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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 […]

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antimicrobial resistance clinical microbiology tuberculosis

New publication: CRyPTIC GWAS of antitubercular resistance

Since the primary goal of CRyPTIC was to map the genetic variants in M. tuberculosis associated with resistance to different antibiotics, this genome-wide association study is one of the key research outputs of the project. It brings together all the samples with genetic and drug susceptibility testing (DST) data and therefore relies on all the […]

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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. (Update on 19 July 2022: the final formatted version of the paper has been posted on eLife). Through BashTheBug we asked for volunteers to classify images of M. tuberculosis growing on a range […]

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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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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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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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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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antimicrobial resistance clinical microbiology computing grants research tuberculosis

Postdoctoral position advertised

Through the CompBioMed2 EU Centre of Excellence project I have funding to appoint a postdoctoral researcher to develop machine-learning models to predict whether an infection is susceptible to an antibiotic. The need for predictive methods, such as these, will grow in the coming years as more of clinical microbiology transitions to using genetics to infer […]

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antimicrobial resistance clinical microbiology computing distributed computing grants

GPAS

I’ve been working on this for the last few months and very happy that we can now share our plans. Through a very generous donation by ORACLE, a group of researchers led by ModMedMicro at Oxford, are developing a cloud-based clinical microbiology genetics processing service, called the Global Pathogen Analysis System (GPAS). GPAS is still […]

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antimicrobial resistance clinical microbiology publication

New preprint: Deciphering bedaquiline and clofazimine resistance in tuberculosis

In this preprint we examine 14,151 clinical isolates drawn from the CRyPTIC dataset. Each isolate had its minimum inhibitory concentration (MIC) to bedaquiline and clofazimine measured and hence we were able to identify the transcription regulator Rv0678, as the current main source of elevated MICs to both these drugs. Lindsay┬áSonnenkalb, who is studying for her […]