, on GitHub here and there is a longer description here.

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 Adlard and Philip Fowler all had posters and there were another three posters from the MMM Unit. At the least minute we were offered a short ten minute talk as another speaker could not travel so we gladly accepted the chance and Philip Fowler presented some work analysing 56,306 Mycobacterial samples sequenced by UKHSA between 2016 and 2024. The main aim was to develop and validate an approach that can identify the species present.

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 we should expect subpopulations in our analysis but most bioinformatics tools and file formats inherently assume a homogenous sample with a single genome.

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 minimum inhibitory concentrations (MICs) of 13 different antibiotics was tested using a bespoke 96-well broth microdilution plate. The project also aggregated previously published samples which has had pDST data and had undergone WGS.

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…