Francois Lebreton, Ph.D.

Research Summary

Research Summary

Dr. Francois Lebreton applies genomic technologies to the important and rapidly growing problem of microbial antibiotic resistance. His research focuses on discovering new insights into the evolution of hospital adapted bacterial pathogens and developing new ways to treat and prevent antibiotic resistant infections of the eye, ear, skin and other sites. He is extensively trained in the epidemiology and molecular aspects of bacterial antimicrobial resistance. He worked with Dr. Michael Gilmore on developing comparative and functional genomic analyses to identify traits that make bacterial infections naturally refractory to antibiotic treatment; factors that allow enterococci bacterial cells to colonize the various ecologies in humans and other hosts; and characteristics that predispose hospital adapted bacteria to readily develop drug resistance.

His most notable work consists of a technical tour de force and shows that the terrestrialization of animals, 425 MYA, foreordained the enterococci bacteria to become leading hospital pathogens in the 20th and 21st centuries. This is a unique story in relating the evolution of specific microbial traits to planetary events.

Selected Publications

For a full publication list, please see his CV.

Zhang S*, Lebreton F*, Mansfield MJ*, Miyashita SI, Zhang J, Schwartzman JA, Tao L, Masuyer G, Martínez-Carranza M, Stenmark P, Gilmore MS, Doxey AC, Dong M. Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host Microbe. 2018 Feb 14;23(2):169-176.e6. *authors contributed equally

Lebreton F, Manson A, Saavedra J, Straub T, Earl A and Gilmore MS.  Tracing the Enterococci from Paleozoic Origins to the Hospital. Cell. 2017 May 18; 169: 1–13.

Gilmore MS, Rauch M, Ramsey MM, Himes PR, Varahan S, Manson JM, Lebreton F, Hancock LE. Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strainsProc Natl Acad Sci U S A. 2015 Jun 9;112(23):7273-8.

Lebreton F, van Schaik W, McGuire AM, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJ, Earl AM, Gilmore MS. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strainsMBio. 2013 Aug 20;4(4). pii:e00534-13.

Lebreton F, van Schaik W, Sanguinetti M, Posteraro B, Torelli R, Le Bras F, Verneuil N, Zhang X, Giard JC, Dhalluin A, Willems RJ, Leclercq R, Cattoir V. AsrR is an oxidative stress sensing regulator modulating Enterococcus faecium opportunistic traits, antimicrobial resistance, and pathogenicityPLoS Pathog. 2012;8(8):e1002834.

Lebreton F, Depardieu F, Bourdon N, Fines-Guyon M, Berger P, Camiade S, Leclercq R, Courvalin P, Cattoir V. D-Ala-d-Ser VanN-type transferable vancomycin resistance in Enterococcus faecium. Antimicrob Agents Chemother. 2011 Oct;55(10):4606-12.

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2006: B.Sc., Biochemistry, Faculty of Sciences, University of Caen, France

2008: M.Sc., Molecular and Cellular Biology, Faculty of Sciences, University of Caen, France

2011: Ph.D., Molecular and Cellular Biology, Medical School of the University of Caen, France

Postgraduate Training

2011-2013: Research Associate, Microbiology, Harvard Medical School/Mass. Eye and Ear

2011-2016: Research Associate, Microbial genomics, The Broad Institute

2013-2016: Senior Research Associate, Microbiology, Harvard Medical School/Mass. Eye and Ear

Academic Appointments

2016-present: Instructor in Ophthalmology, Harvard Medical School

Professional Memberships

2010-present: American Society for Microbiology (ASM)

2009-present: Societe Francaise de Microbiologie (SFM)


2008: Award for academic excellence, University of Caen, France

2012: Organizer/Chair of Mini-Symposium on Enterococci and Streptococci at Institut Pasteur, Paris, France

2013: Recommended publication (F1000 Prime)

2013: Editor’s pick (mBio)

2013: Research highlight (Nature Reviews in Microbiology)

2013: Invited speaker, Antimicrobial Agents Section of the French Society of Microbiology. Paris, France

2014: Citation of scholarship in PCAST report to US President

2014: Best presentation, EMBO Conference on Microbiology after the genomics revolution, Pasteur, Paris

2014: Invited speaker, Bacterial Evolution Seminar. Massachusetts Institute of Technology. Cambridge, USA

2014: Invited speaker, 4th ASM conference on enterococci. Carthagena, Colombia

2015: Best presentation, Gordon Research Seminar, Newport, USA

2016: Invited speaker, Fellows’ Recognition Day, Schepens Eye Research Institute, Boston, USA

2016: Invited speaker, ASM Microbe, Boston, USA      

2017: Participation to TV show (Microbe Apocalypse, NowThis production)

2017: Research highlight (Nature Reviews in Microbiology)

2017: Commentary (Cell Host and Microbe)

2018: Organizer 5th International Conference on Enterococci (April 2018), Chamonix, France

2018: Commentary (Cell Host and Microbe)

2018: Editor’s pick (Cell Host and Microbe)

2018: Invited speaker annual meeting of French Society for Microbiology, Paris, France

2018: Organizer 6th annual meeting of the Boston Area Antibiotic Resistance Network, Boston, USA

2018: Core faculty member International Course on Antibiotic Resistance, Institut Pasteur, Annecy, France