Category: publications
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CRyPTIC ECOFF/ECV paper attracts two letters
The paper we, as a consortium, published last year in Eur Rest J, described the ECOFF/ECV values we had determined for research use. The Editor received two letters about our paper which you can read here and here. Our response is here.
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Two new publications: Data compendium and GWAS
These two papers, just published in PLoS Biology, are amongst the primary research outputs of the CRyPTIC project. The first, entitled “A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics” describes in detail the large dataset of clinical tuberculosis isolates collected by CRyPTIC, including examining the probability of a sample…
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CRyPTIC papers covered by CIDRAP
The Center for Infectious Disease Research and Policy (CIDRAP) has written a news story on the two CRyPTIC papers recently published in PLoS Biology. Click here to read more.
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New publication: BashTheBug!
We enlisted citizen scientists to help us classify the many thousands of photographs of the different samples of M. tuberculosis collected by CRyPTIC growing on different concentrations of antibiotics by launching the BashTheBug project on the Zooniverse platform back in April 2017. In this paper, published in eLife, we investigate how to form a consensus from the many classifications made by the volunteers and…
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Press release – Largest ever global study of tuberculosis identifies genetic causes of drug resistance
Using cutting-edge genomic sequencing techniques, researchers at the University of Oxford have identified almost all the genomic variation that gives people resistance to 13 of the most common tuberculosis (TB) drug treatments. The Comprehensive Resistance Prediction for Tuberculosis International Consortium (CRyPTIC) research project has collected the largest ever global dataset of clinical M. tuberculosis samples…
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New publication: Structure of MmpL3 protein
Oliver Adams, as part of his DPhil studies in Simon Newstead’s group at the University of Oxford, has resolved the structure of MmpL3 which is the only essential member of the mmpL family of genes. It is a mycolic acid transporter that is targeted by a number of antituberculars under active development, for example SQ109 which is in Phase 3 clinical trials. This…
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WHO tuberculosis mutation catalogue released
Last Friday 25 June 2021, the World Health Organization released their first report containing a catalogue of mutations in Mycobacterium tuberculosis and their association with drug resistance. The CRyPTIC project shared its large and comprehensive dataset, as well as providing its genetic processing pipeline, to the group compiling that data and producing the report. We are very pleased that…
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New preprint: Deciphering bedaquiline and clofazimine resistance in tuberculosis
Stefan Niemann, a CRyPTIC partner, led this combined experimental and modelling study looking at how resistance is conferred to bedaquline and clofazimine in Mycobacterial tuberculosis. The CRyPTIC project provided 14,151 clinical isolates, each with minimum inhibitory concentrations (MICs) to bedaquiline and clofazimine. This dataset was used to pinpoint genetic variation in Rv0678, a transcription regulator of a…
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New preprint: Establishing epidemiological cutoffs for the CRyPTIC UKMYC microdilution plates.
The CRyPTIC project has measured the minimum inhibitory concentrations (MICs) of 20,637 isolates to 13 different anti-TB drugs using a bespoke 96-well broth microdilution plate. These samples were collected by 14 partner laboratories based in 11 countries and span five continents. In this preprint, we use this large dataset to determine epidemiological cutoffs (ECOFF or ECV)…
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New paper: Estimating genetic adaption in 10,000 M. tuberculosis genomes
Daniel Wilson, one of the CRyPTIC partners, has recently published a paper where he introduces a new approach, genomegaMap, which estimates the ratio of non-synonymous to synonymous mutations (usually referred to as dN/dS) at sites across the genome. This ratio can provide important clues to which parts of the genome are under selection pressure, which can lead…