A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections
Abstract Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak detection and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infe...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60045-4 |
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| author | Stefano G. Giulieri Marcel Leroi Diane Daniel Roy Chean Katherine Bond Harry Walker Natasha E. Holmes Nomvuyo Mothobi Adrian Alexander Adam Jenney Carolyn Beckett Andrew Mahony Kerrie Stevens Norelle L. Sherry Benjamin P. Howden |
| author_facet | Stefano G. Giulieri Marcel Leroi Diane Daniel Roy Chean Katherine Bond Harry Walker Natasha E. Holmes Nomvuyo Mothobi Adrian Alexander Adam Jenney Carolyn Beckett Andrew Mahony Kerrie Stevens Norelle L. Sherry Benjamin P. Howden |
| author_sort | Stefano G. Giulieri |
| collection | DOAJ |
| description | Abstract Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak detection and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infections, driving precision medicine strategies. Here, we present a clinician-driven bacterial genomics framework that applies within-patient evolutionary analysis to identify in real-time microbial genetic changes that have an impact on treatment outcomes of severe Staphylococcus aureus infections, a strategy that is increasingly used in cancer genomics. Our approach uses a combination of bacterial genomics and antibiotic susceptibility testing to identify and track bacterial adaptive mutations that underlie microbiologically documented treatment failure (i.e. ongoing positive cultures [persistent infection] or new positive cultures after initial response [recurrent infection]). We show the potential added value of our approach to clinicians and propose a roadmap for the use of bacterial genomics to advance the management of severe bacterial infections. |
| format | Article |
| id | doaj-art-838963145a9044cc997af01a2e149ca1 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-838963145a9044cc997af01a2e149ca12025-08-20T03:22:12ZengNature PortfolioNature Communications2041-17232025-05-011611910.1038/s41467-025-60045-4A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infectionsStefano G. Giulieri0Marcel Leroi1Diane Daniel2Roy Chean3Katherine Bond4Harry Walker5Natasha E. Holmes6Nomvuyo Mothobi7Adrian Alexander8Adam Jenney9Carolyn Beckett10Andrew Mahony11Kerrie Stevens12Norelle L. Sherry13Benjamin P. Howden14Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and ImmunityDepartment of Infectious Diseases and Immunology, Austin HealthDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and ImmunityDepartment of Microbiology, Eastern HealthDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and ImmunityDorevitch PathologyDepartment of Infectious Diseases and Immunology, Austin HealthDepartment of Infectious Diseases, University Hospital GeelongDepartment of Infectious Diseases, The Alfred HospitalDepartment of Infectious Diseases, The Alfred HospitalEpworth HealthCareDepartment of Infectious Diseases and Immunology, Austin HealthMicrobiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and ImmunityDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and ImmunityDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and ImmunityAbstract Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak detection and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infections, driving precision medicine strategies. Here, we present a clinician-driven bacterial genomics framework that applies within-patient evolutionary analysis to identify in real-time microbial genetic changes that have an impact on treatment outcomes of severe Staphylococcus aureus infections, a strategy that is increasingly used in cancer genomics. Our approach uses a combination of bacterial genomics and antibiotic susceptibility testing to identify and track bacterial adaptive mutations that underlie microbiologically documented treatment failure (i.e. ongoing positive cultures [persistent infection] or new positive cultures after initial response [recurrent infection]). We show the potential added value of our approach to clinicians and propose a roadmap for the use of bacterial genomics to advance the management of severe bacterial infections.https://doi.org/10.1038/s41467-025-60045-4 |
| spellingShingle | Stefano G. Giulieri Marcel Leroi Diane Daniel Roy Chean Katherine Bond Harry Walker Natasha E. Holmes Nomvuyo Mothobi Adrian Alexander Adam Jenney Carolyn Beckett Andrew Mahony Kerrie Stevens Norelle L. Sherry Benjamin P. Howden A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections Nature Communications |
| title | A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections |
| title_full | A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections |
| title_fullStr | A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections |
| title_full_unstemmed | A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections |
| title_short | A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections |
| title_sort | multi hospital clinician initiated bacterial genomics programme to investigate treatment failure in severe staphylococcus aureus infections |
| url | https://doi.org/10.1038/s41467-025-60045-4 |
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