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Activated ClpP kills persisters and eradicates a chronic biofilm infection

Nature volume 503, pages 365370 (21 November 2013) | Download Citation



Chronic infections are difficult to treat with antibiotics but are caused primarily by drug-sensitive pathogens. Dormant persister cells that are tolerant to killing by antibiotics are responsible for this apparent paradox. Persisters are phenotypic variants of normal cells and pathways leading to dormancy are redundant, making it challenging to develop anti-persister compounds. Biofilms shield persisters from the immune system, suggesting that an antibiotic for treating a chronic infection should be able to eradicate the infection on its own. We reasoned that a compound capable of corrupting a target in dormant cells will kill persisters. The acyldepsipeptide antibiotic (ADEP4) has been shown to activate the ClpP protease, resulting in death of growing cells. Here we show that ADEP4-activated ClpP becomes a fairly nonspecific protease and kills persisters by degrading over 400 proteins, forcing cells to self-digest. Null mutants of clpP arise with high probability, but combining ADEP4 with rifampicin produced complete eradication of Staphylococcus aureus biofilms in vitro and in a mouse model of a chronic infection. Our findings indicate a general principle for killing dormant cells—activation and corruption of a target, rather than conventional inhibition. Eradication of a biofilm in an animal model by activating a protease suggests a realistic path towards developing therapies to treat chronic infections.

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We thank B. Wright and C. Blinn of AstraZeneca for assisting with the establishment of the mouse infection model, R. E. Lee, M. Pollastri and Z. Maglika for critical discussions and advice, I. Keren and S. Rowe for reading of the manuscript, H. Brewer, V. Petyuk and D. Camp II for assistance with proteomics, and Z. Zheng for assistance with ChemDraw. This work was supported by NIH award T-RO1 AI085585 to K.L., by Arietis Corporation to M.D.L and K.C., by the NIH-NIAID IAA Y1-AI-8401 to J.N.A. and P41 GM103493-11 to R.D.S. Proteomic analysis was performed in the EMSL, a DOE-BER national scientific user facility at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle Memorial Institute for the DOE under contract DE-AC05-76RLO 1830.

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Author notes

    • E. S. Nakayasu

    Present address: Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA.


  1. Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA

    • B. P. Conlon
    • , L. E. Fleck
    • , V. M. Isabella
    •  & K. Lewis
  2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA

    • E. S. Nakayasu
    • , R. D. Smith
    •  & J. N. Adkins
  3. Arietis Corporation, Boston, Massachusetts 02118, USA

    • M. D. LaFleur
    •  & K. Coleman
  4. Bouvé College of Health Sciences, School of Pharmacy, Northeastern University, Boston, Massachusetts 02115, USA

    • S. N. Leonard


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B.P.C., M.D.L., K.C. and K.L. designed the study, analysed results and wrote the manuscript. B.P.C. performed in vitro antibiotic susceptibility assays, collected samples for proteomics, and performed biofilm susceptibility studies and mouse infection models. V.M.I. assisted with in vitro susceptibility assays. E.S.N. and J.N.A. performed i-TRAQ proteomics and analysed results. L.E.F. participated in mouse infection model experiments. S.N.L performed hollow-fibre experiments. M.D.L. was responsible for histopathology. R.D.S. provided the proteomics measurement capabilities.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to K. Lewis.

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