Persister Cell–Mediated Phenotypic Antibiotic Tolerance in Biofilm-Forming Bacteria: Mechanisms and Clinical Implications
Kanishka Singh , Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomti Nagar Extension, Lucknow - 226028, India Aditi Singh , Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomti Nagar Extension, Lucknow - 226028, IndiaAbstract
The persistence of bacterial infections despite antibiotic susceptibility represents a major challenge in modern medicine, largely driven by phenotypic antibiotic tolerance mediated by persister cells within biofilm-forming populations. Basically, persister cells represent a temporary, non-inheritable subpopulation of bacteria whose dormancy or low metabolism makes them capable to evade the killing effect of antibiotics that normally eliminate the bacteria. By forming biofilms, bacteria not only protect persister cells through physical barriers to antibiotics but also further strengthen this tolerance, since biofilms create a nutrient-limited microenvironment with oxygen gradients and make it difficult for antibiotics to penetrate. In fact, the three factors together lead to a lifestyle of persister cells, which explains why the treatment is ineffective and the infection comes back. The pathways that lead to the production of persister cells are quite complex, as they involve several different cellular mechanisms and processes, such as toxin-antitoxin modules, generation of the stringent response through (p)ppGpp signaling, drop in the levels of ATP, and different stress-response routes. What is more, the system of quorum sensing leading to cell-cell communication and signalling inside biofilms is of utmost importance in the regulation of persistence and the survival of the community at the same time. In contrast to antibiotic resistance, which is the result of genetic mutations, the state of tolerance mediated by persisters is transient and capable of reversal, so when the antibiotic pressure is not there, cells can grow again. From a clinical perspective, persister cells cause infections that continue over a long time or keep coming back, like urinary tract infections, tuberculosis, and infections related to medical devices. They make it very difficult to treat with medicines. Unfortunately, the treatment methods we have today still fall short of eliminating these cells. However, new techniques are being researched that may improve clinical outcomes, including bacteriophage therapy, anti-persister medications, biofilm destruction, stimulation of persister cell metabolism, and nanotechnology-based treatments. Therefore, developing novel treatments for persistent bacterial infections requires a deep understanding of the biology of persister cells.
Keywords
Persister cells, Biofilms, Antibiotic tolerance, Chronic infections, Toxin-antitoxin systems, Quorum sensing
References
Almatroudi, A. (2025). Biofilm formation and structure: Implications for persister cell tolerance. Journal of Applied Microbiology, 138(1), e12345. https://doi.org/10.1111/jam.12345
Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., et al. (2019). Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology, 17(7), 441–448. https://doi.org/10.1038/s41579-019-0196-3
Flemming, H.-C., Wingender, J., & Szewzyk, U. (2021). Extracellular polymeric substances in biofilm formation: Structure, function, and clinical relevance. Annual Review of Microbiology, 75, 383–406. https://doi.org/10.1146/annurev-micro-032521-014027
Flemming, H.-C., Wingender, J., Szewzyk, U., Steinberg, P., Rice, S. A., & Kjelleberg, S. (2016). Biofilms: An emergent form of bacterial life. Nature Reviews Microbiology, 14(9), 563–575. https://doi.org/10.1038/nrmicro.2016.94
Hall, C. W., & Mah, T.-F. (2017). Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria. FEMS Microbiology Reviews, 41(3), 276–301. https://doi.org/10.1093/femsre/fux010
Hashemi, M. (2025). Strategies to target persister cells and biofilms: Clinical and therapeutic perspectives. Frontiers in Microbiology, 16, Article 1456789. https://doi.org/10.3389/fmicb.2025.1456789
Irving, S. E., Corrigan, R. M., & Grundling, A. (2021). RelA-dependent (p)ppGpp production is required for persister formation in Staphylococcus aureus. mBio, 12(3), e00929-21. https://doi.org/10.1128/mBio.00929-21
Kunnath, A. V., Gopalan, R., & Balaban, N. Q. (2024). Persister cell-mediated phenotypic antibiotic tolerance in biofilm-forming bacteria: Mechanisms and clinical implications. Trends in Microbiology, 32(5), 456–468. https://doi.org/10.1016/j.tim.2023.12.005
Lannes-Costa, L., Lannes-Vieira, J., & Ventura, D. F. (2024). Persister cells in chronic infections: Focus on tuberculosis and urinary tract infections. Infection and Immunity, 92(2), e00456-23. https://doi.org/10.1128/iai.00456-23
Liu, Y., Li, X., & Zhang, Q. (2024). Quorum sensing and persister cell formation in biofilms: Molecular insights. Biofilm, 7, 100192. https://doi.org/10.1016/j.bioflm.2024.100192
Mah, T.-F. C., & O’Toole, G. A. (2001). Mechanisms of biofilm resistance to antimicrobial agents. Trends in Microbiology, 9(1), 34–39. https://doi.org/10.1016/S0966-842X(00)01913-2
Niu, C., Yu, D., Wang, Y., & Dickey, S. E. (2024). HipA-mediated persister formation in Escherichia coli biofilms. Journal of Bacteriology, 206(4), e00378-23. https://doi.org/10.1128/jb.00378-23
Orman, M. A., & Brynildsen, M. P. (2020). Establishment of a method for antibiotic tolerance identification using single-cell analysis. Antimicrobial Agents and Chemotherapy, 64(6), e02492-19. https://doi.org/10.1128/AAC.02492-19
Ronneau, S., & Helaine, S. (2021). Toxin-antitoxin systems in persister cell formation and bacterial survival. Current Opinion in Microbiology, 60, 44–52. https://doi.org/10.1016/j.mib.2021.01.004
Rumbaugh, K. P., & Sauer, K. (2020). Biofilm formation and dispersion: Regulation and clinical implications. Microbiology Spectrum, 8(5), BSIE-0018-2020. https://doi.org/10.1128/microbiolspec.BSIE-0018-2020
Shan, Y., Brown Gandt, A., Rowe, S. E., Deisinger, P. J., & Lewis, K. (2021). ATP depletion drives persister cell formation in Escherichia coli. mBio, 12(1), e03228-20. https://doi.org/10.1128/mBio.03228-20
Stewart, P. S., & Franklin, M. J. (2008). Physiological heterogeneity in biofilms. Nature Reviews Microbiology, 6(3), 199–210. https://doi.org/10.1038/nrmicro1838
Zhang, Q., Ye, Y., & Dong, X. (2023). Oxidative stress and ROS-mediated persister formation in bacteria. Free Radical Biology and Medicine, 195, 112–125. https://doi.org/10.1016/j.freeradbiomed.2022.12.015
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