Tuberculosis bacteria show lineage-linked drug tolerance

Drug tolerance lets bacteria survive long exposures to drugs that would normally kill them, and it is thought to help explain how drug resistance evolves. In tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), outbreaks of multidrug resistant TB (MDR-TB) are often linked to particular branches of the bacterium’s family tree. Because of that pattern, Sònia Borrell and her team set out to test whether some of those branches are intrinsically better at tolerating drugs and therefore more likely to evolve resistance. To do this, the researchers developed a high throughput in vitro assay to measure drug tolerance in Mtb. They assembled a representative group of strains drawn from the most common global human-adapted phylogenetic lineages, L1 through L4, so they could compare intrinsic tolerance across the major branches of Mtb found worldwide. The study was designed to determine whether tolerance is tied to lineage — that is, whether closely related strains share similar abilities to survive prolonged drug exposure — and to look for genetic signals that might explain differences in tolerance.

Using their high throughput in vitro assay, the team measured tolerance to two important TB drugs, rifampicin and bedaquiline. These experiments revealed clear differences between lineages: strains from lineage L3 and lineage L4 showed higher tolerance to the tested drugs than strains from lineage L1 and lineage L2. The researchers also found that strains that are phylogenetically closely related tended to have similar levels of tolerance, a pattern that suggests tolerance is a heritable trait within the Mtb family tree. Beyond measuring tolerance, they examined genes previously reported to be associated with tolerance in Mtb. In the strains with high tolerance, there was a significant enrichment of mutations in genes involved in cell wall and cell processes, intermediary metabolism and respiration, as well as lipid metabolism. Those enriched genetic changes point to biological systems that may underlie the observed differences in drug tolerance among lineages.

The findings build a link between the evolutionary history of Mtb and how well different strains survive drug exposure. That link matters because intrinsic differences in tolerance can shape how readily a strain evolves drug resistance: if tolerance allows bacteria to survive long enough under drug pressure, resistant mutants have more opportunity to arise and spread. The discovery that tolerance clusters by phylogenetic lineage and that specific functional gene categories are enriched for mutations in high-tolerance strains offers a clearer picture of where researchers should look for tolerance mechanisms. While the study does not itself change treatment, it points to the value of combining lineage information and genetic analysis to understand which strains may pose greater risk for the development and spread of MDR-TB, and it suggests molecular pathways that could be studied further to reduce tolerance and slow resistance evolution.