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antimicrobial resistance clinical microbiology publication tuberculosis

New publication: reply to letters about CRyPTIC ECOFF/ECVs

Last year, the CRyPTIC Consortium published a detailed study establishing epidemiological cutoff values (ECOFFs or ECVs) so that it could binarise the minimum inhibitory concentrations it measured for 13 antibiotics for over 15,000 samples of M. tuberculosis collected worldwide. This paper attracted two letters to the editor of the journal, Eur Resp J, which you […]

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New publication: detecting minor populations important for predicting fluoroquinolone resistance

When predicting if an infection is resistant or susceptible to a specific antibiotic, it is all too easy to think that the infection is homogeneous and, in fact, many bioinformatic variant callers encourage that point of view. Or, at best, you can subvert the format of, say, a variant call file (VCF) by using the […]

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antimicrobial resistance clinical microbiology publication research tuberculosis

New publication: determining novel mechanisms of bedaquiline resistance

A new paper with Lindsay Sonnenkalb as first-author has just been published in The Lancet Microbe. It is a collaboration between a ¬†number of groups, led by Stefan Niemann and in it we evolved resistance to bedaquiline in vitro. Sequencing revealed 265 genetic variants with 250 affecting Rv0678, which is the transcription regulator of mmpL5, […]

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DPhil in Computational Discovery

I have a project advertised as part of the DPhil in Computational Discovery programme at the University of Oxford to start in October 2023. This programme is jointly run with IBM and benefits from their applied research in machine learning and other shared areas of interest. The project (Project 6) aims to develop graph-based convolutional […]

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Congratulations Dr Brankin!

Alice successfully defended her thesis “Predicting Fluoroquinolone Resistance in¬†Mycobacterium tuberculosis” yesterday. Her examiners were Professor Philip Biggin and Dr Esther Robinson. Much of Alice’s research was done during various SARS-CoV-2 lockdowns and I doubt she thought at the start she’d be using Microsoft Teams so much. Despite this she has produced some excellent research and […]

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Philip Fowler appointed as Associate Professor

More good news for the group! Philip was awarded an Associate Professorship by the Nuffield Department of Medicine along with two other researchers.