A new assay testing antibiotics’ ability to kill bacteria—not just inhibit their growth—may help researchers develop more effective antimicrobial drugs.
Antimicrobial resistance is a serious public health problem, but it is not the only reason why some antibiotics don’t work. Some bacteria, such as tuberculosis-causing Mycobacterium tuberculosis, can withstand antibiotic treatment without developing resistance in a phenomenon called antibiotic tolerance. When antibiotics just block bacterial growth, the cells can lay low for months, dormant but alive.
Existing tests for how well antibiotics work against infections typically focus on the evaluating the drugs’ ability to inhibit bacterial growth, not kill them. This can lead to long treatment courses and poor outcomes.
To identify antibiotics that will kill bacteria outright, Lucas Boeck, a biomedical researcher at the University of Basel, and his colleagues recently developed a workflow called antimicrobial single-cell testing (ASCT).1 This test quantifies how well antibiotics kill bacteria at single-cell resolution. The method, published in Nature Microbiology, can help predict how well human patients will respond to specific antibiotic treatments.
Lucas Boeck, a biomedical researcher at the University of Basel, investigates pathogenic microorganisms’ response to drug treatment.
Lucas Boeck
“The better bacteria tolerate an antibiotic, the lower the chances of therapeutic success are for the patients,” said Boeck in a statement.
To demonstrate how ASCT works, Boeck’s team placed Mycobacterium abscessus in a 1,536-well plate. This lung infection-causing pathogen is related to M. tuberculosis, but it poses less of a biosafety hazard to the researchers.
The team stained M. abscessus with a dye that signals viability and treated them with eight antibiotic drugs for three days. To monitor killing, they took images every two to four hours for three days. The researchers tracked the “time-kill kinetics” for each cell, a metric which indicates how quickly each drug kills the bacteria. Next, the team tested if ASCT is more predictive of antibiotic treatment outcomes for M. tuberculosis infections in living organisms than in a standard growth inhibition assay. They first used ASCT to evaluate how well the 65 antibiotic combinations killed two avirulent strains of M. tuberculosis. Then, they leveraged data from existing mouse and human studies and categorized antibiotic drug combinations depending on how well they mitigate M. tuberculosis infections in mice and humans relative to the standard-of-care regimen.2-5 The researchers found that ASCT could distinguish between drugs that were “similar to” standard-of-care and their “better than” counterparts, but the growth inhibition assay could not.
To better understand how different strains of mycobacteria tolerate antibiotic treatment, Boeck’s team studied clinical isolates of M. abscessus from 405 patients. The researchers investigated how well M. abscessus tolerated eight commonly used antibiotics for up to 72 hours, tracking more than 100 million individual cells in total. They discovered that the isolates’ responses to antibiotics were different from one another, indicating that bacterial strain differences influence antibiotic tolerance.
Boeck hopes that ASCT can one day help personalize drug regimens to each patient and the pathogen they are fighting.
- Jovanovic A, et al. Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes. Nat Microbiol. 2026.
- Larkins-Ford J, et al. Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis. Cell Syst. 2021;12(11):1046-1063.e7.
- Larkins-Ford J, et al. Design principles to assemble drug combinations for effective tuberculosis therapy using interpretable pairwise drug response measurements. Cell Rep Med. 2022;3(9):100737.
- Cevik M, et al. Bedaquiline-pretomanid-moxifloxacin-pyrazinamide for drug-sensitive and drug-resistant pulmonary tuberculosis treatment: a phase 2c, open-label, multicentre, partially randomised controlled trial. Lancet Infect Dis. 2024;24(9):1003-1014.
- Tweed CD, et al. Bedaquiline, moxifloxacin, pretomanid, and pyrazinamide during the first 8 weeks of treatment of patients with drug-susceptible or drug-resistant pulmonary tuberculosis: a multicentre, open-label, partially randomised, phase 2b trial. Lancet Respir Med. 2019;7(12):1048-1058.
