This citizen science project is part of a larger project developing a new way of diagnosing infections resistant to antibiotics and brings together researchers from Medical Sciences, Physics and Oxford University Hospitals NHS Trust and is funded by the Oxford Martin School.
From 5-7pm you can find out more about some of the projects through Science on the Sofa where Oli Moore will talk to some of scientists behind the different public engagement projects on display during the day, including our very own Carla Wright and Emma Pritchard!
You can register to attend in person, or follow the livestream, via this link.
Read the first scientific paper published in eLife. Anyone can go to the website and read it, there is no paywall.
Each image is looked at by up to 17 different citizen scientists — in this paper we show that taking the median of these classifications is both reproducible and accurate.
In fact, if you apply the criteria defined by the relevant ISO standard their results are sufficient accurate but not quite reproducible enough to qualify as an Antibiotic Susceptibility Testing device.
Professor Sarah Walker has been Principal Investigator of the ONS Covid Infection Survey since it started in April 2020. By regularly testing random samples of the UK population for infection and Covid antibodies, this has provided hugely valuable information as the Covid pandemic has progressed and has helped inform public health policy.
You can listen to her talk about the survey in the first episode of the new Statistically Speaking podcast by the Office of National Statistics (ONS), along with other people heavily involved in the survey.
Listen to Professor Tim Peto be interviewed on Radio 4’s PM programme about the UK validation of SARS-CoV-2 lateral flow tests. You’ll need to go to about 15 minutes in to hear the start of the piece.
You can hear the CRyPTIC Principal Investigator, Prof Derrick Crook, talking about the project and its impact on tuberculosis on News Hour on the BBC World Service here. The segment starts about 35 minutes in. You will need a BBC login so this link may not work for everyone.
The CRyPTIC project, which is coordinated by us (Derrick Crook is the Principal Investigator) has released the largest ever global study of tuberculosis aimed at identifying all the genetic variants responsible for antibiotic resistance.
The Comprehensive Resistance Prediction for Tuberculosis International Consortium (CRyPTIC) research project has collected the largest ever global dataset of clinical M. tuberculosis samples from across the world consisting of 15,211 samples from 27 countries on five continents.
Using two key advances: a new quantitative test for drug resistance and a new approach which identifies all the genetic changes in a sample of drug-resistant TB bacteria the researchers have generated a unique dataset which the team has used to quantify how changes in the genetic code of M. tuberculosis reduce how well different drugs kill these bacteria that cause TB. These innovations, combined with ongoing work in the field, promise to profoundly improve how patients with TB are treated in the future.
Tuberculosis kills more people each year than any other bacterium, virus, or parasite, except for SARS-CoV-2. Although it is treatable, drug resistance has emerged as a major problem over the past 3 decades. Testing for mutations in the M. tuberculosis genome to determine which drugs will give a patient the best chance of cure is the most realistic way of getting drug resistance testing to every patient who needs it.
“This innovative, large-scale, international collaboration has enabled us to create possibly the most comprehensive map yet of the genetic changes responsible for drug resistance in tuberculosis.”Dr. Derrick Crook, Professor of Microbiology at the University of Oxford.
In a series of nine new preprint manuscripts, each documenting a different aspect of how the CRyPTIC project has advanced the field, the researchers reveal:
- How the new drug resistance tests should be interpreted and how a massive citizen science project helped solve this problem
- How a new approach to detecting and describing genetic changes in the whole TB genome sequence improved the way genetic changes driving drug resistance can be detected
- How these data were used to scan the TB genome sequence for changes not previously known to cause drug resistance
- How individual mutations, and combinations of mutations, can be related not just to blunt measures of ‘resistance’ or ‘susceptibility’, but also to even minor changes in the way a drug kills M. tuberculosis, thereby reducing the effectiveness of treatment with special attention being paid to two novel compounds being used to treat tuberculosis.
- How artificial intelligence can predict drug resistance from signatures in the DNA sequence
- How these data contributed to the first list of drug resistance mutations in the TB genome to be endorsed for global use by the World Health Organization
These results aim to help improve control of tuberculosis and facilitate the World Health Organisation’s end TB strategy through better, faster and more targeted treatment of drug-resistant tuberculosis via genetic resistance prediction, paving the way towards universal drug susceptibility testing (DST).
“Our ultimate goal is to achieve a sufficiently accurate genetic prediction of resistance to most anti-tuberculosis drugs, so that whole genome sequencing can replace culture-based DST for TB. This will enable rapid-turnaround near-to-patient assays to revolutionise MDR-TB identification and management.”Professor Derrick Crook
The data, which are now freely available, can be used by the wider scientific community to improve our understanding of drug resistance in TB and how to best treat this important disease.
The work of Prof Crook’s team is supported through the NIHR Oxford Biomedical Research Centre’s Antimicrobial Resistance and Microbiology Theme.
The first scientific paper investigating how we can best use all the classifications done by our volunteers is now available for anyone to download and read here.
If you like it, please retweet one of @BashTheBug’s tweets about it.
Note that since it is only considering about 20% of the full dataset you might not find your name on the montage of volunteers in Figure S1 — don’t worry there will be other papers!
This is a “preprint” which means whilst we have written the manuscript it hasn’t yet been reviewed by several other independent scientists which will happen when we submit it to a scientific journal for consideration. It is free to download and when it is published in a scientific journal it will also be free to download, thanks to support from the Wellcome Trust.