antimicrobial resistance research tuberculosis

New publication: WHO catalogue of Mycobacterium tuberculosis resistant mutations

The CRyPTIC project collecting over 20,000 clinical samples of TB and for each, sequencing its genome and testing its susceptibility to 13 different antibiotics. A lovely unintended consequence of compiling such a large high-quality dataset is that CRyPTIC was invited to form part of the team that collected data and compiled the first catalogue of […]

clinical microbiology computing gpas

GPAS stopover on the ORACLE road trip

You can listen to Philip Fowler talk about the Global Pathogen Analysis System (GPAS) as part of the ORACLE Road Show by clicking here. We hope in the long term to translate into GPAS the predictive models we are creating for tuberculosis.


New preprint: Rapid decontamination of SARS-CoV-2 genetic reads

This preprint describes some software, ReadItAndKeep, that rapidly removes host (i.e. human) genetic information from a sample. This is necessary to ensure that a sample containing SARS-CoV-2 genetic reads cannot be linked to the individual who gave the sample whilst it is being processed by GPAS in the cloud. Martin Hunt and Zam Iqbal did […]

antimicrobial resistance clinical microbiology computing group molecular dynamics publication research tuberculosis

New preprint: Predicting antibiotic resistance in complex protein targets

In this preprint, which Alice has been working on for several years, we show how alchemical free energy methods can predict whether an amino acid mutation confers resistance to an antitubercular, but only in cases where the change in binding free energy is large. This is mainly because the confidence limits on the change in […]


Alice Brankin wins NDM Prize

Congratulations to Alice who last night was awarded an NDM prize for the work she’s done in the third year of her DPhil! Very well deserved – despite locating away from Oxford due to the pandemic Alice has, amongst other things, become a key member of the CRyPTIC analysis group of the past year.

antimicrobial resistance publication research tuberculosis

New Publication: Structure of MmpL3

Oliver Adams successfully elucidated the structure of the M. tuberculosis MmpL3 membrane transporter using cryo-EM and this has recently been published online in Structure. This was the main aim of his PhD studies in Simon Newstead‘s group in the Department of Biochemistry here in Oxford. It is an important protein structure since although other MmpL3 […]