A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates

Abstract

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, Using 96-well broth micro dilution plates with each well containing a lyophilised predetermined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11-17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing.

Data availability

The data tables and a Jupyter notebook that allows the user to recreate the majority of figures and tables in both the manuscript and the supplemental information is freely available here: https://github.com/fowler-lab/bashthebug-consensus-datasetIt is setup so a user can either clone the repository and run the jupyter-notebook on their local computer (the installation process having installed the pre-requisites) or by clicking the "Launch Binder" button in the README, they can access and run the jupyter-notebook via their web browser, thereby avoiding any installation.I've added a short statement to the manuscript -- please advise if you think it needs changing.

The following data sets were generated

Article and author information

Author details

  1. Philip W Fowler

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    For correspondence
    philip.fowler@ndm.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0912-4483
  2. Carla Wright

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Helen Spiers

    Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Tingting Zhu

    Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Elisabeth ML Baeten

    Department of Physics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Sarah W Hoosdally

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Ana L Gibertoni Cruz

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9473-2215
  8. Aysha Roohi

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Samaneh Kouchaki

    Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Timothy M Walker

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0421-9264
  11. Timothy EA Peto

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  12. Grant Miller

    Department of Physics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  13. Chris Lintott

    Department of Physics, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  14. David Clifton

    Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  15. Derrick W Crook

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0590-2850
  16. A Sarah Walker

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0412-8509

Funding

Wellcome Trust (200205/Z/15/Z)

  • Philip W Fowler
  • Carla Wright
  • Sarah W Hoosdally
  • Ana L Gibertoni Cruz
  • Aysha Roohi
  • Samaneh Kouchaki
  • Timothy M Walker
  • Timothy EA Peto
  • David Clifton
  • Derrick W Crook
  • A Sarah Walker

Bill and Melinda Gates Foundation (OPP1133541)

  • Philip W Fowler
  • Carla Wright
  • Sarah W Hoosdally
  • Ana L Gibertoni Cruz
  • Aysha Roohi
  • Samaneh Kouchaki
  • Timothy M Walker
  • Timothy EA Peto
  • David Clifton
  • Derrick W Crook
  • A Sarah Walker

Wellcome Trust (203141/Z/16/Z)

  • Philip W Fowler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Version history

  1. Preprint posted: July 21, 2021 (view preprint)
  2. Received: October 28, 2021
  3. Accepted: May 15, 2022
  4. Accepted Manuscript published: May 19, 2022 (version 1)
  5. Accepted Manuscript updated: May 20, 2022 (version 2)
  6. Version of Record published: July 15, 2022 (version 3)

Copyright

© 2022, Fowler et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,084
    Page views
  • 239
    Downloads
  • 5
    Citations

Article citation count generated by polling the highest count across the following sources: PubMed Central, Crossref, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Philip W Fowler
  2. Carla Wright
  3. Helen Spiers
  4. Tingting Zhu
  5. Elisabeth ML Baeten
  6. Sarah W Hoosdally
  7. Ana L Gibertoni Cruz
  8. Aysha Roohi
  9. Samaneh Kouchaki
  10. Timothy M Walker
  11. Timothy EA Peto
  12. Grant Miller
  13. Chris Lintott
  14. David Clifton
  15. Derrick W Crook
  16. A Sarah Walker
(2022)
A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates
eLife 11:e75046.
https://doi.org/10.7554/eLife.75046

Further reading

    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease
    Vanessa Dumeaux, Samira Massahi ... Michael T Hallett
    Research Article Updated

    Candida albicans, an opportunistic human pathogen, poses a significant threat to human health and is associated with significant socio-economic burden. Current antifungal treatments fail, at least in part, because C. albicans can initiate a strong drug tolerance response that allows some cells to grow at drug concentrations above their minimal inhibitory concentration. To better characterize this cytoprotective tolerance program at the molecular single-cell level, we used a nanoliter droplet-based transcriptomics platform to profile thousands of individual fungal cells and establish their subpopulation characteristics in the absence and presence of antifungal drugs. Profiles of untreated cells exhibit heterogeneous expression that correlates with cell cycle stage with distinct metabolic and stress responses. At 2 days post-fluconazole exposure (a time when tolerance is measurable), surviving cells bifurcate into two major subpopulations: one characterized by the upregulation of genes encoding ribosomal proteins, rRNA processing machinery, and mitochondrial cellular respiration capacity, termed the Ribo-dominant (Rd) state; and the other enriched for genes encoding stress responses and related processes, termed the Stress-dominant (Sd) state. This bifurcation persists at 3 and 6 days post-treatment. We provide evidence that the ribosome assembly stress response (RASTR) is activated in these subpopulations and may facilitate cell survival.

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Taylor J Abele, Zachary P Billman ... Edward A Miao
    Research Article

    Pyroptosis and apoptosis are two forms of regulated cell death that can defend against intracellular infection. When a cell fails to complete pyroptosis, backup pathways will initiate apoptosis. Here, we investigated the utility of apoptosis compared to pyroptosis in defense against an intracellular bacterial infection. We previously engineered Salmonella enterica serovar Typhimurium to persistently express flagellin, and thereby activate NLRC4 during systemic infection in mice. The resulting pyroptosis clears this flagellin-engineered strain. We now show that infection of caspase-1 or gasdermin D deficient macrophages by this flagellin-engineered S. Typhimurium induces apoptosis in vitro. Additionally, we engineered S. Typhimurium to translocate the pro-apoptotic BH3 domain of BID, which also triggers apoptosis in macrophages in vitro. During mouse infection, the apoptotic pathway successfully cleared these engineered S. Typhimurium from the intestinal niche but failed to clear the bacteria from the myeloid niche in the spleen or lymph nodes. In contrast, the pyroptotic pathway was beneficial in defense of both niches. To clear an infection, cells may have specific tasks that they must complete before they die; different modes of cell death could initiate these ‘bucket lists’ in either convergent or divergent ways.