Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

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Abstract

During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues, and is exposed to new selective pressures, thus potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation, however a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2,590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single-nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file 1-6.The code to call, filter and annotated within-host variants and to perform the enrichment analysis is available on github at https://github.com/stefanogg/staph_adaptation_paper

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Article and author information

Author details

Stefano G Giulieri

Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia

Competing interests
The authors declare that no competing interests exist.
Romain Guérillot

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.
Sebastian Duchene

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.
Abderrahman Hachani

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8032-2154
Diane Daniel

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.
Torsten Seemann

Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.
Joshua S Davis

Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia

Competing interests
The authors declare that no competing interests exist.
Steven YC Tong

Victorian Infectious Diseases Service, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1368-8356
Bernadette C Young

University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6071-6770
Daniel J Wilson

University of Oxford, Oxford, United Kingdom

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0940-3311
Timothy P Stinear

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.
Benjamin P Howden

Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia

For correspondence
bhowden@unimelb.edu.au

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0237-1473

Funding

National Health and Medical Research Council

Timothy P Stinear

National Health and Medical Research Council

Benjamin P Howden

The University of Melbourne

Stefano G Giulieri

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

Ethics

Human subjects: Ethics approval was obtained at each partecipating site to the CAMERA2 trial and written informed onsent was obtained from each participant or surrogate decision maker.

Copyright

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.