Research Topics
Genomes and Genes | Kim LewisSummaryAffiliation: Northeastern University Country: USA Publications
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Publications
Persister eradication: lessons from the world of natural productsIris Keren
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, Massachusetts, USA Electronic address
Methods Enzymol 517:387-406. 2012..Finally, one of the best bactericidal agents is rifampin, an inhibitor of RNA polymerase, and we suggest that it "kills" by preventing persister resuscitation...
Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coliIris Keren
Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115
J Bacteriol 186:8172-80. 2004..The function of these specialized dormant cells is to ensure the survival of the population in the presence of lethal factors...
Surpassing nature: rational design of sterile-surface materialsKim Lewis
Department of Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
Trends Biotechnol 23:343-8. 2005..These sterile-surface materials kill both air- and waterborne pathogens and are not susceptible to existing resistance mechanisms...
Persister cells and the riddle of biofilm survivalK Lewis
Northeastern University, Boston, MA 02115, USA
Biochemistry (Mosc) 70:267-74. 2005..Persisters are essentially altruistic cells that forfeit propagation in order to ensure survival of kin cells in the presence of lethal factors...
Persister cells, dormancy and infectious diseaseKim Lewis
Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
Nat Rev Microbiol 5:48-56. 2007..The molecular mechanisms that underlie the formation of dormant persister cells are now being unravelled and are the focus of this Review...
Intact DNA in ancient permafrostKim Lewis
Department of Biology, Northeastern University, Boston, MA 02115, USA
Trends Microbiol 16:92-4. 2008..The data presented in this work raise intriguing questions about the nature of bacteria in many of the ancient samples reported to date: are they spores, persisters, sessile vegetative cells or do they make up a slow-growing population?..
Multidrug tolerance of biofilms and persister cellsK Lewis
Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02459, USA
Curr Top Microbiol Immunol 322:107-31. 2008..Other approaches to the problem include sterile-surface materials, prodrug antibiotics, and cyclical application of conventional antimicrobials...
Prospects for plant-derived antibacterialsKim Lewis
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
Nat Biotechnol 24:1504-7. 2006..Can weakly active phytochemicals be combined synergistically to produce new antibacterial treatments?..
Persister cellsKim Lewis
Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA
Annu Rev Microbiol 64:357-72. 2010..Stress responses may act as general activators of persister formation. Proteins required for maintaining persisters may represent realistic targets for discovery of drugs capable of effectively treating chronic infections...
Uncultured microorganisms as a source of secondary metabolitesKim Lewis
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, MA, USA
J Antibiot (Tokyo) 63:468-76. 2010..The new cultivation approaches allow for the exploitation of the secondary metabolite potential of the previously inaccessible microorganisms...
Conjugating berberine to a multidrug efflux pump inhibitor creates an effective antimicrobialAnthony R Ball
Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA
ACS Chem Biol 1:594-600. 2006..The hybrid molecule showed good efficacy in a Caenorhabditis elegans model of enterococcal infection, curing worms of the pathogen...
High-throughput screen for novel antimicrobials using a whole animal infection modelTerence I Moy
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
ACS Chem Biol 4:527-33. 2009..elegans animals but do not affect the growth of the pathogen in vitro, thus acting by a mechanism of action distinct from antibiotics currently in clinical use...
Role of oxidative stress in persister toleranceYanxia Wu
Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
Antimicrob Agents Chemother 56:4922-6. 2012..These findings show that induction of a classical resistance mechanism, MDR efflux, by oxidative stress leads to an increase in multidrug-tolerant persister cells...
Persisters: a distinct physiological state of E. coliDevang Shah
Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115, USA
BMC Microbiol 6:53. 2006..Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944...
Persister cells and tolerance to antimicrobialsIris Keren
Department of Biology, Northeastern University, Boston, MA 02115, USA
FEMS Microbiol Lett 230:13-8. 2004..This suggests that persisters are not at a particular stage in the cell cycle, neither are they defective cells nor cells created in response to antibiotics. Our data indicate that persisters are specialized survivor cells...
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coliFrederick F Correia
Department of Biology, Northeastern University, 405 Mugar Hall, 360 Huntington Avenue, Boston, MA 02115, USA
J Bacteriol 188:8360-7. 2006..Taken together, these results suggest that the protein kinase activity of HipA is essential for persister formation...
Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coliSonja Hansen
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, MA 02115, USA
Antimicrob Agents Chemother 52:2718-26. 2008..Consistent with this scenario, the overexpression of both genes produced increased tolerance to ofloxacin...
Isolation and physiology of bacteria from contaminated subsurface sedimentsAnnette Bollmann
Northeastern University, Department of Biology, Boston, MA 02115, USA
Appl Environ Microbiol 76:7413-9. 2010....
Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosisLawrence R Mulcahy
Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA
J Bacteriol 192:6191-9. 2010..Persisters may play a similarly critical role in the recalcitrance of other chronic infections...
SOS response induces persistence to fluoroquinolones in Escherichia coliTobias Dörr
Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
PLoS Genet 5:e1000760. 2009..This unique survival mechanism may be an important factor influencing the outcome of antibiotic therapy in vivo...
Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coliTobias Dörr
Department of Biology, Northeastern University, Antimicrobial Discovery Center, Boston, Massachusetts, United States of America
PLoS Biol 8:e1000317. 2010..These results suggest that a DNA damage-induced toxin controls production of multidrug tolerant cells and thus provide a model of persister formation...
Siderophores from neighboring organisms promote the growth of uncultured bacteriaAnthony D'Onofrio
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, MA 02115, USA
Chem Biol 17:254-64. 2010....
Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profileNiilo Kaldalu
Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
Antimicrob Agents Chemother 48:890-6. 2004..Among the repressed genes were those required for flagellar synthesis, energy metabolism, transport of small molecules, and protein synthesis...
Novel high-throughput screen against Candida albicans identifies antifungal potentiators and agents effective against biofilmsMichael D LaFleur
Antimicrobial Discovery Center and Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02118, USA
J Antimicrob Chemother 66:820-6. 2011..The screen was performed against C. albicans biofilms grown in microtitre plates in order to target the most resilient forms of the pathogen...
A trap for in situ cultivation of filamentous actinobacteriaEkaterina Gavrish
Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
J Microbiol Methods 72:257-62. 2008..Importantly, the trap cultivation resulted in the isolation of unusual and rare actinomycetes...
GlpD and PlsB participate in persister cell formation in Escherichia coliAmy L Spoering
Northeastern University, Department of Biology, 405 Mugar Hall, 360 Huntington Ave, Boston, MA 02115, USA
J Bacteriol 188:5136-44. 2006....
Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysisSonja Hansen
Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
PLoS ONE 7:e39185. 2012....
Patients with long-term oral carriage harbor high-persister mutants of Candida albicansMichael D LaFleur
Antimicrobial Discovery Center and Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Hall, Boston, MA 02115, USA
Antimicrob Agents Chemother 54:39-44. 2010..The drug tolerance of persisters may be a critical but overlooked component responsible for antimicrobial drug failure and relapsing infections...
Candida albicans biofilms produce antifungal-tolerant persister cellsMichael D LaFleur
Department of Biology, Northeastern University, 360 Huntington Ave, 134 Mugar Hall, Boston, MA 02115, USA
Antimicrob Agents Chemother 50:3839-46. 2006..It remains to be seen whether attachment initiates dormancy that leads to the formation of fungal persisters. This study suggests that persisters may be largely responsible for the multidrug tolerance of fungal biofilms...
Short peptide induces an "uncultivable" microorganism to grow in vitroD Nichols
Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
Appl Environ Microbiol 74:4889-97. 2008..Access to cultures of some of these species should be possible through identification of the signaling compounds necessary for growth, their addition to standard medium formulations, and eventual domestication...
Identification of novel antimicrobials using a live-animal infection modelTerence I Moy
Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
Proc Natl Acad Sci U S A 103:10414-9. 2006..Our findings indicate that the whole-animal C. elegans screen identifies not only traditional antibiotics, but also compounds that target bacterial virulence or stimulate host defense...
Prokaryotic real-time gene expression profiling for toxicity assessmentAnnalisa Onnis-Hayden
Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, USA
Environ Sci Technol 43:4574-81. 2009..A mechanism-based evaluation of toxins based on real-time gene expression profiles promises, to be an efficient and informative method for toxicity assessment in environmental samples...
Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolatesAnnette Bollmann
Northeastern University, Department of Biology, 134 Mugar Life Science Building, 360 Huntington Ave, Boston, MA 02115, USA
Appl Environ Microbiol 73:6386-90. 2007..This suggests that continuous cultivation in diffusion chambers adapts some microorganisms for growth under otherwise prohibitive in vitro conditions...
Characterization and transcriptome analysis of Mycobacterium tuberculosis persistersIris Keren
Antimicrobial Discovery Center and Department of Biology, Northeastern University, Boston, Massachusetts, USA
MBio 2:e00100-11. 2011..A comparison of the persister transcriptome with transcriptomes obtained for several in vitro dormancy models identified a small number of genes upregulated in all cases, which may represent a core dormancy response...
Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobialsA L Spoering
Department of Biology, Northeastern University, 405 Mugar, 360 Huntington Ave, Boston, MS 02115, USA
J Bacteriol 183:6746-51. 2001..We further suggest that tolerance to antibiotics in stationary-phase or biofilm cultures is largely dependent on the presence of persister cells...
Tackling antibiotic resistanceKaren Bush
Department of Biology, 1001 E Third Street, Indiana University, Bloomington, IN 47405, USA
Nat Rev Microbiol 9:894-6. 2011..From these discussions there emerged a priority list of steps that need to be taken to resolve this global crisis...
Multidrug pump inhibitors uncover remarkable activity of plant antimicrobialsGeorge Tegos
Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
Antimicrob Agents Chemother 46:3133-41. 2002..These findings also suggest that plant antimicrobials might be developed into effective, broad-spectrum antibiotics in combination with inhibitors of MDRs...
Isolating "uncultivable" microorganisms in pure culture in a simulated natural environmentT Kaeberlein
Biology Department, Northeastern University, Boston, MA 02115, USA
Science 296:1127-9. 2002..These isolates did not grow on artificial media alone but formed colonies in the presence of other microorganisms. This observation may help explain the nature of microbial uncultivability...
Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial speciesD Nichols
134 Mugar Hall, Department of Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
Appl Environ Microbiol 76:2445-50. 2010..The new method allows access to a large and diverse array of previously inaccessible microorganisms and is well suited for both fundamental and applied research...
Metabolites of the "smoke tree", Dalea spinosa, potentiate antibiotic activity against multidrug-resistant Staphylococcus aureusGil Belofsky
Department of Chemistry and Biochemistry, The University of Tulsa, Tulsa, Oklahoma 74101, USA
J Nat Prod 69:261-4. 2006..aureus overexpression and knockout isogenic efflux mutants for the NorA pump were done in order to assess whether the potentiating effects were associated with inhibition of this known pump mechanism...
Immobilized N-alkylated polyethylenimine avidly kills bacteria by rupturing cell membranes with no resistance developedNebojsa M Milovic
Department of Chemistry and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biotechnol Bioeng 90:715-22. 2005..Finally, the immobilized N-alkyl-PEI, while deadly to bacteria, is determined to be harmless to mammalian (monkey kidney) cells...
Synthesis of functionalized 2-aryl-5-nitro-1H-indoles and their activity as bacterial NorA efflux pump inhibitorsSiritron Samosorn
Institute for Biomolecular Science, Department of Chemistry, University of Wollongong, NSW 2522, Australia
Bioorg Med Chem 14:857-65. 2006..The compound [4-benzyloxy-2-(5-nitro-1H-2-yl)-phenyl]-methanol was the most potent pump inhibitor...
Drastically lowering the titer of waterborne bacteriophage PRD1 by exposure to immobilized hydrophobic polycationsFaina Gelman
Department of Chemistry and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Biotechnol Lett 26:1695-700. 2004..The greatest loss of infectivity--up to a 4-log reduction in the titer--was observed with immobilized hydrophobic polyethylenimine-based and dendrimer-based polycations...
Polyacylated neohesperidosides from Geranium caespitosum: bacterial multidrug resistance pump inhibitorsFrank R Stermitz
Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
Bioorg Med Chem Lett 13:1915-8. 2003..aureus, but potentiated activity of the antibiotics berberine, rhein, ciprofloxacin and norfloxacin. Cellular concentrations of berberine were greatly increased in the presence of active esters...
Phenolic metabolites of Dalea versicolor that enhance antibiotic activity against model pathogenic bacteriaGil Belofsky
Department of Chemistry and Biochemistry, The University of Tulsa, Tulsa, Oklahoma 74101, USA
J Nat Prod 67:481-4. 2004..cereus. Compounds 4 and 7 were also found to potentiate the activity of berberine and of prescribed antibiotics, with 4 demonstrating a mode of action consistent with inhibition of the NorA MDR efflux pump in S. aureus...
Isoflavones as potentiators of antibacterial activityCécile Morel
Department of Chemistry, Colorado State University, Fort Collins, CO 80523 1872, USA
J Agric Food Chem 51:5677-9. 2003..Thus, L. argenteus contains a weak antibacterial and also MDR pump inhibitors, which increase its potency...
Polymer surfaces derivatized with poly(vinyl-N-hexylpyridinium) kill airborne and waterborne bacteriaJoerg C Tiller
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Biotechnol Bioeng 79:465-71. 2002..Various commercial synthetic polymers derivatized in this manner become bactericidal-they kill up to 99% of deposited, from either an aerosol or an aqueous suspension, Gram-positive and Gram-negative bacteria on contact...
Structure-activity relationships of 2-aryl-1H-indole inhibitors of the NorA efflux pump in Staphylococcus aureusJoseph I Ambrus
School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
Bioorg Med Chem Lett 18:4294-7. 2008..A promising new antibacterial lead compound against S. aureus (2-phenyl-1H-indol-5-yl)-methanol, was also found...
Bactericidal properties of flat surfaces and nanoparticles derivatized with alkylated polyethyleniminesJian Lin
Department of Chemistry and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biotechnol Prog 18:1082-6. 2002..Systematic chemical modifications of the immobilized PEI conducted herein shed light on the relationship between the structure of the polymer and the antibacterial efficiency of the resultant coating...
Mechanism of bactericidal and fungicidal activities of textiles covalently modified with alkylated polyethylenimineJian Lin
Department of Chemistry and Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biotechnol Bioeng 83:168-72. 2003..The bactericidal textiles prepared herein are lethal not only to pathogenic bacteria but to fungi as well...
Two flavonols from Artemisa annua which potentiate the activity of berberine and norfloxacin against a resistant strain of Staphylococcus aureusFrank R Stermitz
Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
Planta Med 68:1140-1. 2002..aureus multidrug resistance (MDR) pump. These same two flavonols were earlier reported to potentiate the activity of artemisinin against Plasmodium falciparum...
Research Grants
- SCREEN DEVELOPMENT FOR ANTIMICROBIAL PRODRUGSKim Lewis; Fiscal Year: 2009..key personnel in alphabetical order, last name first; Name eRA Commons User Name Organization Role on Project Kim Lewis k.lewis@neu...
- A GENOMICS APPROACH TO DRUG TOLERANCEKim Lewis; Fiscal Year: 2009..Persisters are largely responsible for many serious relapsing infections. Identifying genes responsible for persister formation will lead to targets for developing an anti-persister therapy. ..
- A synergy-based therapy against C. difficileKim Lewis; Fiscal Year: 2010..We will develop an effective therapeutic against drug-resistant C. difficile by disabling the mechanism of resistance to berberine, a widely used antimicrobial from medicinal plants. ..
- Super-persistent cells and the paradox of untreatable infectionsKim Lewis; Fiscal Year: 2009..Our findings are likely to change the way we view infectious diseases and will provide rational approaches for discovering drugs that completely eradicate the infection. ..
- A GENOMICS APPROACH TO DRUG TOLERANCEKim Lewis; Fiscal Year: 2010..Persisters are largely responsible for many serious relapsing infections. Identifying genes responsible for persister formation will lead to targets for developing an anti-persister therapy. ..
- A GENOMICS APPROACH TO DRUG TOLERANCEKim Lewis; Fiscal Year: 2009....
- Culturing Uncultivatable Gut MicroorganismsKim Lewis; Fiscal Year: 2010....
- Super-persistent cells and the paradox of untreatable infectionsKim Lewis; Fiscal Year: 2010..Our findings are likely to change the way we view infectious diseases and will provide rational approaches for discovering drugs that completely eradicate the infection. ..
- The Nature of Bacterial UncultivabilityKim Lewis; Fiscal Year: 2007..Unculturable bacteria are an enormous untapped source of potentially useful pharmaceutical compounds. Unculturable bacteria also make up most of the human oral and intestinal microflora. ..
- SCREEN DEVELOPMENT FOR ANTIMICROBIAL PRODRUGSKim Lewis; Fiscal Year: 2007....
- NATURAL SUBSTRATES AND INHIBITORS OF MICROBIAL MDR PUMPSKim Lewis; Fiscal Year: 2002..MDR inhibitors will potentiate the action of conventional antibiotics, aiding eradication of multidrug resistant human pathogens. ..
- A GENOMICS APPROACH TO P. AERUGINOSA BIOFILMSKim Lewis; Fiscal Year: 2003..This information will likely contribute to the understanding of the mechanism of resistance. Resistance genes identified in this project will serve as targets for drug discovery and development of effective anti-biofilm therapies. ..
- NOVEL METHODS FOR DISCOVERY OF ANTI-MICROBIALSKim Lewis; Fiscal Year: 2005..Determination of chemical structure will be performed by a combination of MS and NMR methods. ..
- BIODEFENSE THERAPEUTICS FROM UNCULTURED MICROORGANISMSKim Lewis; Fiscal Year: 2005..Determination of chemical structure will be performed by a combination of MS and NMR methods. ..
- A GENOMICS APPROACH TO BIOFILMSKim Lewis; Fiscal Year: 2007..These studies will form the basis for understanding biofilm infections and developing drugs that target persister proteins. ..
- A High-Throughput Screen for Specific Anti-M. tuberculosis CompoundsKim Lewis; Fiscal Year: 2010..We will also look for compounds that act specifically against the pathogen M. tuberculosis, which will avoid killing of the good bacteria of our gut flora. ..
