Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection

  1. Karthik Hullahalli  Is a corresponding author
  2. Matthew K Waldor  Is a corresponding author
  1. Harvard Medical School, United States
  2. Brigham and Women's Hospital, United States


The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underly pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic E. coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.

Data availability

Barcode and TIS read counts, in addition to all scripts required to analyze these data, are provided at Sequencing reads have been deposited in SRA

Article and author information

Author details

  1. Karthik Hullahalli

    Department of Biological Sciences, Harvard Medical School, Boston, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3064-2090
  2. Matthew K Waldor

    Division of Infectious Diseases, Brigham and Women's Hospital, Boston, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1843-7000


Howard Hughes Medical Institute

  • Matthew K Waldor

National Science Foundation

  • Karthik Hullahalli

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


Animal experimentation: All animal experiments were conducted in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and the Animal Welfare Act of the United States Department of Agriculture using protocols reviewed and approved by Brigham and Women's Hospital Committee on Animals (Institutional Animal Care and Use Committee protocol number 2016N000416 and Animal Welfare Assurance of Compliance number A4752-01)

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Publication history

  1. Preprint posted: May 17, 2021 (view preprint)
  2. Received: June 2, 2021
  3. Accepted: October 7, 2021
  4. Accepted Manuscript published: October 12, 2021 (version 1)
  5. Version of Record published: October 25, 2021 (version 2)


© 2021, Hullahalli & Waldor

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.


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  1. Karthik Hullahalli
  2. Matthew K Waldor
Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection
eLife 10:e70910.

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