A one-two punch knocks out biofilms

Biofilm formation, a tactic used by some bacterial pathogens to evade drug treatment and the human immune response, is a growing threat to human health. Now, Conlon et al.¹ describe a novel strategy to destroy biofilm-associated Staphylococcus aureus, a pathogen that can cause a range of severe diseases. They report in Nature that two antibiotics, when used together, eliminate S. aureus growing in biofilms, kill methicillin-resistant S. aureus (MRSA) and eradicate a deep-seated S. aureus infection in mice.

The two antibiotics are acyldepsipeptide 4 (ADEP4) and rifampicin. ADEP4 had been shown to kill replicating S. aureus² but it had not been tested against so-called bacterial persisters, phenotypic variants that tend to grow in biofilms. Because commonly used antibiotics target processes essential to bacterial replication, they are often ineffective against metabolically inactive persisters.

Conlon et al.¹ show that, whereas antibiotics such as vancomycin and ciprofloxacin are only marginally effective against S. aureus persisters, ADEP4 reduces their numbers exponentially within a day. ADEP4 acts by binding to ClpP, the catalytic core of a bacterial protease, activating it to degrade proteins indiscriminately². A large quantitative proteomics study reveals that ADEP4-ClpP targets more than 400 proteins for degradation, and first among them are essential ribosomal proteins¹. Conlon et al.¹ suggest that the efficacy of ADEP4 against persisters may be linked to its ability to uncouple ClpP from ATP dependency², activating the protease in dormant cells that have low energy levels.

“It's really important to find new antibiotics, particularly those that are active against S. aureus and against bacteria in biofilms,” says Carl Nathan of Weill Cornell Medical College in New York. “The discovery that ADEP4-mediated activation of ClpP is efficacious against S. aureus is significant because it represents a way to kill a group of nonreplicating or slowly replicating bacteria by targeting a pathway that is not on the classical list.” Conlon et al.¹ find that the effects of ADEP4 are impressive but transient, because bacterial growth quickly rebounds as clpP mutants arise that are resistant to ADEP4. But clpP mutants have lower fitness and are 10–100 times more susceptible to rifampicin compared with wild-type S. aureus. So even though rifampicin on its own is ineffective against S. aureus persisters, when combined with ADEP4 it reduces S. aureus cell counts to extremely low levels.

The problem of antibiotic-resistant biofilms is becoming increasingly acute with the rise in medical interventions such as insertions of catheters and prostheses and the paucity of new antibiotics with unconventional mechanisms of action. The efficacy of ADEP4 and rifampicin against S. aureus biofilms and MRSA is a tale of success, but more work is needed to determine whether this approach will work against other biofilm-forming and antibiotic-resistant pathogens. “It would be a big mistake to assume that the word 'biofilm' refers to exactly the same thing no matter what community of organisms is causing it, which anatomical site you find it in or how long it's been there,” says Nathan. Similarly, “persistence is an operational definition, and we still don't know whether bacteria that persist against one antibiotic are similar to those that persist against a different antibiotic,” Nathan adds.

The principle that bacterial persisters can be killed by activating an inactive target represents a promising alternative to the conventional approach of seeking to inhibit active pathways. A deeper understanding of the processes that are active and inactive in persisters and in biofilm formation will be critical to the identification of additional drug targets. While the hunt for new antibiotics continues, activating ClpP to kill S. aureus persisters holds promise for treatment of a dangerous human pathogen.