Single-cell pathogen diagnostics for combating antibiotic resistance

Bacterial infections and antimicrobial resistance are a major cause for morbidity and mortality worldwide. Antimicrobial resistance often arises from antimicrobial misuse, where physicians empirically treat suspected bacterial infections with broad-spectrum antibiotics until standard culture-based diagnostic tests can be completed. There has been a tremendous effort to develop rapid diagnostics in support of the transition from empirical treatment of bacterial infections towards a more precise and personalized approach. Single-cell pathogen diagnostics hold particular promise, enabling unprecedented quantitative precision and rapid turnaround times. This Primer provides a guide for assessing, designing, implementing and applying single-cell pathogen diagnostics. First, single-cell pathogen diagnostic platforms are introduced based on three essential capabilities: cell isolation, detection assay and output measurement. Representative results, common analysis methods and key applications are highlighted, with an emphasis on initial screening of bacterial infection, bacterial species identification and antimicrobial susceptibility testing. Finally, the limitations of existing platforms are discussed, with perspectives offered and an outlook towards clinical deployment. This Primer hopes to inspire and propel new platforms that can realize the vision of precise and personalized bacterial infection treatments in the near future.

This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at:



Work Title Single-cell pathogen diagnostics for combating antibiotic resistance
Open Access
  1. Hui Li
  2. Kuangwen Hsieh
  3. Pak Kin Wong
  4. Kathleen E. Mach
  5. Joseph C. Liao
  6. Tza-Huei Wang
License In Copyright (Rights Reserved)
Work Type Article
  1. Nature Reviews Methods Primers
Publication Date February 2, 2023
Publisher Identifier (DOI)
Deposited February 19, 2024




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Work History

Version 1

  • Created
  • Added Single-cell_pathogen_diagnostics_for_upload.docx
  • Added Creator Hui Li
  • Added Creator Kuangwen Hsieh
  • Added Creator Pak Kin Wong
  • Added Creator Kathleen E. Mach
  • Added Creator Joseph C. Liao
  • Added Creator Tza Huei Wang
  • Published
  • Updated Publication Date Show Changes
    Publication Date
    • 2023-12-01
    • 2023-02-02
  • Renamed Creator Tza-Huei Wang Show Changes
    • Tza Huei Wang
    • Tza-Huei Wang
  • Updated