New Method Developed to Quantify Bacterial Killing in Real Time

Antibiotics are traditionally tested for how effectively they inhibit bacterial growth in laboratory conditions, but a crucial question is whether they truly eliminate bacteria inside the body. At the University of Basel, researchers led by Lucas Boeck have developed a new approach to measure how well antibiotics actually kill bacterial pathogens rather than just stop their growth. 

Antibiotic-resistant bacteria remain one of the most serious health issues of modern times. As bacteria mutate, they increasingly resist many standard drugs, making infections harder to treat. Even in the absence of resistance, some bacteria can survive antibiotic exposure by entering a dormant state in which they remain inactive but alive. These dormant cells can later “wake up,” allowing infection to return after treatment ends. This is particularly significant for diseases such as tuberculosis, where selecting drugs that fully sterilize the infection over many months of therapy is vital.

Traditional antimicrobial tests only measure growth inhibition and cannot reliably predict whether antibiotics fully eradicate pathogens. To overcome this limitation, Boeck’s team created a method called antimicrobial single-cell testing (ASCT). This technique involves microscopic imaging of millions of individual bacteria under thousands of treatment conditions. “We use it to film each individual bacterium over several days and observe whether and how quickly a drug actually kills it,” explains Boeck, senior author on the study published in Nature Microbiology. The method quantifies what proportion of bacteria die and how efficiently, giving a clearer picture of a drug’s true action.

To validate their approach, the team tested 65 antibiotic combinations on Mycobacterium tuberculosis and analyzed 400 samples from patients infected with Mycobacterium abscessus, a related lung pathogen. They observed significant differences between therapies and among bacterial strains from different patients. This variation, known as antibiotic tolerance, was linked to specific genetic traits that allow some bacteria to survive antibiotic exposure. “The better bacteria tolerate an antibiotic, the lower the chances of therapeutic success are for the patients,” says Boeck. 

Results from antimicrobial single-cell testing aligned closely with outcomes seen in animal and clinical studies. Though currently a research tool, the method could eventually guide personalized antibiotic treatments and assist drug developers. According to Boeck, it may also shed light on bacterial survival strategies and support future efforts to design more effective therapies.