Persister Cells: Molecular Mechanisms Related to Antibiotic Tolerance

Part of the Handbook of Experimental Pharmacology book series (HEP, volume 211)


It is a given that new antibiotics are needed to combat drug-resistant pathogens. However, this is only a part of the need—we actually never had antibiotics capable of eradicating an infection. All pathogens produce a small subpopulation of dormant persister cells that are highly tolerant to killing by antibiotics. Once an antibiotic concentration drops, surviving persisters re-establish the population, causing a relapsing chronic infection. Persisters are especially significant when the pathogen is shielded from the immune system by biofilms, or in sites where the immune components are limited—in the nervous system, the stomach, or inside macrophages.

Antibiotic treatment during a prolonged chronic infection of P. aeruginosa in the lungs of patients with cystic fibrosis selects for high-persister (hip) mutants. Similarly, treatment of oral thrush infection selects for hip mutants of C. albicans. These observations suggest a direct causality between persisters and recalcitrance of the disease. It appears that tolerance of persisters plays a leading role in chronic infections, while resistance is the leading cause of recalcitrance to therapy in acute infections. Studies of persister formation in E. coli show that mechanisms of dormancy are highly redundant. Isolation of persisters produced a transcriptome which suggests a dormant phenotype characterized by downregulation of energy-producing and biosynthetic functions. Toxin–antitoxin modules represent a major mechanism of persister formation. The RelE toxin causes dormancy by cleaving mRNA; the HipA toxin inhibits translation by phosphorylating elongation factor Ef-Tu, and the TisB toxin forms a membrane pore, leading to a decrease in pmf and ATP.


Biofilm Drug tolerance High-persister mutants Persister Toxin/antitoxins 


  1. Al-Dhaheri RS, Douglas LJ (2008) Absence of amphotericin B-tolerant persister cells in biofilms of some Candida species. Antimicrob Agents Chemother 52:1884–7PubMedCrossRefGoogle Scholar
  2. Alix E, Blanc-Potard A (2009) Hydrophobic peptides: novel regulators within bacterial membranes. Mol Microbiol 72:5–11PubMedCrossRefGoogle Scholar
  3. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008PubMedCrossRefGoogle Scholar
  4. Barry CE 3rd, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ, Young D (2009) The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nat Rev Microbiol 7:845–55PubMedGoogle Scholar
  5. Bigger JW (1944) Treatment of staphylococcal infections with penicillin. Lancet II:497–500CrossRefGoogle Scholar
  6. Christensen SK, Gerdes K (2004) Delayed-relaxed response explained by hyperactivation of RelE. Mol Microbiol 53:587–97PubMedCrossRefGoogle Scholar
  7. Correia FF, D'Onofrio A, Rejtar T, Li L, Karger BL, Makarova K, Koonin EV, Lewis K (2006) Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol 188:8360–7PubMedCrossRefGoogle Scholar
  8. Costerton JW, Stewart PS, Greenberg EP (1999) Bacterial biofilms: a common cause of persistent infections. Science 284:1318–22PubMedCrossRefGoogle Scholar
  9. Courcelle J, Khodursky A, Peter B, Brown P, Hanawalt P (2001) Comparative gene expression profiles following UV exposure in wild type and SOS-deficient Escherichia coli. Genetics 158:41–64PubMedGoogle Scholar
  10. De Groote VN, Verstraeten N, Fauvart M, Kint CI, Verbeeck AM, Beullens S, Cornelis P, Michiels J (2009) Novel persistence genes in Pseudomonas aeruginosa identified by high-throughput screening. FEMS Microbiol Lett 297:73–9PubMedCrossRefGoogle Scholar
  11. Del Pozo J, Patel R (2007) The challenge of treating biofilm-associated bacterial infections. Clinical Pharmacol Ther 82:204–9CrossRefGoogle Scholar
  12. Dörr T, Lewis K, Vulic M (2009) SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet 5:e1000760PubMedCrossRefGoogle Scholar
  13. Dorr T, Vulic M, Lewis K (2010) Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol 8:e1000317PubMedCrossRefGoogle Scholar
  14. Falla TJ, Chopra I (1998) Joint tolerance to beta-lactam and fluoroquinolone antibiotics in Escherichia coli results from overexpression of hipA. Antimicrob Agents Chemother 42:3282–4PubMedGoogle Scholar
  15. Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol 35:1560–72PubMedCrossRefGoogle Scholar
  16. Garcia-Olmedo F, Molina A, Alamillo JM, Rodriguez-Palenzuela P (1998) Plant defense peptides. Biopolymers 47:479–91PubMedCrossRefGoogle Scholar
  17. Gerdes K, Bech FW, Jorgensen ST, Lobner-Olesen A, Rasmussen PB, Atlung T, Boe L, Karlstrom O, Molin S, von Meyenburg K (1986a) Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J 5:2023–9PubMedGoogle Scholar
  18. Gerdes K, Rasmussen PB, Molin S (1986b) Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci USA 83:3116–20PubMedCrossRefGoogle Scholar
  19. Gibson RL, Burns JL, Ramsey BW (2003) Pathophysiology and management of pulmonary infections in cystic fibrosis. Am J Respir Crit Care Med 168:918–51PubMedCrossRefGoogle Scholar
  20. Hansen S, Lewis K, Vulić M (2008) The role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli. Antimicrob Agents Chemother 52:2718–2726PubMedCrossRefGoogle Scholar
  21. Harrison JJ, Ceri H, Roper NJ, Badry EA, Sproule KM, Turner RJ (2005a) Persister cells mediate tolerance to metal oxyanions in Escherichia coli. Microbiology 151:3181–95PubMedCrossRefGoogle Scholar
  22. Harrison JJ, Turner RJ, Ceri H (2005b) Persister cells, the biofilm matrix and tolerance to metal cations in biofilm and planktonic Pseudomonas aeruginosa. Environ Microbiol 7:981–94PubMedCrossRefGoogle Scholar
  23. Harrison JJ, Turner RJ, Ceri H (2007) A subpopulation of Candida albicans and Candida tropicalis biofilm cells are highly tolerant to chelating agents. FEMS Microbiol Lett 272:172–81PubMedCrossRefGoogle Scholar
  24. Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H (2009) The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Antimicrob Agents Chemother 53:2253–8PubMedCrossRefGoogle Scholar
  25. Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496–9PubMedCrossRefGoogle Scholar
  26. Honda H, Warren DK (2009) Central nervous system infections: meningitis and brain abscess. Infect Dis Clin North Am 23:609–23PubMedCrossRefGoogle Scholar
  27. Hu Y, Coates AR (2005) Transposon mutagenesis identifies genes which control antimicrobial drug tolerance in stationary-phase Escherichia coli. FEMS Microbiol Lett 243:117–24PubMedCrossRefGoogle Scholar
  28. Jesaitis AJ, Franklin MJ, Berglund D, Sasaki M, Lord CI, Bleazard JB, Duffy JE, Beyenal H, Lewandowski Z (2003) Compromised host defense on Pseudomonas aeruginosa biofilms: characterization of neutrophil and biofilm interactions. J Immunol 171:4329–39PubMedGoogle Scholar
  29. Kawano M, Aravind L, Storz G (2007) An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64:738–54PubMedCrossRefGoogle Scholar
  30. Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004) Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186:8172–80PubMedCrossRefGoogle Scholar
  31. LaFleur MD, Kumamoto CA, Lewis K (2006) Candida albicans biofilms produce antifungal-tolerant persister cells. Antimicrob Agents Chemother 50:3839–46PubMedCrossRefGoogle Scholar
  32. Lafleur MD, Qi Q, Lewis K (2010) Patients with long-term oral carriage harbor high-persister mutants of Candida albicans. Antimicrob Agents Chemother 54:39–44PubMedCrossRefGoogle Scholar
  33. Leid JG, Shirtliff ME, Costerton JW, Stoodley AP (2002) Human leukocytes adhere to, penetrate, and respond to Staphylococcus aureus biofilms. Infect Immun 70:6339–45PubMedCrossRefGoogle Scholar
  34. Levin BR, Rozen DE (2006) Non-inherited antibiotic resistance. Nat Rev Microbiol 4:556–62PubMedCrossRefGoogle Scholar
  35. Lewis K (2001) Riddle of biofilm resistance. Antimicrob Agents Chemother 45:999–1007PubMedCrossRefGoogle Scholar
  36. McKenzie MD, Lee PL, Rosenberg SM (2003) The dinB operon and spontaneous mutation in Escherichia coli. J Bacteriol 185:3972–7PubMedCrossRefGoogle Scholar
  37. Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E (2007) Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. FEMS Microbiol Lett 268:112–9PubMedCrossRefGoogle Scholar
  38. Moyed HS, Bertrand KP (1983) hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 155:768–75PubMedGoogle Scholar
  39. Mulcahy LR, Burns JL, Lory S, Lewis K (2010) Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J Bacteriol 192:6191–6199Google Scholar
  40. Pandey DP, Gerdes K (2005) Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 33:966–76PubMedCrossRefGoogle Scholar
  41. Pedersen K, Christensen SK, Gerdes K (2002) Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol 45:501–10PubMedCrossRefGoogle Scholar
  42. Pedersen K, Gerdes K (1999) Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol 32:1090–102PubMedCrossRefGoogle Scholar
  43. Peterson WL, Fendrick AM, Cave DR, Peura DA, Garabedian-Ruffalo SM, Laine L (2000) Helicobacter pylori-related disease: guidelines for testing and treatment. Arch Intern Med 160:1285–1291PubMedCrossRefGoogle Scholar
  44. Phillips I, Culebras E, Moreno F, Baquero F (1987) Induction of the SOS response by new 4-quinolones. J Antimicrob Chemother 20:631–8PubMedCrossRefGoogle Scholar
  45. Ramage HR, Connolly LE, Cox JS (2009) Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet 5:e1000767PubMedCrossRefGoogle Scholar
  46. Sahl HG, Bierbaum G (1998) Lantibiotics: biosynthesis and biological activities of uniquely modified peptides from gram-positive bacteria. Annu Rev Microbiol 52:41–79PubMedCrossRefGoogle Scholar
  47. Schmelzle T, Hall MN (2000) TOR, a central controller of cell growth. Cell 103:253–62PubMedCrossRefGoogle Scholar
  48. Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG (2009) Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 323:396–401PubMedCrossRefGoogle Scholar
  49. Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K (2006) Persisters: a distinct physiological state of E. coli. BMC Microbiol 6:53–61PubMedCrossRefGoogle Scholar
  50. Singletary LA, Gibson JL, Tanner EJ, McKenzie GJ, Lee PL, Gonzalez C, Rosenberg SM (2009) An SOS-regulated type 2 toxin-antitoxin system. J Bacteriol 191:7456–7465PubMedCrossRefGoogle Scholar
  51. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, D'Argenio DA, Miller SI, Ramsey BW, Speert DP, Moskowitz SM, Burns JL, Kaul R, Olson MV (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 103:8487–92PubMedCrossRefGoogle Scholar
  52. Spoering A (2006) GlpD and PlsB participate in persister cell formation in Escherichia coli. J Bacteriol 188:5136–5144PubMedCrossRefGoogle Scholar
  53. Spoering AL, Lewis K (2001) Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J Bacteriol 183:6746–6751PubMedCrossRefGoogle Scholar
  54. Stewart PS, Costerton JW (2001) Antibiotic resistance of bacteria in biofilms. Lancet 358:135–8PubMedCrossRefGoogle Scholar
  55. Unoson C, Wagner E (2008) A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Mol Microbiol 70:258–70PubMedCrossRefGoogle Scholar
  56. Vazquez-Laslop N, Lee H, Neyfakh AA (2006) Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol 188:3494–7PubMedCrossRefGoogle Scholar
  57. Vogel J, Argaman L, Wagner EG, Altuvia S (2004) The small RNA Istr inhibits synthesis of an SOS-induced toxic peptide. Curr Biol 14:2271–2276PubMedCrossRefGoogle Scholar
  58. Vuong C, Voyich JM, Fischer ER, Braughton KR, Whitney AR, DeLeo FR, Otto M (2004) Polysaccharide intercellular adhesin (PIA) protects Staphylococcus epidermidis against major components of the human innate immune system. Cell Microbiol 6:269–75PubMedCrossRefGoogle Scholar
  59. Walters MC 3rd, Roe F, Bugnicourt A, Franklin MJ, Stewart PS (2003) Contributions of antibiotic penetration, oxygen limitation, and low metabolic activity to tolerance of Pseudomonas aeruginosa biofilms to ciprofloxacin and tobramycin. Antimicrob Agents Chemother 47:317–23PubMedCrossRefGoogle Scholar
  60. Wolfson JS, Hooper DC, McHugh GL, Bozza MA, Swartz MN (1990) Mutants of Escherichia coli K-12 exhibiting reduced killing by both quinolone and beta-lactam antimicrobial agents. Antimicrob Agents Chemother 34:1938–43PubMedCrossRefGoogle Scholar
  61. Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415:389–95PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Antimicrobial Discovery Center and Department of BiologyNortheastern UniversityBostonUSA

Personalised recommendations