New publication: CRyPTIC GWAS of antitubercular resistance Philip Fowler, 16th August 202216th August 2022 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 efforts to reduce the errors in the DST data, for example using AMyGDA to read the photographs of the 96-well plates and the efforts of the BashTheBug volunteers. In addition to associating genes already known to confer resistance to specific antibiotics, putative resistance genes are proposed for each of the thirteen drugs on the UKMYC series of broth microdilution plates. Danny Wilson and Sarah Earle led the GWAS analysis, which is complicated not only by the population structure (lineages) of M. tuberculosis but also by the fact that the resistance to each drug correlates with resistance to other drugs. Our involvement was mainly in improving the quality of the DST data, thereby improving the signal-to-noise ratio. Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance clinical microbiology tuberculosis
antimicrobial resistance New software: gemucator 4th September 20184th September 2018 Short for “Genbank Mutation Locator”. A simple Python3 package that if you pass it a… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance Accelerating Oxford Nanopore basecalling 26th January 20175th August 2018 It looks innocuous sitting on the desk, an Oxford Nanopore MinION, but it can produce… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
Desirable features for any antibiotic resistance catalogue 31st October 202331st October 2023 In the past few years a growing number of catalogues containing mutations associated with resistance… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More