Abstract

Effective antibiotic use that minimizes treatment failures remains a challenge. A better understanding of how bacterial populations respond to antibiotics is necessary. Previous studies of large bacterial populations established the current deterministic framework of pharmacodynamics. Here, characterizing the dynamics of population extinction, we demonstrated the stochastic nature of eradicating bacteria with antibiotics. Antibiotics known to kill bacteria (bactericidal) induced population fluctuations. Thus, at high antibiotic concentrations, the dynamics of bacterial clearance were heterogeneous. At low concentrations, clearance still occurred with a non-zero probability. These striking outcomes of population fluctuations were well captured by our probabilistic model. Our model further suggested a strategy to facilitate eradication by increasing extinction probability. We experimentally tested this prediction for antibiotic-susceptible and clinically-isolated resistant bacteria. This new knowledge exposes fundamental limits in our ability to predict bacterial eradication. Additionally, it demonstrates the potential of using antibiotic concentrations that were previously deemed inefficacious to eradicate bacteria.

Article and author information

Author details

  1. Jessica Coates

    Microbiology and Molecular Genetics Graduate Program, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Bo Ryoung Park

    Department of Physics, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Dai Le

    Department of Physics, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Emrah Şimşek

    Department of Physics, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Waqas Chaudhry

    Department of Physics, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Minsu Kim

    Microbiology and Molecular Genetics Graduate Program, Emory University, Atlanta, United States
    For correspondence
    minsu.kim@emory.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1594-4971

Funding

Research Corporation for Science Advancement (24097)

  • Jessica Coates
  • Bo Ryoung Park
  • Dai Le
  • Emrah Şimşek
  • Minsu Kim

Human Frontier Science Program (RGY0072/2015)

  • Jessica Coates
  • Bo Ryoung Park
  • Dai Le
  • Emrah Şimşek
  • Minsu Kim

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

Reviewing Editor

  1. Aleksandra M Walczak, Ecole Normale Superieure, France

Version history

  1. Received: October 20, 2017
  2. Accepted: February 15, 2018
  3. Accepted Manuscript published: March 6, 2018 (version 1)
  4. Version of Record published: March 12, 2018 (version 2)
  5. Version of Record updated: March 15, 2018 (version 3)

Copyright

© 2018, Coates 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

  • 5,769
    views
  • 735
    downloads
  • 52
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Jessica Coates
  2. Bo Ryoung Park
  3. Dai Le
  4. Emrah Şimşek
  5. Waqas Chaudhry
  6. Minsu Kim
(2018)
Antibiotic-induced population fluctuations and stochastic clearance of bacteria
eLife 7:e32976.
https://doi.org/10.7554/eLife.32976

Share this article

https://doi.org/10.7554/eLife.32976

Further reading

    1. Cell Biology
    2. Computational and Systems Biology
    Thomas Grandits, Christoph M Augustin ... Alexander Jung
    Research Article

    Computer models of the human ventricular cardiomyocyte action potential (AP) have reached a level of detail and maturity that has led to an increasing number of applications in the pharmaceutical sector. However, interfacing the models with experimental data can become a significant computational burden. To mitigate the computational burden, the present study introduces a neural network (NN) that emulates the AP for given maximum conductances of selected ion channels, pumps, and exchangers. Its applicability in pharmacological studies was tested on synthetic and experimental data. The NN emulator potentially enables massive speed-ups compared to regular simulations and the forward problem (find drugged AP for pharmacological parameters defined as scaling factors of control maximum conductances) on synthetic data could be solved with average root-mean-square errors (RMSE) of 0.47 mV in normal APs and of 14.5 mV in abnormal APs exhibiting early afterdepolarizations (72.5% of the emulated APs were alining with the abnormality, and the substantial majority of the remaining APs demonstrated pronounced proximity). This demonstrates not only very fast and mostly very accurate AP emulations but also the capability of accounting for discontinuities, a major advantage over existing emulation strategies. Furthermore, the inverse problem (find pharmacological parameters for control and drugged APs through optimization) on synthetic data could be solved with high accuracy shown by a maximum RMSE of 0.22 in the estimated pharmacological parameters. However, notable mismatches were observed between pharmacological parameters estimated from experimental data and distributions obtained from the Comprehensive in vitro Proarrhythmia Assay initiative. This reveals larger inaccuracies which can be attributed particularly to the fact that small tissue preparations were studied while the emulator was trained on single cardiomyocyte data. Overall, our study highlights the potential of NN emulators as powerful tool for an increased efficiency in future quantitative systems pharmacology studies.

    1. Computational and Systems Biology
    2. Neuroscience
    Domingos Leite de Castro, Miguel Aroso ... Paulo Aguiar
    Research Article Updated

    Closed-loop neuronal stimulation has a strong therapeutic potential for neurological disorders such as Parkinson’s disease. However, at the moment, standard stimulation protocols rely on continuous open-loop stimulation and the design of adaptive controllers is an active field of research. Delayed feedback control (DFC), a popular method used to control chaotic systems, has been proposed as a closed-loop technique for desynchronisation of neuronal populations but, so far, was only tested in computational studies. We implement DFC for the first time in neuronal populations and access its efficacy in disrupting unwanted neuronal oscillations. To analyse in detail the performance of this activity control algorithm, we used specialised in vitro platforms with high spatiotemporal monitoring/stimulating capabilities. We show that the conventional DFC in fact worsens the neuronal population oscillatory behaviour, which was never reported before. Conversely, we present an improved control algorithm, adaptive DFC (aDFC), which monitors the ongoing oscillation periodicity and self-tunes accordingly. aDFC effectively disrupts collective neuronal oscillations restoring a more physiological state. Overall, these results support aDFC as a better candidate for therapeutic closed-loop brain stimulation.