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antimicrobial resistance citizen science clinical microbiology publication research tuberculosis

New publication: BashTheBug works!

Yesterday eLife published the first paper from our citizen science project, BashTheBug, which was launched in April 2017 on the Zooniverse platform. Through BashTheBug we asked for volunteers to classify images of M. tuberculosis growing on a range of concentrations of 13 different antibiotics. The images were derived from photographs of 96-well plates taken after […]

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clinical microbiology computing gpas

New publication: fast human read decontamination for SARS-CoV-2

ReadItAndKeep is a new human-read decontamination algorithm that works by mapping the reads in a FASTQ file to the reference SARS-CoV-2 genome. This works because SARS-CoV-2 genetic variation is not so high as to lead to reads being incorrectly discarded and means the algorithm, which relies on minimap2, is both fast and has a low […]

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group

Group photo

From left to right: Dylan, Alice, Charlotte, Matty and Phil (Viktoria had only just left the month before) See Members page.

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antimicrobial resistance citizen science clinical microbiology tuberculosis

New refereed preprint: BashTheBug

BashTheBug is a citizen science project hosted on the Zooniverse platform that we launched in April 2017 and asked volunteers to help us assess how well 20,637 clinical samples of M. tuberculosis grow on one of 13 different antibiotics. To help engage with the volunteers it has its own blog, that has grown into the […]

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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 […]

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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.

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Uncategorised

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 […]

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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 […]

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group

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.

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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 […]