Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes

In vitro antibiotic testing is important for guiding therapy and drug development. Current methods are focused on growth inhibition in bulk bacterial populations but often fail to accurately predict treatment responses. Here we introduce Antimicrobial Single-Cell Testing (ASCT), a large-scale live-cell imaging approach that quantifies bacterial killing in real time at single-cell resolution. By tracking over 140 million mycobacteria and analysing ~20,000 time-kill curves, we identify key determinants of antibiotic killing and its clinical relevance. For Mycobacterium tuberculosis, we found that drug-specific killing dynamics in starved bacteria, rather than growth inhibition or killing of growing cells, predict regimen efficacy in mice and humans. Extending this approach to Mycobacterium abscessus and comparing 405 bacterial strains, we show that antibiotic killing is also a genetically encoded bacterial trait (drug tolerance). We demonstrate that tolerance patterns cluster by antibiotic targets, identify a phage protein that modulates antibiotic killing, and show that strain-specific killing dynamics are associated with individual patient outcomes independent of drug resistance. Together, these findings establish a framework that reveals how drug properties and bacterial diversity shape treatment responses, offering a path to more effective and personalized therapies.

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Publication Details

Journal
Nature Microbiology
Published
2026-01-09
DOI
https://doi.org/10.1038/s41564-025-02217-y
Citations
2
Primary Topic
Cell Image Analysis Techniques
Type
article
Field-Weighted Citation Impact
73.59
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article

Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes

Basil Wicki, Scott C. Bell, Loïc Sauteur, Johannes Nemeth et al.
2 citations
Nature Microbiology
Cell Image Analysis Techniques
73.59
article

Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes

Basil Wicki, Scott C. Bell, Loïc Sauteur, Johannes Nemeth, Lucas Boeck, Andréanne Lupien, Dorothy Grogono, Andreas M. Wüst, Nicole E. Wheeler, Gagneux Sebastien, Josephine M. Bryant, Frederick K. Bright, Sònia Borrell, Alexander Jovanovic, Philippe Dehio, Santiago E. Caño Muñiz, Anna Rodoni, Hans Pargger, Rachel Thomson, Ahmad Sadeghi, Michael Abanto, R. Andres Floto, Sara Toprak, Andreas H. Diacon, Greta C. Giannini
article en
2 citations

Abstract

In vitro antibiotic testing is important for guiding therapy and drug development. Current methods are focused on growth inhibition in bulk bacterial populations but often fail to accurately predict treatment responses. Here we introduce Antimicrobial Single-Cell Testing (ASCT), a large-scale live-cell imaging approach that quantifies bacterial killing in real time at single-cell resolution. By tracking over 140 million mycobacteria and analysing ~20,000 time-kill curves, we identify key determinants of antibiotic killing and its clinical relevance. For Mycobacterium tuberculosis, we found that drug-specific killing dynamics in starved bacteria, rather than growth inhibition or killing of growing cells, predict regimen efficacy in mice and humans. Extending this approach to Mycobacterium abscessus and comparing 405 bacterial strains, we show that antibiotic killing is also a genetically encoded bacterial trait (drug tolerance). We demonstrate that tolerance patterns cluster by antibiotic targets, identify a phage protein that modulates antibiotic killing, and show that strain-specific killing dynamics are associated with individual patient outcomes independent of drug resistance. Together, these findings establish a framework that reveals how drug properties and bacterial diversity shape treatment responses, offering a path to more effective and personalized therapies.

Nature MicrobiologyVol. 11(2)
Griffith University (AU), University of Ulster (GB), Swiss Tropical and Public Health Institute (CH), The University of Queensland (AU), MRC Laboratory of Molecular Biology (GB), University of Basel (CH), University of Cambridge (GB), Royal Papworth Hospital (GB), Gold Coast Hospital (AU), Greenslopes Private Hospital (AU), McGill University Health Centre (CA), Wellcome Sanger Institute (GB), University Hospital of Basel (CH), Center for Environmental Health (US), Helmholtz Zentrum München (DE), Task Applied Science (ZA), University Hospital of Zurich (CH), Gallipoli Medical Research Foundation (AU), Department of Biomedicine Basel (CH), Royal Victoria Hospital (GB), McGill University (CA), University of Birmingham (GB)
Good health and well-being
Openalex Percentile: Top 0%
Cell Image Analysis Techniques
73.59
DOIOpen Access PDFOpenAlex
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