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In situ genotyping of a pooled strain library after characterizing complex phenotypes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
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2017 (English)In: Molecular Systems Biology, ISSN 1744-4292, E-ISSN 1744-4292, Vol. 13, no 10, article id 947Article in journal (Refereed) Published
Abstract [en]

In this work, we present a proof-of-principle experiment that extends advanced live cell microscopy to the scale of pool-generated strain libraries. We achieve this by identifying the genotypes for individual cells in situ after a detailed characterization of the phenotype. The principle is demonstrated by single-molecule fluorescence time-lapse imaging of Escherichia coli strains harboring barcoded plasmids that express a sgRNA which suppresses different genes in the E.coli genome through dCas9 interference. In general, the method solves the problem of characterizing complex dynamic phenotypes for diverse genetic libraries of cell strains. For example, it allows screens of how changes in regulatory or coding sequences impact the temporal expression, location, or function of a gene product, or how the altered expression of a set of genes impacts the intracellular dynamics of a labeled reporter.

Place, publisher, year, edition, pages
2017. Vol. 13, no 10, article id 947
Keywords [en]
DuMPLING, live cell, microfluidic, single cell, strain libraries
National Category
Biochemistry Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-342924DOI: 10.15252/msb.20177951ISI: 000416160000004PubMedID: 29042431OAI: oai:DiVA.org:uu-342924DiVA, id: diva2:1185625
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilEU, European Research CouncilAvailable from: 2018-02-26 Created: 2018-02-26 Last updated: 2026-02-05Bibliographically approved
In thesis
1. 30-Minute Antibiotic Susceptibility Testing at the Point-of-Care using Nanofluidics
Open this publication in new window or tab >>30-Minute Antibiotic Susceptibility Testing at the Point-of-Care using Nanofluidics
2026 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Antimicrobial resistance (AMR) is a global health crisis driven significantly by the overuse of antibiotics. Most of this systemic misuse in human healthcare is a direct consequence of a diagnostic void created by the temporal gap between patient presentation and microbiological results. Traditional Antibiotic Susceptibility Testing (AST) relies on macroscopic biomass accumulation, a process constrained by bacterial generation times, and requires 48 to 72 hours. This delay forces clinicians to rely on empirical guidelines, treating patients based on probability rather than diagnostic certainty. Dependence on empirical therapy drives antibiotic overuse, fueling AMR. However, as resistance rates rise, the utility of empirical guidelines diminishes, creating a paradox where increasing resistance demands immediate diagnostic answers that current technology cannot provide.

This thesis demonstrates that the temporal constraints of AST are not immutable biological constants, but technological artifacts resulting from limited detection sensitivity. It establishes that bacterial cells respond to effective antibiotics within minutes, and that detecting these immediate physiological changes requires only a sufficiently sensitive method. This detection is enabled by a novel nanofluidic platform that actively captures, maintains, and images individual bacterial cells. By utilizing phase-contrast microscopy, the method quantifies instantaneous single-cell growth rates in real-time. Paper I establishes the "Fast Antibiotic Susceptibility Testing" (FASTest) method, demonstrating that susceptibility profiles for Escherichia coli against nine antibiotics can be determined in 30 minutes, and that it correctly distinguishes resistant bacteria from susceptible ones across 49 uropathogenic E. coli isolates. Paper II validates the platform's robustness through a complex "lab-on-a-chip" application involving a multi-step molecular biology protocol for in situ genotyping. Finally, Paper III shows clinical feasibility of the method for 30-minute AST for sepsis using either positive blood cultures or isolated colonies.

The research presented in this thesis has been successfully translated from an academic concept into a fully automated medical device, the PA-100 AST System, which was recently awarded the Longitude Prize on Antimicrobial Resistance. This technology demonstrates that shifting observation from the population to the single cell bridges the diagnostic void, enabling the transition from empirical prescribing to evidence-based precision medicine for urinary tract infections at the Point-of-Care.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2026. p. 97
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2637
Keywords
Antimicrobial resistance, Antibiotic susceptibility testing, Nanofluidics, Single-cell analysis, Microfluidics, Point-of-Care diagnostics, Urinary tract infection, Sepsis, PA-100, Rapid diagnostics, IVD, In vitro diagnostics, Point-of-care
National Category
Medical Biotechnology (Focus on Cell Biology, (incl. Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Biology with specialization in Molecular Biotechnology
Identifiers
urn:nbn:se:uu:diva-578489 (URN)978-91-513-2735-8 (ISBN)
Public defence
2026-03-27, B21 Biomedicinskt centrum (BMC), Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2026-03-06 Created: 2026-02-05 Last updated: 2026-03-06

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Lawson, Michael J.Camsund, DanielLarsson, JimmyBaltekin, ÖzdenFange, DavidElf, Johan

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