Evidence map›Paper›PMID 40419483›Full record

ArticleNature communications2025

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections.

Stefano G Giulieri, Marcel Leroi, Diane Daniel, Roy Chean, Katherine Bond, Harry Walker, Natasha E Holmes, Nomvuyo Mothobi, Adrian Alexander, Adam Jenney and 5 more

Abstract readMulticenter Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Stefano G GiulieriDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia. stefano.giulieri@unimelb.edu.au.ORCID http://orcid.org/0000-0001-5366-1943
Marcel LeroiDepartment of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia.
Diane DanielDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
Roy CheanDepartment of Microbiology, Eastern Health, Box Hill, VIC, Australia.
Katherine BondDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
Harry WalkerDorevitch Pathology, Footscray, VIC, Australia.
Natasha E HolmesDepartment of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia.ORCID http://orcid.org/0000-0001-8501-4054
Nomvuyo MothobiDepartment of Infectious Diseases, University Hospital Geelong, Geelong, VIC, Australia.
Adrian AlexanderDepartment of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia.
Adam JenneyDepartment of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia.
Carolyn BeckettEpworth HealthCare, Richmond, VIC, Australia.
Andrew MahonyDepartment of Infectious Diseases and Immunology, Austin Health, Heidelberg, VIC, Australia.
Kerrie StevensMicrobiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
Norelle L SherryDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.ORCID http://orcid.org/0000-0002-7789-8360
Benjamin P HowdenDepartment of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.ORCID http://orcid.org/0000-0003-0237-1473

Funding

Department of Health | National Health and Medical Research Council (NHMRC) GNT1196103
6 · The paper itself

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.

Indexed as

Anti-Bacterial AgentsGenome, BacterialGenomicsStaphylococcal InfectionsStaphylococcus aureusDrug Resistance, BacterialHumansMicrobial Sensitivity TestsMutationTreatment FailureWhole Genome SequencingAnti-Bacterial Agents

Identifiers

PMID40419483
PMCPMC12106732

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.