pH shifts help tuberculosis bacteria survive antibiotic treatment

Tuberculosis (TB) is notoriously hard to cure in part because some Mycobacterium tuberculosis (Mtb) cells enter a drug-tolerant persister state: they survive antibiotic treatment without showing genetic resistance. To better define what causes this difficult-to-study phenotype, researchers led by David R. Sherman screened 2,336 FDA-approved drugs looking for compounds that affect persistence. The search turned up an unexpected result. Instead of finding a drug that kills persisters, the team identified a strong inducer of drug tolerance: the antiparasitic niclosamide (NCA), a compound known to disrupt the proton motive force. This finding contrasted with earlier reports suggesting niclosamide (NCA) might have promising anti-TB activity. The work reframes how some chemical effects on bacterial physiology — in this case disruption of proton motive force — can push Mtb into a protected state that survives otherwise lethal antibiotic exposure. By deliberately inducing this state in the lab, the researchers aimed to create a reproducible way to study persisters and to map the molecular changes that accompany their emergence.

The study combined a broad drug screen with focused mechanistic experiments. From the 2,336 FDA-approved drugs tested, niclosamide (NCA) emerged as a strong inducer of tolerance. Follow-up tests showed that niclosamide (NCA) protected Mtb from bactericidal doses of isoniazid, rifampicin, and other standard TB drugs. To understand how this protection worked, the team separated effects on the proton motive force into its components. They showed that disruption of the pH gradient and the resulting intracellular acidification are required to induce tolerance, whereas disruption of membrane potential is not sufficient. They also found that the degree of protection is tunable by external pH. Transcriptomic analysis of these chemically-induced persister (CIP) cells implicated specific genes in the tolerance phenotype, and targeted knockdowns confirmed roles for three genes in either promoting or mitigating the tolerance state. Together the methods link a clear chemical perturbation to a reproducible drug-tolerant state and to gene-level contributors.

These findings carry two important messages. First, chemical disruption of the pH gradient is a facile and rapid means to induce drug tolerance, so researchers now have a practical tool to generate reproducible chemically-induced persister (CIP) cells for study. That will help dissect the molecular and genetic basis of persistence in TB and potentially in other infectious diseases. Second, the study cautions against assuming that compounds such as niclosamide (NCA) will always be helpful as anti-TB agents: under some conditions they can protect Mtb from frontline drugs like isoniazid and rifampicin. The demonstration that protection is driven by intracellular acidification and is tunable by external pH points to new experimental levers — and new risks — when manipulating bacterial physiology. Ultimately, this work provides both a warning and a new laboratory approach for tackling the stubborn problem of TB persisters.