antimicrobial resistance clinical microbiology computing tuberculosis

AMyGDA now available from GitHub

AMyGDA is a python module that analyses photographs of 96-well plates and, by examining each well for bacterial growth, is able to read a series of minimum inhibitory concentrations for the antibiotics present on a plate. Previously it was only available to download from this website (due to licensing) if you gave your email address […]

antimicrobial resistance clinical microbiology computing GPUs molecular dynamics publication research

New preprint: rapid prediction of AMR by free energy methods

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.

antimicrobial resistance citizen science clinical microbiology

BashTheBug Coordinator post advertised

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 […]

antimicrobial resistance molecular dynamics publication

New publication: Predicting resistance is (not) futile

Our “First Reactions” article has been published in ACS Central Science. We discuss the paper, Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches, by Matteo Aldeghi, Vytautas Gapsys and Bert de Groot, which is in the same issue of the journal. Aldeghi et al. apply a series of methods to try and predict the effect […]

antimicrobial resistance tuberculosis

Genetics and Tuberculosis: A Case of New Meets Old

I was very pleased to be invited to contribute to this “Voices” article organised by the journal Cell Host and Microbe. You can read it here.

antimicrobial resistance computing meetings molecular dynamics

BioExcel Alchemical Free Energy workshop

Last month I was invited to give a talk on using alchemical free energy methods to predict antimicrobial resistance at a workshop in Göttingen organised by the Max Planck Institute for Biophysical Chemistry on behalf of BioExcel. You can read more about the meeting, which I hope will become a biennial event, here.

antimicrobial resistance clinical microbiology publication research tuberculosis

New preprint: Predicting pyrazinamide resistance by machine learning

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 […]

antimicrobial resistance clinical microbiology miscellaneous

GARC: A Grammar for Antimicrobial Resistance Catalogues

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 […]

antimicrobial resistance citizen science clinical microbiology publication tuberculosis

New publication: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of M. tuberculosis

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 […]

antimicrobial resistance citizen science clinical microbiology tuberculosis

BashTheBug reaches one million classifications

  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 […]