antimicrobial resistance computing tuberculosis

New software: gemucator

Short for “Genbank Mutation Locator”. A simple Python3 package that if you pass it a mutation it will give you the location in the specified genbank file. > –mutation rpoB_S450L rpoB_S450L: 761153 t 761154 c 761155 g (H37rV.gbk for M. tuberculosis is loaded by default). Or you can go the other way > –location […]

antimicrobial resistance clinical microbiology publication tuberculosis

New publication: Validating a bespoke 96-well plate for high-throughput drug susceptibility testing of M. tuberculosis

This paper, published in Antimicrobial Agents and Chemotherapy, determines the reproducibility and accuracy of minimum inhibitory concentrations for a panel of 14 different anti-TB compounds using a specifically designed 96-well plate (called UKMYC5) manufactured by Thermo Fisher.

citizen science clinical microbiology computing research tuberculosis

Automated detection of bacterial growth on 96-well plates (AMyGDA)

I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC), that is collecting 30-50,000 clinical samples from patients with tuberculosis (TB). Although often viewed as a historical disease, TB kills more people globally than any other infectious disease, with 1.7 million people dying from it in 2016. The ultimate […]

antimicrobial resistance clinical microbiology teaching tuberculosis

2018 PhD projects announced

As described here, one of the main ways of getting funding to studying for a DPhil with me is to apply for an NDM Prize Studentship. There is a competition held each year and the successful applicants have all their fees paid and get a generous £18,000 pa tax-free stipend. The deadline is 12 noon […]

citizen science tuberculosis

BashTheBug has won an NIHR Let’s Get Digital Award!

The National Institute for Health Research hold an annual competition, called Let’s Get Digital, to “recognise those people involved in NIHR research using video, photography, websites, infographics and online communities to promote research”. I was encouraged to enter BashTheBug back in June 2017 and was pleased to see in August that we had been shortlisted […]

antimicrobial resistance clinical microbiology meetings tuberculosis

Twitter at #ECCMID

A bit over two years ago I was a guest blogger at the US Biophysical Society Annual Meeting in Baltimore. I was disappointed by the lack of Tweeting at the conference – there were 208 tweets using the #bps15 hashtag when I wrote a blog post in which I speculated that, one day, there might […]