In this preprint, the CRyPTIC project proposes the maximum value of minimum inhibitory concentration (MIC) for 13 different anti-TB drugs below which a sample can be considered to be ‘genotypically wild-type’. It is necessary to establish these values, called epidemiological cutoff values (ECOFFs or ECVs), so that the MICs measured can be converted into binary […]
Come and work with me on antimicrobial resistance! Advert here. Broadly the idea is to develop our work using machine learning and molecular simulation to predict whether individual bacterial protein mutations confer resistance to an antibiotic (or not). Any questions please get in touch. For more details please see the advert, especially the lists of […]
A second Covid-19 publication I’m proud to be (a small) part of has recently published been in the New England Journal of Medicine. Given the Oxford University Hospital’s Staff Covid testing has been running for months, as described in our first publication, the team was able to show that having antibodies led to a substantially […]
Very pleased and proud to be included on this manuscript, which has been published in eLife (and is also available as a preprint); the observations are drawn from the large and comprehensive SARS-CoV-2 testing programme run by Oxford University Hospitals NHS Trust. I helped develop the internal website used by staff to book appointments and […]
Clinical microbiology often assumes a sample is resistant or susceptible. Making such a classification relies on applying a threshold (usually called a cutoff) to quantitative data, such as minimum inhibitory concentrations (MICs). If the MICs are strongly bimodal, then this is trivial and reproducibility is guaranteed. If the MICs are unimodal, then one is left […]
Although the population structure M. tuberculosis is clonal, one must be careful when inferring the effect of individual mutations on the effect of an antibiotic. Purely because a mutation appears to define a phylogeny does not mean it has no effect on the minimum inhibitory concentration. Read more here (Open Access).