Yu Imai, Glenn Hauk, Jeffrey Quigley, Libang Liang, Sangkeun Son, Meghan Ghiglieri, Michael F. Gates, Madeleine Morrissette, Negar Shahsavari, Samantha Niles, Donna Baldisseri, Chandrashekhar Honrao, Xiaoyu Ma, Jason J. Guo, James M. Berger and Kim Lewis. (2022) Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis. Nature Chemical Biology. full-text

R. Shukla, F. Lavore, S. Maity, M.G.N. Derks, C.R. Jones, B.J.A. Vermeulen, A. Melcrová, M.A. Morris, L.M Becker, X. Wang, R. Kumar, J. Medeiros-Silva, R.A.M. van Beekveld, A.M.J.J. Bonvin, J. Lorent, M. Lelli, J. Nowick, H.D. MacGillavry, A.J. Peoples, A.L. Spoering, L.L. Ling, D.E. Hughes, W.H. Roos, E. Breukink, K. Lewis, and M. Weingarth (2022) Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature (Published online: 03 August 2022).full-text

Nadja Leimer*, Xiaoqian Wu*, Yu Imai*, Madeleine Morrissette, Norman Pitt, Quentin Favre-Godal, Akira Iinishi, Samta Jain, Mariaelena Caboni, Inga V. Leus, Vincent Bonifay, Samantha Niles, Rachel Bargabos, Meghan Ghiglieri, Rachel Corsetti, Megan Krumpoch, Gabriel Fox, Sangkeun Son, Dorota Klepacki, Yury S. Polikanov, Cecily Freliech, Julie McCarthy, Diane G. Edmondson, Steven J. Norris, Anthony D’Onofrio, Linden Hu, Helen I. Zgurskaya, Kim Lewis. (2021) A Selective Antibiotic for Lyme Disease. Cell. full-text

Manuse S*, Shan Y*, Canas-Duarte SJ*, Bakshi S, Sun WS, Mori H, Paulsson J, Lewis K. (2021) Bacterial persisters are a stochastically formed subpopulation of low-energy cells. PLoS Biology. 19(4):e3001194. PubMed / PLoS Biology

Kaur H*, Jakob RP*, Marzinek JK, Green R, Imai Y, Bolla JR, Agustoni E, Robinson CV, Bond PJ, Lewis K, Maier T, Hiller S. (2021) The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature. 593(7857):125-129. PubMed / Nature

Morrissette M*, Pitt N*, González A, Strandwitz P, Caboni M, Rebman AW, Knight R, D’Onofrio A, Aucott JN, Soloski MJ, Lewis K. (2020) A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients. mBio. 11:e02310-20. PubMed / mBio

Quigley J, Peoples A, Sarybaeva A, Hughes D, Ghiglieri M, Achorn C, Desrosiers A, Felix C, Liang L, Malveira S, Millett W, Nitti A, Tran B, Zullo A, Anklin C, Spoering A, Ling LL, Lewis K. (2020) Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis. mBio. 11(4):e01516-20. PubMed / mBio

Lewis K. (2020) The Science of Antibiotic Discovery. Cell. 181(1):29-45. PubMed / Cell

Imai Y*, Meyer KJ*, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O’Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D’Onofrio A, and Lewis K. (2019) A new antibiotic selectively kills Gram-negative pathogens. Nature. 576(7787):459-464. Full-text access / PubMed / Nature

Zalis EA*, Nuxoll AS*, Manuse S, Clair G, Radlinski LC, Conlon BP, Adkins J, Lewis K. (2019) Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. mBio. e01930-19. PubMed / mBio

Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K. (2018) GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 4(3):396-403. PubMed / Nat Microbiol

Wu X, Sharma B, Niles S, O’Connor K, Schilling R, Matluck N, D’Onofrio A, Hu LT, Lewis K. (2018) Identifying Vancomycin as an effective antibiotic for killing Borrelia Burgdorferi. Antimicrob. Agents Chemother. e01201-18. PubMed / Antimicrob Agents Chemother

Cameron DR, Shan Y, Zalis EA, Isabella V, Lewis K. (2018) A genetic determinant of persister cell formation in bacterial pathogens. J Bacteriol. e00303-18. PubMed / J Bacteriol

Fenn K*, Strandwitz P*, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K. (2017) Quinones are growth factors for the human gut microbiota. Microbiome. 5(1):161. PubMed / Microbiome

Shan Y*, Brown Gandt A*, Rowe SE, Deisinger JP, Conlon BP, Lewis K. (2017) ATP dependent persister formation in Escherichia coli. mBio. 8:e02267-16. PubMed / mBio

Conlon B, Rowe SE, Brown Gandt A, Nuxoll A, Donegan N, Zalis E, Clair G, Adkins J, Cheung A, Lewis K. (2016) Persister formation in Staphylococcus aureus is associated with ATP depletion. Nat Microbiol. 1:16051. PubMed / Nat Microbiol

Schumacher, M., Balani, P., Min, J., Chinnam, N., Hansen, S., Vulić, M., Lewis, K.*, Brennan, R.* (2015) HipAB-promoter structures reveal basis of heritable multidrug tolerance. Nature. 524:59-64. PubMed / Nature

Sharma, B., Brown, A., Matluck, N., Hu, L., Lewis, K. (2015) Borrelia burgdorferi, the causative agent of Lyme disease, forms drug-tolerant persister cells. Antimicrob Agents Chemother. 59:4616-24. Pubmed / Antimicrob Agents Chemother

Shan, Y., Lazinski, D., Rowe, S., Camilli, A., Lewis, K. (2015) Genetic basis of persister tolerance to aminoglycosides in Escherichia coli. mBio. e00078-15. PubMed / mBio

Ling, L., Schneider, T., Peoples, A., Spoering, A., Engels, I., Conlon, B., Mueller, A., Schäberle, T., Hughes, D., Epstein, S., Jones, M., Lazarides, L., Steadman, V., Cohen, D., Felix C., Fetterman, K., Millett, W., Nitti, A.,Zullo, A., Chen, C., and Lewis, K. (2015) A novel antibiotic kills pathogens without detectable resistance. Nature. 517:455-459. PubMed / Nature

Gavrish, E., C. S. Sit, S. Cao, O. Kandror, A. Spoering, A. Peoples, L. Ling, A. Fetterman, D. Hughes, A. Bissell, H. Torrey, T. Akopian, A. Mueller, S. Epstein, A. Goldberg, J. Clardy and K. Lewis. (2014) Lassomycin, a ribosomally synthesized cyclic peptide, kills Mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem Biol. 21: 509-518. PubMed / Chem Biol

Fleck, L., North E., Lee R., Mulcahy L., Casadei G., Lewis K. (2014) A screen for and validation of prodrug antimicrobials. Antimicrob Agents Chemother. 58:1410-9. PubMed / Antimicrob Agents Chemother

Theodore, A.,Lewis, K., Vulic, M. (2013) Tolerance of Escherichia coli to fluoroquinolone antibiotics depends on specific components of the SOS response pathway. Genetics. 195(4):1265-76. PubMed / Genetics

Conlon, B., Nakayasu, E., Fleck, L., LaFleur, M., Isabella, V., Coleman, K., Leonard, S., Smith, R., Adkins, J. and Lewis, K. (2013) Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature. 503(7476):365-370. PubMed / Nature

Balaban, N., Gerdes, K., Lewis, K., McKinney, J. (2013) A problem of persistence: still more questions than answers. Nat Rev Microbiol. 11, 587-591. PubMed / Nat Rev Microbiol

Lewis, K. (2013) Platforms for antibiotic discovery. Nat Rev Drug Discov. 12, 371-387. PubMed / Nat Rev Drug Discov

Keren, I., Wu, Y., Innocencio, J., Mulcahy, L., and Lewis, K. (2013) Killing by bactericidal antibiotics does not depend on reactive oxygen species. Science. 339: 1213-1216. PubMed / Science

Wu, Y., Vulić, M., Keren, I., Lewis, K. (2012) Role of oxidative stress in persister tolerance. Antimicrob Agents Chemother. 56(9): 4922-4926. PubMed / Antimicrob Agents Chemother

Lewis, K. (2012) Antibiotics: Recover the lost art of drug discovery. Nature. 485:439-440. PubMed / Nature

Keren, I., Minami, S., Rubin, E. and Lewis, K. (2011) Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters. mBio. e00100-11. PubMed / mBio

Mulcahy, L., Burns, J., Lory, S., Lewis, K. (2010) Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. Journal of bacteriology. 192:6191–6199. PubMed / J Bacteriol

  • Microbe (2011) “Persister Cells Fingered in Chronic CF”. (Feature).

Lewis, K. (2010) Persister cells. Annu Rev Microbiol. 64:357-372. PubMed / Annu Rev Microbiol

D’Onofrio, A., Crawford, J., Stewart, E., Witt, K., Gavrish, E., Epstein, S., Clardy, J., Lewis, K. (2010) Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria. Chem Biol. 17(3):254-264. PubMed / Chem Biol

  • Discover Magazine (2010) “Luring Out the Missing Biosphere” by Carl Zimmer.
  • Faculty of 1000 Biology (2010), A “Must read” by Harald Labischinski.
  • Microbe Feature (2010), by Carol Potera, and Podcast.

Dörr, T., Vulić, M., Lewis, K. (2010) Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli. PLoS Biol. e1000317. PubMed / PLoS Biol

  • Faculty of 1000 Biology (2010) Review by Daniel Madar and Uri Alon.
  • Boston Globe (2010) “Outwitting germs that never say die”. Carolyn Y. Johnson.

LaFleur, M., Qi, Q., Lewis, K. (2010) Patients with long-term oral carriage harbor high-persister mutants of Candida albicans. Antimicrob Agents Chemother. 54:39–44. PubMed / Antimicrob Agents Chemother

Dörr T, Lewis K, Vulic M, (2009) SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet. e1000760. PubMed / PLoS Genet

Schumacher, M., Piro, K., Xu, W., Hansen, S., Lewis, K., and Brennan, R. (2009) Molecular mechanisms of HipA mediated multidrug tolerance and its neutralization by HipB. Science. 323:396-401. PubMed / Science

Hansen, S., Lewis, K., Vulic, M. (2008) Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli. Antimicrob Agents Chemother. 52:2716-26. PubMed / Antimicrob Agents Chemother

  • Microbe, Current Topics. (2008) “Genes Underlying Bacterial ‘Persister Cells’ Identified”. 3:399-400.

Moy, T., Ball, A., Anklesaria, Z., Casadei, G., Lewis, K., Ausubel F. (2006) Identification of novel antimicrobials using a live-animal infection model. PNAS. 103:10414-9. PubMed / PNAS

  • PNAS In the News (July 2006). “Identification of novel antimicrobials using a live-animal infection model”.
  • Nature Reviews: Microbiology, Research Highlights (August 2006). “Anti-infectives Worming a way to better drugs”.
  • Nature Biotechnology, Research Highlights (September 2006). “The worm turns for antimicrobial discovery”.