Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant

  1. Dallas L Mould
  2. Mirjana Stevanovic
  3. Alix Ashare
  4. Daniel Schultz
  5. Deborah A Hogan  Is a corresponding author
  1. Geisel School of Medicine at Dartmouth, United States
  2. Dartmouth-Hitchock Medical Center, United States

Abstract

Microbes frequently evolve in reproducible ways. Here, we show that differences in specific metabolic regulation rather than inter-strain interactions explain the frequent presence of lasR loss-of-function mutations in the bacterial pathogen Pseudomonas aeruginosa. While LasR contributes to virulence through its role in quorum sensing, lasR mutants have been associated with more severe disease. A model based on the intrinsic growth kinetics for a wild type strain and its LasR- derivative, in combination with an experimental evolution based genetic screen and further genetics analyses, indicated that differences in metabolism were sufficient to explain the rise of these common mutant types. The evolution of LasR- lineages in laboratory and clinical isolates depended on activity of the two-component system CbrAB, which modulates substrate prioritization through the catabolite repression control pathway. LasR- lineages frequently arise in cystic fibrosis lung infections and their detection correlates with disease severity. Our analysis of bronchoalveolar lavage fluid metabolomes identified compounds that negatively correlate with lung function, and we show that these compounds support enhanced growth of LasR- cells in a CbrB-controlled manner. We propose that in vivo metabolomes contribute to pathogen evolution, which may influence the progression of disease and its treatment.

Data availability

All sequencing data is available on the Sequence Read Archive with accession number PRJNA786588 upon publication. All data generated or analyzed and all code used during this study are included in the manuscript or associated files.

The following data sets were generated

Article and author information

Author details

  1. Dallas L Mould

    Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Mirjana Stevanovic

    Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Alix Ashare

    Department of Medicine, Dartmouth-Hitchock Medical Center, Lebanon, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Daniel Schultz

    Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Deborah A Hogan

    Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
    For correspondence
    dhogan@dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6366-2971

Funding

Cystic Fibrosis Foundation (HOGAN19G0)

  • Dallas L Mould
  • Deborah A Hogan

Cystic Fibrosis Foundation (ASHARE20P0)

  • Alix Ashare

Cystic Fibrosis Foundation (STANTO19R0)

  • Daniel Schultz

Cystic Fibrosis Foundation (T32AI007519)

  • Dallas L Mould

National Institutes of Health (R01HL122372)

  • Alix Ashare

National Institutes of Health (GM130454)

  • Mirjana Stevanovic
  • Daniel Schultz

National Institutes of Health (P20GM113132)

  • Dallas L Mould
  • Deborah A Hogan

National Institutes of Health (DK117469)

  • Dallas L Mould
  • Alix Ashare
  • Daniel Schultz
  • Deborah A Hogan

National Institutes of Health (P30CA023108)

  • Dallas L Mould
  • Alix Ashare
  • Daniel Schultz
  • Deborah A Hogan

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

Reviewing Editor

  1. Vaughn S Cooper, University of Pittsburgh, United States

Publication history

  1. Received: December 21, 2021
  2. Preprint posted: January 14, 2022 (view preprint)
  3. Accepted: April 24, 2022
  4. Accepted Manuscript published: May 3, 2022 (version 1)
  5. Version of Record published: June 23, 2022 (version 2)

Copyright

© 2022, Mould 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

  • 1,642
    Page views
  • 317
    Downloads
  • 5
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Dallas L Mould
  2. Mirjana Stevanovic
  3. Alix Ashare
  4. Daniel Schultz
  5. Deborah A Hogan
(2022)
Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant
eLife 11:e76555.
https://doi.org/10.7554/eLife.76555

Further reading

    1. Cell Biology
    2. Microbiology and Infectious Disease
    Emma M Briggs, Catarina A Marques ... Keith R Matthews
    Research Article Updated

    African trypanosomes proliferate as bloodstream forms (BSFs) and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single-cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated (CCR) transcriptomes of both procyclic and slender BSF Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze–thawing protocol that allows single-cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the CCR transcriptomes of both forms, which are available for further interrogation via an interactive webtool.

    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease
    Kennedy Lushasi, Kirstyn Brunker ... Katie Hampson
    Research Article

    Background:

    Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle.

    Methods:

    We combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010-2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba Island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data we inferred transmission chains and estimated case detection. Using a decision tree model we quantified the public health burden and evaluated the impact and cost-effectiveness of interventions over a ten-year time horizon.

    Results:

    We resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were projected to be highly cost-effective ($256 per death averted), only dog vaccination interrupts transmission. A combined One Health approach of routine annual dog vaccination together with free post-exposure vaccines for bite victims, rapidly eliminates rabies, is highly cost-effective ($1657 per death averted) and by maintaining rabies freedom prevents over 30 families from suffering traumatic rabid dog bites annually on Pemba island.

    Conclusions:

    A One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere.

    Funding:

    Wellcome [207569/Z/17/Z, 095787/Z/11/Z, 103270/Z/13/Z], the UBS Optimus Foundation, the Department of Health and Human Services of the National Institutes of Health [R01AI141712] and the DELTAS Africa Initiative [Afrique One-ASPIRE/DEL-15-008] comprising a donor consortium of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), the New Partnership for Africa's Development Planning and Coordinating (NEPAD) Agency, Wellcome [107753/A/15/Z], Royal Society of Tropical Medicine and Hygiene Small Grant 2017 [GR000892] and the UK government. The rabies elimination demonstration project from 2010-2015 was supported by the Bill & Melinda Gates Foundation [OPP49679]. Whole-genome sequencing was partially supported from APHA by funding from the UK Department for Environment, Food and Rural Affairs (Defra), Scottish government and Welsh government under projects SEV3500 & SE0421.