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…

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 In August 2022 seven laboratories across the world uploaded their SARS-CoV-2 genetics files for processing to an online cloud processing platform. Since then the pipeline that is run (the Tiled Amp…

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...