Note that it is behind a pay wall, but you can always buy a copy of the print edition when it comes out on Friday 23 October 2021!
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.
We gave a talk, “Setting up an online citizen science project on the Zooniverse is easy: the BashTheBug experience” to other researchers at the University of Oxford as part of this week-long online public engagement with research conference. In it, we talk our experiences with BashTheBug and setup live a demo project “Chihuahua or Muffin?”. Although aimed at other researchers, feel free to have a look! You can find the video of our talk here.
We hope you are all well and keeping safe and sane during these trying and daunting times
We wanted to say Thank You!
You have helped BashtheBug reach over 4 million classifications:
Total classifications since the project began: 4, 028, 152
You have looked at over 15,000 samples, which has helped the *CRyPTIC project prepare its first dataset for release, which will form the basis of: several big publications and a number of smaller ones including machine learning, a new catalogue and a genome-wide association study to look for genes that confer resistance no one has noticed yet.
Well done to all our volunteers for making this happening!
*The project is part of the CRyPTIC Comprehensive Resistance Prediction for Tuberculosis: an International Consortium is a world-wide collaboration between tuberculosis (TB) research institutions all over the world to achieve better, faster and more targeted treatment of multidrug-resistant TB via genetic resistance prediction.
In response to the COVID pandemic, UN Environment (UNEP), TED Education, and many other partners and contributors around the world launched Earth School, which aims to give kids, parents, and teachers 30 days of daily “quests,” or curated learning experiences that highlight how we are connected to nature from home. Quests began on Earth Day, April 22nd, and will continue to be released until World Environment Day, on June 5th.
The Citizen Science Quest of Earth School launched on Wednesday 27 May 2020 and BashTheBug was chosen by SciStarter as one of the Citizen Science projects.
Ariel Zych and Diana Montano team from Science Friday hosted a discussion with Philip Fowler (BashTheBug lead), Carla Wright (BashTheBug coordinator) and Helen Spiers (Zooniverse liaison) yesterday on Facebook.
You can watch a recording of the livestream here.
This was a first time the BashTheBug has ever done anything like this, so let us know if you’d like more, or equally if you’d like something different.
Last Friday 24 April 2020, Laura Trouille, who is Co-Principal Investigator for the Zooniverse and Vice President of Citizen Science at the Adler Planetarium, was interviewed on the popular North American radio show, ScienceFriday.
Laura talked about four Zooniverse projects, and BashTheBug was one of them!