Email: k.lewis@neu.edu

Phone: 617.373.8238
Fax: 617.373.3724

Location: 406 Mugar Life Sciences
Mail: NU/Biology
         134 Mugar Life Sciences
         360 Huntington Avenue
         Boston, MA 02115 USA

Lewis Lab

Research Description

Molecular Microbiology/Biotechnology
My Laboratory works on antibiotic resistance and drug discovery, persister cells, and unculturable bacteria.

1. Persister cells and infectious diseases.

Many human disease such as tuberculosis or biofilm infections are very difficult to eradicate with existing antibiotics. Microbial biofilms are responsible for over 60% of all infections, according to the CDC. We found that biofilm tolerance is largely due to the presence of a small fraction of persister cell essentially invulnerable to antibiotics (Brooun et al., 2000; Spoering and Lewis, 2001). Persisters are not mutants, but phenotypic variants of the wild type. We developed a method to isolate persisters and obtained their gene profile, which points to a dormancy program that is turned on in these cells (Keren et al., 2004). We find that proteins known as “toxins” that form toxin/antitoxin modules participate in persister formation.  “Toxins” appear to be the exact opposite of what their name suggests, they reversibly block important processes such as translation, protecting the cell from bactericidal antibiotics that are ineffective against inactive targets. Our current focus is to understand the workings of this dormancy program. The same program may be responsible for the tolerance of M. tuberculosis to antibiotics as well, leading to a latent form of the disease which which can then relapse into a life-threatening infection. We are currently testing whether persister cells are responsible for latency of M. tuberculosis. On the applied side, we are developing drugs that can kill persister cells.

2. Discovery of “unculturable” microorganisms; Novobiotic Pharmaceuticals (in collaboration with Professor Slava Epstein)

It has been known for over half a century that 99% of all microbial species from most environments are unculturable. Microbiology as a discipline has been focusing by necessity on the 1% of cultivable species.  Attempts to culture more species in the lab by manipulating growth media were unsuccessful.

We have recently designed a diffusion chamber for growing unculturable organisms. The idea was to provide a simulated natural environment by growing microorganisms in a chamber that allows exchange of chemicals with the environment, but restricts movement of cells (Kaeberlein et al., 2002).

The chamber enables growth of unculturable organisms. We also find that many unculturable organisms will grow on synthetic media in the presence of other, neighboring species, and are currently isolating substances that act as growth promoters. Apparently, lack of growth on foreign media is due to choice, rather than a missing metabolic ability. We were able to mutate/select a large number of unculturable species for growth on regular media in a Petri dish. The previously uncultured bacteria are an attractive source for natural product discovery, and we are screening them for novel antibiotics. The focus of current research is understanding the molecular nature of uncultivability, and finding novel microorganisms. About a third of bacterial domains do not have a single cultivable representative, and we know of their existence only from DNA extracted from the environment.

3. Natural inhibitors of microbial resistance from medicinal plants.

Bacteria have an unusual ability to resist chemically unrelated antimicrobials, including ones they never encountered in nature. This ability is largely due to the presence of Multidrug Resistance Pumps, membrane translocases that pump out antibiotics from the cell (Lomovskaya and Lewis, 1992). MDRs are found in all microorganisms, and we wondered whether organisms that produce antibiotics learned how to combat this resistance.

Medicinal plants make many different types of antimicrobials, but these are rather weak when tested in vitro. We find that this is due to their efflux by MDRs (Tegos et al., 2002). But why should plants keep on producing antibiotics if microorganisms have MDR pumps that make these substances essentially ineffective? We reasoned that plants are “smart” and have developed MDR inhibitors that act synergistically with antibiotics. We indeed discovered a compound that specifically disrupts this bacterial resistance mechanism. Barberry plants make an ineffective antibiotic berberine. We found that barberry also produces 5'-methoxyhydnocarpin-D (5'-MHC), that is a potent inhibitor of MDRs (Stermitz et al., 2000). When combined with berberine, 5'-MHC has effective antimicrobial action. Importantly, 5'-MHC has no antimicrobial activity on its own. This finding provides an important precedent for the idea that synergistic interaction among different compounds (antimicrobial or not) explains the frequent failures to isolate single active substances from medicinal plants. Plants have faced the problem of microbial multidrug resistance for far longer than we have, and their solution is apparently to use a combination of an antibiotic with an MDR inhibitor. Emulating Nature's strategy and potentiating antibiotics with MDR inhibitors can be an effective strategy against drug-resistant microorganisms.

4. Sterile surface materials.

We have recently developed a “sterile” surface material in collaboration with Professor Alexander Klibanov of MIT (Tiller et al., 2001; Lewis and Klibanov, 2005).
Antimicrobial action requires the active molecule to penetrate into the cell in order to reach its target. This would seemingly preclude creation of a surface to which antimicrobials are bound covalently and are therefore immobilized. We reasoned that an antimicrobial molecule tethered covalently to the surface by a long polymer “thread” will retain its mobile properties and will be able to penetrate into cells and reach its targets. N-hexylated poly(4-vinylpyridine) coupled to the surface of amino-glass produced a polymer material that kills bacteria on contact. Interestingly, resistance does not develop to antimicrobial polymers, probably because nature has not encountered this design before. Sterile surface materials promise to provide a new class of antimicrobials for hospitals to stem the spread of drug-resistant pathogens, and to prevent biofilm formation on indwelling devices such as catheters.

Selected Publications

Lewis, K. (2007) Persister cells, dormancy and infectious disease. Nat. Rev. Microbiol. 5:48-56. [PDF]

Lewis, K. and Ausubel, FM. (2006) Prospects for plant-derived antibacterials. Nat. Biotechnol. 24:1504-7. [PDF]

Correia, FF., D’Onofrio, A., Rejtar, T., Li, L., Karger, BL., Makarova, K., Koonin, EV., and Lewis, K. (2006) Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J. Bacteriol. 188:8360-7. [PDF]

Ball, AR., Casadei, G., Samosorn, S., Bremner, JB., Moy, TI., and Lewis, K. (2006) Conjugating berberine to a multidrug efflux pump inhibitor creates an effective antimicrobial. ACS Chem. Biol. 1:594-600. [PDF]

LaFleur, MD., Kumamoto, CA., and Lewis, K. (2006) Candida albicans biofilms produce antifungal-tolerant persister cells. Antimicrob. Agents Chemother. 50:3839-46. [PDF]

Belofsky, G., Carreno, R., Lewis, K., Ball, A., Casadei, G., and Tegos, G.P. (2006) Metabolites of the ‘Smoke Tree’ Dalea spinosa Potentiate Antibiotic Activity against Multi-Drug Resistant (MDR) Staphylococcus aureus. J. Nat. Prod. Chem. 69:261-4. [PDF]

Moy, T.I., Ball, A.R., Anklesaria, Z., Casadei, G., Lewis, K., and Ausubel F.M. (2006) From the Cover: Identification of novel antimicrobials using a live-animal infection model. Proc. Natl. Acad. Sci. U S A. 103:10414-9. [PDF]

Shah, D.V., Zhang, Z., Kurg, K., Kaldalu, N, Khodursky, A, and Lewis, K. (2006) Persisters: A distinct physiological state of E. coli. BMC Microbiol. 6:53. [PDF]

Spoering, A.L., Vulic, M., Lewis, K. (2006) GlpD and PlsB Participate in Persister Cell Formation in Escherichia coli. J. Bacteriol. 188:5136-44. [PDF]

Samosorn, S., Bremner, J.B., Ball A., and Lewis, K. (2006) Synthesis of functionalised 2-aryl-5-nitro-1H-indoles and their activity as bacterial NorA efflux pump inhibitors. Bioorg. Med. Chem. 14:857-865. [PDF]

Milovic, N.M., Wang, J., Lewis, K., and Klibanov, A.M. (2005) Immobilized N-alkylated polyethylenimine avidly kills bacteria by rupturing cell membranes with no resistance developed. Biotechnol Bioeng. 90:715-722.

Lewis, K. and Klibanov, A.M. (2005) Surpassing nature: rational design of sterile-surface materials. Trends Biotechnol. 23:343-248. [PDF]

Lewis, K., Spoering, A., Kaldalu, N., Keren, I., and Shah, D. (2005) Persisters: Specialized Cells Responsible For Biofilm Tolerance To Antimicrobial Agents. In Biofilms, Infection, and Antimicrobial Therapy. Pace, J., Rupp, M.E. and Finch, R.G. (eds). Boca Raton, London, New York, Singapore: Taylor & Francis, pp. 241-256.

Keren, I., Shah, D., Spoering, A., Kaldalu, N., and Lewis, K. (2004) Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186:8172-80. [PDF]

Keren, I., Kaldalu, N., Spoering, A., Wang, Y., and Lewis, K. (2004). Persister cells and tolerance to antimicrobials. FEMS Microbiol. Lett. 230: 13-18. [PDF]

Kaldalu, N., Mei, R., and Lewis, K. (2004) Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profile. Antimicrob. Agents Chemother. 48:890-896.

Stermitz, Frank R., Cashman, Kevin K., Halligan, Kathleen M., Morel, Cécile, Tegos, George P., Lewis, Kim (2003) Polyacylated Neohesperidosides From Geranium caespitosum: Bacterial Multidrug Resistance Pump Inhibitors. Bioorganic & Medicinal Chemistry Letters 13. [PDF]

Kaeberlein, T., Lewis, K., and Epstein, S.S. (2002) Isolating "uncultivable" microorganisms in pure culture using a simulated natural environment. Science 296:1127-1129. [PDF]

Tiller, J.C., Liao, C.J., Lewis, K., and Klibanov, A.M. (2001) Designing surfaces that kill bacteria on contact. Proc. Natl. Acad. Sci. U S A. 22:5981-5985.

Spoering, A.L. and Lewis, K. (2001) Biofilms and Planktonic Cells of Pseudomonas aeruginosa Have Similar Resistance to Killing by Antimicrobials. J. Bacteriol. 183:6746-6751. [PDF]

Guz, Nathan R., Stermitz, Frank R., Johnson, Jeffrey B., Beeson, Teresa D., Willen, Seth, Hsiang, Jen-Fang, and Lewis, Kim. Flavonolignan and Flavone Inhibitors of a Staphylococcus aureus Multidrug Resistance Pump: Structure-Activity Relationships. J. Med. Chem. 44, 261-268. [PDF]

Stermitz, F.R., Lorenz, P., Tawara, J.N., Zenewicz, L., and Lewis, K. (2000) Synergy in a medicinal plant: antimicrobial action of berberine potentiated by 5'-methoxyhydnocarpin, a multidrug pump inhibitor. Proc. Natl. Acad. Sci. USA 97:1433-1437. [PDF]

Brooun, A., Liu, S., and Lewis, K. (2000) A Dose-Response Study of Antibiotic Resistance in Pseudomonas aeruginosa Biofilms. Antimicrob. Agents Chemother. 44:640-646. [PDF]

Brooun, A., Tomashek, J.J., and Lewis, K.(1999) Purification and ligand binding of EmrR, a regulator of a multidrug transporter. J. Bacteriol. 181:5131-5133.[PDF]

Lewis, K. (1998) Pathogen resistance as the origin of kin altruism. J. Theor. Biol. 43:359-363.

Hsieh, P.C., Siegel, S.A., Rogers, B., Davis, D., and Lewis, K. (1998) Bacteria lacking a multidrug pump: a sensitive tool for drug discovery. Proc. Natl. Acad. Sci. USA. 95:6602-6606. [PDF]

Ferrante, A., Augliera, J., Lewis, K., and Klibanov, M.A. (1995) Cloning of an organic solvent resistance gene in E. coli : the unexpected role of alkylhydroperoxide reductase. Proc. Natl. Acad. Sci. USA 92:7617-7621.

Lomovskaya, O. and Lewis, K. (1992) EMR, an Escherichia coli locus for multidrug resistance. Proc. Natl. Acad. Sci. USA 89: 8938-8942.


Papers from the Lewis lab recently featured in the media:

1. Belofsky, G., Carreno, R., Lewis, K., Ball, A., Casadei, G., and Tegos, G.P. (2006) Metabolites of the ‘Smoke Tree’ Dalea spinosa Potentiate Antibiotic Activity against Multi-Drug Resistant (MDR) Staphylococcus aureus. J. Nat. Prod. Chem. 69:261-4. [PDF]

2. American Society of Pharmacognosy (ASP) Newsletter, Clearing the Air on the Smoke Tree, Vol. 42(2) 2006. [PDF]

3. Moy, T.I., Ball, A.R., Anklesaria, Z., Casadei, G., Lewis, K., and Ausubel F.M. (2006) From the Cover: Identification of novel antimicrobials using a live-animal infection model. Proc. Natl. Acad. Sci. U S A. 103:10414-9. [PDF]

4. Proceedings of the National Academy of Sciences of the United States of America (PNAS) In the News. Identification of novel antimicrobials using a live-animal infection model, July 2006.

5. Nature Reviews: Microbiology, Research Highlights. Anti-infectives Worming a way to better drugs August 2006. [PDF]

6. Nature Biotechnology, Research Highlights. The worm turns for antimicrobial discovery. September 2006. [PDF]

7. Kaeberlin, T., Lewis, K., and Epstein, S. S. (2002) Isolating "uncultivable" microorganisms in pure culture using a simulated natural environment. Science 296:1127-1129. [PDF]

Science (News) 296:550 (2002)

8. Lin, J., Tiller, J.C., Lee, S.B., Lewis, K., and Klibanov, A.M. (2002) Insights into bactericidal action of surface-attached poly(vinyl-N-hexylpyridinium) chains. Biotechnol. Lett. 24:801-805. [PDF]

Chem. Engineer. News (2002) 80:22. Surface Designed to Kill Bacteria

9. Spoering, A. L. and Lewis, K. (2001) Biofilms and Planktonic Cells of Pseudomonas aeruginosa Have Similar Resistance to Killing by Antimicrobials. Journal of Bacteriology 183:6746-6751 [PDF]

ASM News Journal Highlights. Persister Cells Responsible for Biofilms' Antimicrobial Resistance. January 2002.

10. Tiller, J.C., Liao, C.J., Lewis, K., and Klibanov, A.M. (2001). Designing surfaces that kill bacteria on contact. Proc. Natl. Acad. Sci. U S A. 22:5981-5985.  [PDF]

Chem. Engineer. News (2001) 79:13. Designed Surface Kills Bacteria.

Chem. Engineer. News (2001) 79:50. Chemistry highlights 2001. Science (News) 159(21):325 (2001)

Technology Review (MIT) 104:19 (2001)

11. Stermitz, F.R., Lorenz, P., Tawar, J.N., Zenewicz, L., and Lewis, K. (2000). Synergy in a medicinal plant: antimicrobial action of berberine potentiated by 5'-methoxyhydnocarpin, a multidrug pump inhibitor. Proc. Natl. Acad. Sci. USA 97:1433-1437. [PDF]

Chem. Engineer. News (2000). 78 (8):6-7. Plant may hold key to ultimate antibiotic.

Chem. Engineer. News (2000). 78 (51):24-31. Chemistry highlights 2000.

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