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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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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 ┬ánumber 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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antimicrobial resistance group meetings tuberculosis

Viki Brunner wins poster prize

The whole group attended the first INEOS Oxford Institute meeting on Multidisciplinary Approaches to AMR on Tuesday 22 November 2022. Great to hear how different research groups around Oxford (and elsewhere) are helping to tackle AMR. Best of all though, Viki Brunner won one of the poster prizes for her poster on Compensatory mutations in […]

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antimicrobial resistance clinical microbiology publication research tuberculosis

New preprint: Including minor alleles improves fluoroquinolone resistance prediction

Fluoroquinolones are used to treat both normal and drug resistant tuberculosis and therefore being able to work out if an infection is resistant or not to fluoroquinolones is very important. Sequencing the genome of an infection is increasingly used to rapidly return which antibiotics could be used to treat a patient with tuberculosis. Genetics-based approaches […]

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antimicrobial resistance computing molecular dynamics tuberculosis

New publication: Predicting antibiotic resistance in complex protein targets using alchemical free energy methods

In this paper, Alice Brankin calculates how different mutations in the DNA gyrase affect the binding of an antibiotic, moxifloxacin, and thereby potentially whether those mutations confer resistance or not. She calculates the relative binding free energy using thermodynamic integration, a method that is derived from classical statistical mechanics. To accompany these results, Philip Fowler, […]

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antimicrobial resistance clinical microbiology tuberculosis

New publication: CRyPTIC Data Compendium

The large and comprehensive dataset of clinical tuberculosis isolates collected by the CRyPTIC project is described in detail by this paper, just published in PLoS Biology. Each isolate was whole genome sequenced and had its minimum inhibitory concentration to 13 different antibiotics measured using a bespoke 96-well broth microdilution plate. Alice Brankin, along with Kerri […]