Real-Time Genome Sequencing Detects Dangerous Superbug Causing Hospital Infections

Superbug infections caused by Staphylococcus aureus, or ‘golden staph’, are notoriously difficult to treat and claim over one million lives globally each year. These bacteria can rapidly develop resistance to even the most powerful antibiotics, making it challenging for clinicians to select effective therapies in time. Now, researchers have demonstrated that real-time genome sequencing can track bacterial mutations during treatment, enabling doctors to adjust therapies early and improve outcomes for patients with severe golden staph infections.

The breakthrough comes from scientists at the Doherty Institute (Melbourne, Australia), who collaborated with seven major hospitals in Victoria. This marks the first time researchers have shown that genome sequencing during active infection, not years later, can guide treatment decisions in real time. Traditional lab tests only identify the bacterial species, but genome sequencing provides a complete genetic profile, revealing how the bacteria are adapting and what traits could lead to treatment failure. In the study published in Nature Communications, the team collected bacterial samples from patients experiencing treatment failure and compared them to earlier samples taken at the start of infection. In one-third of the cases, they discovered new mutations that could compromise therapy effectiveness.

For example, one patient repeatedly relapsed after stopping antibiotics, with each recurrence showing new dangerous mutations. Armed with this data, the clinical team was able to change the antibiotic strategy and successfully cure the infection. To measure the clinical value of this approach, the researchers surveyed 25 infectious disease specialists across Australia, the UK, the US, and Switzerland. The genomic reports received an average usefulness score of 80 out of 100, with more than a third of clinicians reporting that the findings influenced their choice of antibiotic. Until now, genomic evolution during infection has only been studied retrospectively. By enabling real-time tracking, this method could usher infectious diseases into the era of precision medicine, similar to what genomics has achieved in oncology.

“Our study is the first to show that by tracking bacterial evolution in real-time, genome sequencing can reveal tricks bacteria use to survive, giving doctors the power to stay one step ahead and tailor treatment to the specific bacterial strain,” said Dr. Stefano Giulieri, lead author of the study. “This helps avoid unnecessary treatments, minimize side effects for patients, and prevent further antibiotic resistance – ultimately giving patients the best chance of recovery.”