Skip to content
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

  • News
  • Research
    • Overview
    • Manifesto
    • Software
    • Reproducibility
    • Publications
  • Members
  • Teaching
  • Contact
    • PhDs
  • Wiki
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

CRyPTIC datasets available through new website

Philip Fowler, 25th June 20257th July 2025

The CRyPTIC project ran from 2016 to 2022 and collected >20,000 clinical samples from patients with tuberculosis. Each sample underwent whole genome sequencing and also was inoculated onto a 96-well plate containing 13 different antibiotics at a range of concentrations. We also collated some existing datasets and the project continued to collect data following the original data freeze in April 2020. We’ve also made extensive improvements to how both the genetics and plate images are processed.

Hence although the original dataset is available through an FTP site hosted at the European Bioinformatics Institute, we now have a larger dataset available which has benefited from several improvements that I won’t go into here. These have been deposited in Zenodo and at the time of writing the current version is v3.4.0 and contains 53,897 samples with both genetic and drug susceptibility testing data. To give these data some context I’ve setup a new CRyPTIC project website to replace the one that unfortunately died last year.

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 tuberculosis

Post navigation

Previous post
Next post

Related Posts

antimicrobial resistance

New paper: automatically and reproducibly building a catalogue bedaquline resistance-associated variants

18th June 20251st July 2025

Dylan Adlard‘s paper describing how we can rapidly automatically build catalogues of bedaquiline resistance-associated variants…

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

New refereed preprint: BashTheBug

31st March 202231st March 2022

BashTheBug is a citizen science project hosted on the Zooniverse platform that we launched in…

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

New software: pygsi

31st August 2018

Whenever a paper involving sequencing the genome of bacteria (or other species for that matter),…

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

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Privacy & Cookies: This site uses cookies. By continuing to use this website, you agree to their use.
To find out more, including how to control cookies, see here: Cookie Policy
    ©2025 Fowler Lab | WordPress Theme by SuperbThemes