The story behind this preprint goes back to the workshop on free energy methods run by BioExcel in Göttingen in May 2019. I gave a talk, based in part on the work I’d previously published showing how alchemical free energy methods are able to predict which mutations in S. aureus DHFR confer resistance to trimethoprim.
We are advertising for a Part-time Citizen Science Project Co-ordinator to come and work with us in Oxford improving BashTheBug, in particular how the project engages, informs and educates its existing base of volunteers, as well as reaching out to new audiences. The closing date is Monday 25 November 2019. For more information please see […]
Usually, the protein that an antibiotic binds is essential for bacterial survival, which is how the drug has its effect. In this case, relatively few protein mutations arise that confer resistance, they are often subtle in nature and one can try to predict the phenotype of a protein mutation by considering how it affects the […]
During the CRyPTIC project it has become obvious that we need a grammar to describe genetic changes that is readable by both human and code and avoids confusion but also allows for the rather sophisticated rules that are currently being developed. For example, in the supplement of the recent publication of the now-quite extensive genetic resistance […]
In this Microbiology paper we show how a Python package, called the Automated Mycobacterial Detection Growth Algorithm (AMyDGA for short), can be used to independently read a 96-well plate designed for determining the minimum inhibitory concentration of 14 different anti-tubercular drugs. AMyGDA is reproducible and shows promising levels of accuracy. Where it fails, it does in […]
BashTheBug, a citizen science project I run that is helping us measure how different clinical samples of M. tuberculosis grow in the presence of 14 different antibiotics, reached its first million classifications earlier this week. To read more head over to its blog. The photo mosaic on the left is made up of images […]
A paper was published in the New England Journal of Medicine earlier this week by the CRyPTIC project, of which I am part, with help from the 100,000 genomes project. It demonstrates how whole genome sequencing can be used to accurately predict drug susceptibility for the four first-line anti-tubercular drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) […]
This paper, published in Antimicrobial Agents and Chemotherapy, determines the reproducibility and accuracy of minimum inhibitory concentrations for a panel of 14 different anti-TB compounds using a specifically designed 96-well plate (called UKMYC5) manufactured by Thermo Fisher.
Last year I coordinated a bid to the NIHR for capital to improve our research capacity to study antimicrobial resistance (AMR) at the Oxford Biomedical Research Centre. We were successful and were awarded £1.8 million to fund several different activities, including developing vaccines to prevent the spread of AMR. Previously in the John Radcliffe […]
I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC), that is collecting 30-50,000 clinical samples from patients with tuberculosis (TB). Although often viewed as a historical disease, TB kills more people globally than any other infectious disease, with 1.7 million people dying from it in 2016. The ultimate […]