Australian Scientists Pioneer Real-Time Genome Sequencing to Tackle Deadly Superbug

Australian scientists from the Peter Doherty Institute for Infection and Immunity in Melbourne have achieved a pioneering advancement in the battle against Staphylococcus aureus, commonly known as "golden staph", a superbug responsible for over one million deaths globally each year.

This breakthrough revolves around the implementation of real-time genome sequencing of bacterial pathogens during active, severe patient infections, a first in clinical practice. Unlike conventional diagnostics, which typically identify just the bacterial species and reveal resistance only after the fact, this method deciphers the pathogen’s full genetic makeup as the infection progresses.

The initiative was conducted in partnership with seven hospitals across Victoria, Australia. The team sampled S. aureus isolates both at infection onset and upon treatment failure. Genome analysis revealed that in one-third of cases, the bacterium had developed genetic mutations rendering standard antibiotics ineffective

A striking component of the study involved a patient whose infection initially responded to antibiotics but relapsed two months later. Genome sequencing demonstrated that resistance had increased eighty-fold during that interval. With these insights, clinicians modified the treatment, successfully curing the patient.

Published in Nature Communications, the study highlights genome sequencing as a powerful tool for guiding personalized antibiotic therapy and bolstering infection control efforts. ^[2] This real-time approach contrasts sharply with retrospective studies, which analyze bacterial evolution only after patient discharge. ^[1]

This real-time sequencing approach enables the medical team to observe how bacteria evolve within a single patient during treatment. It offers critical insights into resistance patterns that would otherwise go unnoticed until treatment failure. Traditional culture-based methods often take days and may miss emergent genetic changes altogether. By sequencing in real time, clinicians can preemptively switch to more effective antibiotics before the infection becomes life-threatening.

The research team emphasized that the method is not just diagnostic but also predictive, allowing early intervention. Furthermore, the implementation of such sequencing could potentially reduce hospital stays, lower healthcare costs, and improve survival rates in critical care units.

Importantly, the data generated also serves public health surveillance, helping authorities monitor trends in resistance and prepare for outbreaks. Experts believe this advancement could be replicated globally, providing hospitals with a crucial tool in the escalating fight against drug-resistant infections.

Following these findings, Victorian hospitals plan to launch the world’s first clinical genomic service dedicated to treatment-resistant bacterial infections. This initiative could reshape hospital protocols by integrating genome sequencing directly into patient care, supporting swift adjustments and enhancing antimicrobial stewardship.

The study marks a major turning point in the fight against antimicrobial resistance (AMR). As S. aureus continues to cause high mortality worldwide, this method offers a promising path toward timely, patient-specific interventions, potentially slowing resistance spread and improving clinical outcomes.

References:

1. Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ArXiv [Preprint]. 2024 Mar 6:arXiv:2403.03688v1. Update in: Methods Mol Biol. 2025;2866:287-315. doi: 10.1007/978-1-0716-4192-7_16. PMID: 38495572; PMCID: PMC10942477.

2. Zampaloni, C., Mattei, P., Bleicher, K. et al. A novel antibiotic class targeting the lipopolysaccharide transporter. Nature 625, 566–571 (2024). https://doi.org/10.1038/s41586-023-06873-0

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