Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

  1. Robert M Cooper  Is a corresponding author
  2. Lev Tsimring
  3. Jeff Hasty  Is a corresponding author
  1. University of California, San Diego, United States

Abstract

Horizontal gene transfer (HGT) plays a major role in the spread of antibiotic resistance. Of particular concern are Acinetobacter baumannii bacteria, which recently emerged as global pathogens, with nosocomial mortality rates reaching 19-54%. Acinetobacter gains antibiotic resistance remarkably rapidly, with multi drug-resistance (MDR) rates exceeding 60%. Despite growing concern, the mechanisms underlying this extensive HGT remain poorly understood. Here, we show bacterial predation by Acinetobacter baylyi increases cross-species HGT by orders of magnitude, and we observe predator cells functionally acquiring adaptive resistance genes from adjacent prey. We then develop a population-dynamic model quantifying killing and HGT on solid surfaces. We show DNA released via cell lysis is readily available for HGT and may be partially protected from the environment, describe the effects of cell density, and evaluate potential environmental inhibitors. These findings establish a framework for understanding, quantifying, and combating HGT within the microbiome and the emergence of MDR super-bugs.

Article and author information

Author details

  1. Robert M Cooper

    BioCircuits Institute, University of California, San Diego, La Jolla, United States
    For correspondence
    robmcooper@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2136-0403
  2. Lev Tsimring

    BioCircuits Institute, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Jeff Hasty

    BioCircuits Institute, University of California, San Diego, La Jolla, United States
    For correspondence
    jhasty@eng.ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

Hartwell Foundation

  • Robert M Cooper

National Institute of General Medical Sciences (San Diego Center for Systems Biology - P50 GM085764)

  • Robert M Cooper
  • Lev Tsimring
  • Jeff Hasty

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

Reviewing Editor

  1. Ben Cooper, Mahidol Oxford Tropical Medicine Research Unit, Thailand

Version history

  1. Received: February 11, 2017
  2. Accepted: October 10, 2017
  3. Accepted Manuscript published: November 1, 2017 (version 1)
  4. Version of Record published: November 17, 2017 (version 2)

Copyright

© 2017, Cooper 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

  • 10,933
    views
  • 1,436
    downloads
  • 106
    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. Robert M Cooper
  2. Lev Tsimring
  3. Jeff Hasty
(2017)
Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance
eLife 6:e25950.
https://doi.org/10.7554/eLife.25950

Share this article

https://doi.org/10.7554/eLife.25950

Further reading

    1. Computational and Systems Biology
    2. Developmental Biology
    Arya Y Nakhe, Prasanna K Dadi ... David A Jacobson
    Research Article

    The gain-of-function mutation in the TALK-1 K+ channel (p.L114P) is associated with maturity-onset diabetes of the young (MODY). TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion. The KCNK16 gene encoding TALK-1 is the most abundant and β-cell-restricted K+ channel transcript. To investigate the impact of KCNK16 L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the Kcnk16 L114P mutation was generated. Heterozygous and homozygous Kcnk16 L114P mice exhibit increased neonatal lethality in the C57BL/6J and the CD-1 (ICR) genetic background, respectively. Lethality is likely a result of severe hyperglycemia observed in the homozygous Kcnk16 L114P neonates due to lack of glucose-stimulated insulin secretion and can be reduced with insulin treatment. Kcnk16 L114P increased whole-cell β-cell K+ currents resulting in blunted glucose-stimulated Ca2+ entry and loss of glucose-induced Ca2+ oscillations. Thus, adult Kcnk16 L114P mice have reduced glucose-stimulated insulin secretion and plasma insulin levels, which significantly impairs glucose homeostasis. Taken together, this study shows that the MODY-associated Kcnk16 L114P mutation disrupts glucose homeostasis in adult mice resembling a MODY phenotype and causes neonatal lethality by inhibiting islet insulin secretion during development. These data suggest that TALK-1 is an islet-restricted target for the treatment for diabetes.

    1. Computational and Systems Biology
    David Geller-McGrath, Kishori M Konwar ... Jason E McDermott
    Tools and Resources

    The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.