The ability of Mycobacterium tuberculosis to acquire resistance to drug treatments appears to be a multistep process, according to results of a study funded in part by the Massachusetts General Hospital Division of Pulmonary and Critical Care. By leveraging a new method of analyzing whole genome sequences of TB, researchers revealed 39 new genes associated with elevated drug resistance.

“Several of the genes we identified are related to the bacteria’s regulation of cell walls; since many classes of drugs target the cell walls, we speculate that changes to the structure or metabolism of the cell walls might confer resistance to a wide variety of drugs,” said first author Maha Farhat, HMS instructor in medicine and assistant physician at Massachusetts General Hospital.

This changes the current line of thinking, which is that single mutations conferred high-level resistance: a strain either had them or did not, according to co-author Megan Murray, MD, MPH, ScD, professor of Global Health and Social Medicine at Harvard Medical School. “Knowing that small changes early in the evolution of resistance open the door for big changes, or that a single change is a gateway to global resistance, would be important clues in our struggle to outrace evolving drug resistance.”

Investigators adapted tools from evolutionary biology known as “phylogenetics,” which allows the study of relationships within populations of organisms. These tools were used to measure the rapid-fire evolution of drug-resistant TB in the clinic.

Researchers examined the whole genomes of 116 newly sequenced and 7 previously sequenced strains of TB. The project used a large set of clinical strains collected from human populations rather than strains that were developed in the lab. They sampled strains from outbreaks in British Columbia, Rome, South Africa, and Russia. The strains came from dozens of sites around the world, including most of the major lineages of susceptible TB currently circulating around the world.

“We don’t really understand why resistance develops so consistently,” Murray said. “This study may provide a lens that we can use to see a way to develop better diagnostics for impending resistance, or even ways to prevent it from happening.”