Abstract
Persisters are transiently antibiotic-tolerant cells that complicate the treatment of bacterial infections. Both theory and experiments have suggested that persisters facilitate genetic resistance by constituting an evolutionary reservoir of viable cells. Here, we provide evidence for a strong positive correlation between persistence and the likelihood to become genetically resistant in natural and lab strains of E. coli. This correlation can be partly attributed to the increased availability of viable cells associated with persistence. However, our data additionally show that persistence is pleiotropically linked with mutation rates. Our theoretical model further demonstrates that increased survival and mutation rates jointly affect the likelihood of evolving clinical resistance. Overall, these results suggest that the battle against antibiotic resistance will benefit from incorporating anti-persister therapies.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Davies J, Davies D. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev. 2010;74:417–33.
World Health Organization. Antimicrobial resistance: global report on surveillance. WHO press, Geneva, Switzerland; 2014.
Brauner A, Fridman O, Gefen O, Balaban NQ. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat Rev Microbiol. 2016;14:320–30.
Bumann D. Heterogeneous host-pathogen encounters: act locally, think globally. Cell Host Microbe. 2015;17:13–19.
Conlon BP. Staphylococcus aureus chronic and relapsing infections: evidence of a role for persister cells. Bioessays. 2014;36:991–6.
Michiels JE, Van den Bergh B, Verstraeten N, Michiels J. Molecular mechanisms and clinical implications of bacterial persistence. Drug Resist Updat. 2016;29:76–89.
Van den Bergh B, Michiels JE, Fauvart M, Michiels J. Should we develop screens for multidrug tolerance? Expert Rev Anti Infect Ther. 2016;14:613–6.
Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev. 2017;41:219–51.
Harms A, Maisonneuve E, Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science. 2016;354:aaf4268.
Fisher RA, Gollan B, Helaine S. Persistent bacterial infections and persister cells. Nat Rev Microbiol. 2017;15:453–64.
Van den Bergh B, Michiels JE, Wenseleers T, Windels EM, Vanden Boer P, Kestemont D, et al. Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence. Nat Microbiol. 2016;1:16020.
Michiels JE, Van den Bergh B, Verstraeten N, Fauvart M, Michiels J. In vitro emergence of high persistence upon periodic aminoglycoside challenge in the ESKAPE pathogens. Antimicrob Agents Chemother. 2016;60:4630–7.
Fridman O, Goldberg A, Ronin I, Shoresh N, Balaban NQ. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature. 2014;513:418–21.
Mechler L, Herbig A, Paprotka K, Fraunholz M, Nieselt K, Bertram R. A novel point mutation promotes growth phase-dependent daptomycin tolerance in Staphylococcus aureus. Antimicrob Agents Chemother. 2015;59:5366–76.
Moreillon P, Tomasz A. Penicillin resistance and defective lysis in clinical isolates of pneumococci: evidence for two kinds of antibiotic pressure operating in the clinical environment. J Infect Dis. 1988;157:1150–7.
Levin BR, Rozen DE. Non-inherited antibiotic resistance. Nat Rev Microbiol. 2006;4:556–62.
Cohen NR, Lobritz MA, Collins JJ. Microbial persistence and the road to drug resistance. Cell Host Microbe. 2013;13:632–42.
Liu HH, Tomasz A. Penicillin tolerance in multiply drug-resistant natural isolates of Streptococcus pneumoniae. J Infect Dis. 1985;152:365–72.
Novak R, Henriques B, Charpentier E, Normark S, Tuomanen E. Emergence of vancomycin tolerance in Streptococcus pneumoniae. Nature. 1999;399:590–3.
Sebastian J, Swaminath S, Nair RR, Jakkala K, Pradhan A, Ajitkumar P. De novo emergence of genetically resistant mutants of Mycobacterium tuberculosis from the persistence phase cells formed against antituberculosis drugs in vitro. Antimicrob Agents Chemother. 2016;61:AAC.01343-16.
Levin-Reisman I, Ronin I, Gefen O, Braniss I, Shoresh N, Balaban NQ. Antibiotic tolerance facilitates the evolution of resistance. Science. 2017;355:826–30.
Vogwill T, Comfort AC, Furió V, MacLean RC. Persistence and resistance as complementary bacterial adaptations to antibiotics. J Evol Biol. 2016;29:1223–33.
Bjedov I, Tenaillon O, Gérard B, Souza V, Denamur E, Radman M, et al. Stress-induced mutagenesis in bacteria. Science. 2003;300:1404–9.
Al Mamun, AAM Lombardo M, Shee C, Lisewski AM, Gonzalez C, et al. Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science. 2012;338:1344–8.
Poole K. Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria. Trends Microbiol. 2012;20:227–34.
Kussell E, Kishony R, Balaban NQ, Leibler S. Bacterial persistence: a model of survival in changing environments. Genetics. 2005;169:1807–14.
Carja O, Liberman U, Feldman MW. Evolution in changing environments: Modifiers of mutation, recombination, and migration. Proc Natl Acad Sci. 2014;111:17935–40.
Ishii K, Matsuda H, Iwasa Y, Sasaki A. Evolutionarily stable mutation rate in a periodically changing environment. Genetics. 1989;121:163–74.
Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, et al. Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli. eLife. 2017;6:1–24.
Giraud A, Matic I, Radman M, Fons M, Taddei F. Mutator bacteria as a risk factor in treatment of infectious diseases. Antimicrob Agents Chemother. 2002;46:863–5.
Giraud A, Matic I, Tenaillon O, Clara A, Radman M, Fons M, et al. Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut. Science. 2001;291:2606–8.
Ram Y, Hadany L. The evolution of stress-induced hypermutation in asexual populations. Evolution. 2012;66:2315–28.
Pearl S, Gabay C, Kishony R, Oppenheim A, Balaban NQ. Nongenetic individuality in the host-phage interaction. PLoS Biol 2008;6:0957–64.
Wang H, Dzink-Fox J, Chen M, Levy SB. Genetic characterization of highly fluoroquinolone-resistant clinical Escherichia coli strains from China: role of acrR mutations. Antimicrob Agents Chemother. 2001;45:1515–21.
Regoes RR, Wiuff C, Zappala RM, Garner KN, Baquero F, Levin BR. Pharmacodynamic functions: a multiparameter approach to the design of antibiotic treatment regimens. Antimicrob Agents Chemother. 2004;48:3670–6.
Stepanyan K, Wenseleers T, Duéñez-Guzmán EA, Muratori F, Van den Bergh B, Verstraeten N, et al. Fitness trade-offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa. Mol Ecol. 2015;24:1572–83.
Sahl JW, Matalka MN, Rasko DA. Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Appl Environ Microbiol. 2012;78:4884–92.
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–98.
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.
Hamon A, Ycart B. Statistics for the Luria-Delbrück distribution. Electron J Stat. 2012;6:1251–72.
Ycart B, Veziris N. Unbiased estimation of mutation rates under fluctuating final counts. PLoS ONE. 2014;9:e101434.
Mazoyer A, Drouilhet R, Despréaux S, Ycart B. flan: An R package for inference on mutation models. R J. 2017;9:334–51.
Stewart FM. Fluctuation analysis: the effect of plating efficiency. Genetica. 1991;84:51–55.
Ochman H, Selander RK. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984;157:690–3.
Stewart B, Rozen DE. Genetic variation for antibiotic persistence in Escherichia coli. Evolution. 2011;66:933–9.
Cirz RT, Chin JK, Andes DR, de Crécy-Lagard V, Craig WA, Romesberg FE. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 2005;3:1024–33.
Riesenfeld C, Everett M, Piddock LJ, Hall BG. Adaptive mutations produce resistance to ciprofloxacin. Antimicrob Agents Chemother. 1997;41:2059–60.
Alam MK, Alhhazmi A, DeCoteau JF, Luo Y, Geyer CR. RecA inhibitors potentiate antibiotic activity and block evolution of antibiotic resistance. Cell Chem Biol. 2016;23:381–91.
Kaspy I, Rotem E, Weiss N, Ronin I, Balaban NQ, Glaser G. HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nat Commun. 2013;4:3001.
Germain E, Castro-Roa D, Zenkin N, Gerdes K. Molecular mechanism of bacterial persistence by HipA. Mol Cell. 2013;52:248–54.
Allison KR, Brynildsen MP, Collins JJ. Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature. 2011;473:216–20.
Piddock LJ. Mechanisms of fluoroquinolone resistance: an update 1994-1998. Drugs. 1999;58:11–18.
Oz T, Guvenek A, Yildiz S, Karaboga E, Tamer YT, Mumcuyan N, et al. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. Mol Biol Evol. 2014;31:2387–401.
Lázár V, Nagy I, Spohn R, Csörgő B, Györkei Á, Nyerges Á, et al. Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. Nat Commun. 2014;5:4352.
Conrad S, Oethinger M, Kaifel K, Klotz G, Marre R, Kern WV. gyrA mutations in high-level fluoroquinolone-resistant clinical isolates of Escherichia coli. J Antimicrob Chemother. 1996;38:443–55.
Weigel LM, Steward CD, Tenover FC. gyrA mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae. Antimicrob Agents Chemother. 1998;42:2661–7.
Ankomah P, Levin BR. Exploring the collaboration between antibiotics and the immune response in the treatment of acute, self-limiting infections. Proc Natl Acad Sci USA. 2014;111:8331–8.
Putrinš M, Kogermann K, Lukk E, Lippus M, Varik V, Tenson T. Phenotypic heterogeneity enables uropathogenic Escherichia coli to evade killing by antibiotics and serum complement. Infect Immun. 2015;83:1056–67.
Levin BR, Baquero F, Ankomah P, McCall IC. Phagocytes, antibiotics, and self-limiting bacterial infections. Trends Microbiol. 2017;25:878–92.
Normark BH, Normark S. Evolution and spread of antibiotic resistance. J Intern Med. 2002;252:91–106.
Yaakov G, Lerner D, Bentele K, Steinberger J, Barkai N. Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress. Nat Ecol Evol. 2017;1:16.
Kussell E, Leibler S. Phenotypic diversity, population growth, and information in fluctuating environments. Science. 2005;309:2075–8.
Patra P, Klumpp S. Population dynamics of bacterial persistence. PLoS ONE. 2013;8:e62814.
Gardner A, West SA, Griffin AS. Is bacterial persistence a social trait? PLoS ONE. 2007;2:e752.
Méhi O, Bogos B, Csörgo B, Pál C. Genomewide screen for modulators of evolvability under toxic antibiotic exposure. Antimicrob Agents Chemother. 2013;57:3453–6.
Kohanski MA, DePristo MA, Collins JJ. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol Cell. 2010;37:311–20.
Long H, Miller SF, Strauss C, Zhao C, Cheng L, Ye Z, et al. Antibiotic treatment enhances the genome-wide mutation rate of target cells. Proc Natl Acad Sci USA. 2016;113:E2498–E2505.
LaFleur MD, Qi Q, Lewis K. Patients with long-term oral carriage harbor high-persister mutants of Candida albicans. Antimicrob Agents Chemother. 2010;54:39–44.
Mulcahy LR, Burns JL, Lory S, Lewis K. Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J Bacteriol. 2010;192:6191–9.
Bridges BA. DNA turnover and mutation in resting cells. Bioessays. 1997;19:347–52.
Williams AB, Foster PL. Stress-induced mutagenesis. EcoSal Plus. 2012;5:1–29.
Roth JR, Kugelberg E, Reams AB, Kofoid E, Andersson DI. Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol. 2006;60:477–501.
Rosenberg SM, Shee C, Frisch RL, Hastings PJ. Stress-induced mutation via DNA breaks in Escherichia coli: A molecular mechanism with implications for evolution and medicine. Bioessays. 2012;34:885–92.
O’Neill J. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. Review on Antimicrobial Resistance. 2014.
Rosenberg SM, Queitsch C. Combating evolution to fight disease. Science. 2014;343:1088–9.
Cirz RT, Romesberg FE. Controlling mutation: intervening in evolution as a therapeutic strategy. Crit Rev Biochem Mol Biol. 2007;42:341–54.
Goldberg DE, Siliciano RF, Jacobs WR. Outwitting evolution: fighting drug-resistant TB, malaria, and HIV. Cell. 2012;148:1271–83.
Fischbach MA. Combination therapies for combating antimicrobial resistance. Curr Opin Microbiol. 2011;14:519–23.
Imamovic L, Sommer MOA. Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development. Sci Transl Med. 2013;5:204ra132.
Oxnard GR. The cellular origins of drug resistance in cancer. Nat Med. 2016;22:232–4.
Hangauer MJ, Viswanathan VS, Ryan MJ, Bole D, Eaton JK, Matov A, et al. Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition. Nature. 2017;551:247–50.
Acknowledgements
We thank Chris Michiels (KU Leuven) for providing ECOR strains, Abram Aertsen (KU Leuven) for sharing the hipA7 strain, and Bernard Ycart and Adrien Mazoyer (Grenoble Alpes University) for their assistance with fluctuation analysis. EMW and BVdB are Research Foundation—Flanders (FWO)-fellows and JEM is a fellow of the Agency for Innovation by Science and Technology (IWT). This research was funded by the KU Leuven Research Council (PF/10/010; C16/17/006), the Belgian Science Policy Office (IAP P7/28), FWO (G047112N; G0B2515N; G055517N), and the Flemish Institute for Biotechnology (VIB).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
About this article
Cite this article
Windels, E.M., Michiels, J.E., Fauvart, M. et al. Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME J 13, 1239–1251 (2019). https://doi.org/10.1038/s41396-019-0344-9
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41396-019-0344-9
This article is cited by
-
Salmonella stress response systems as targets for anti-virulence strategies
BMC Microbiology (2025)
-
Regulation of antibiotic persistence and pathogenesis in Acinetobacter baumannii by glutamate and histidine metabolic pathways
BMC Microbiology (2025)
-
Trehalose catalytic shift inherently enhances phenotypic heterogeneity and multidrug resistance in Mycobacterium tuberculosis
Nature Communications (2025)
-
Bioenergetic stress potentiates antimicrobial resistance and persistence
Nature Communications (2025)
-
Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks
Molecular Systems Biology (2025)
