Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections
Stefano G Giulieri,
Romain Guérillot,
Sebastian Duchene,
Abderrahman Hachani,
Diane Daniel,
Torsten Seemann,
Joshua S Davis,
Steven YC Tong,
Bernadette C Young,
Daniel J Wilson,
Timothy P Stinear,
Benjamin P Howden
Affiliations
Stefano G Giulieri
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia
Romain Guérillot
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
Sebastian Duchene
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
Diane Daniel
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Australia
Torsten Seemann
Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Australia
Joshua S Davis
Department of Infectious Diseases, John Hunter Hospital, Newcastle, New South Wales, Australia; Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia; Victorian Infectious Disease Service, Royal Melbourne Hospital, and University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
Big Data Institute, Nuffield Department of Population Health, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, University of Oxford, Oxford, United Kingdom
Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Australia
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 2590 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.
