Журналов:     Статей:        

Журнал микробиологии, эпидемиологии и иммунобиологии. 2020; 97: 271-279

Молекулярные механизмы персистенции бактерий

Андрюков Борис Георгиевич, Ляпун Ирина Николаевна

https://doi.org/10.36233/0372-9311-2020-97-3-10

Аннотация

Высокий уровень смертности от инфекционных болезней в значительной степени опосредован повсеместным и бесконтрольным использованием антибиотиков, что привело к появлению лекарственно-резистентных штаммов бактерий. Быстрая эволюция резистентности бактерий к антимикробным препаратам является серьезным вызовом для современного здравоохранения, обусловливает необходимость создания новых антибиотических средств, а также активизации изучения молекулярных механизмов, лежащих в основе формирования устойчивости микроорганизмов. Одним из таких механизмов является бактериальная персистенция, которая проявляется образованием в микробной культуре клеток-персисторов, являющихся фенотипическим вариантом изогенной популяции. Персистенция бактерий может возникать самопроизвольно, независимо от воздействия антимикробных средств или причин, связанных с окружающей средой (недостаток питательных веществ, окислительный стресс или гипоксия). Эта небольшая по численности генерация клеток способна сохранять жизнеспособность даже в присутствии антимикробных средств в концентрациях, многократно превышающих терапевтические. Наличие в организме персисторных клеток патогенных бактерий снижает эффективность антибиотического лечения не в связи с генотипической лекарственной устойчивостью микроорганизма, а вследствие наличия фенотипической резистентности клеток-персисторов. Различие принципиальное, поскольку персисторы нечувствительны ко всем антибиотикам и для их эрадикации необходима разработка принципиально новых антимикробных стратегий. Клетки-персисторы представляют собой фенотипические варианты материнской культуры бактерий, которые присутствуют во всех популяциях микроорганизмов, а после наступления благоприятных условий способны рекультивироваться и сформировать новую генерацию вегетативных бактерий. В обзоре рассмотрены современные концепции молекулярно-генетических механизмов персистенции бактерий с акцентом на их клиническом значении для возникновения персистирующих инфекций, а также обсуждаются инновационные технологии эрадикации устойчивых клеточных форм микроорганизмов.
Список литературы

1. Hobby G.L., Meyer K., Chaffee E. Observations on the mechanism of action of penicillin. Proc. Soc. Exp. Biol. NY. 1942; 50(2): 281-5. DOI: http://doi.org/10.3181/00379727-50-13773

2. Bigger J.W. Treatment of staphylococcal infections with penicillin by intermittent sterilization. Lancet. 1944; 244(6320): 497-500. DOI: http://doi.org/10.1016/S0140-6736(00)74210-3

3. van den Bergh B., Michiels J.E., Fauvart M., Michiels J. Should we develop screens for multi-drug antibiotic tolerance? Expert. Rev. Anti. Infect. Ther. 2016; 14(7): 613-16. DOI: http://doi.org/10.1080/14787210.2016.1194754

4. Rehab Mahmoud abd El-Baky. The future challenges facing antimicrobial therapy: resistance and persistence. Am. J. Microbiol. Res. 2016; 4(1): 1-15. DOI: http://doi.org/10.12691/ajmr-4-1-1

5. Balaban N.Q., Merrin J., Chait R., Kowalik L., Leibler S. Bacterial persistence as a phenotypic switch. Science. 2004; 305(5690): 1622-5. DOI: http://doi.org/10.1126/science.1099390

6. Lewis K. Persister cells. Annu. Rev. Microbiol. 2010; 64: 357- 72. DOI: http://doi.org/10.1146/annurev.micro.112408.134306

7. van Teeseling M.C.F., de Pedro M.A., Cava F. Determinants of bacterial morphology: from fundamentals to possibilities for antimicrobial targeting. Front. Microbiol. 2017; 8: 1264. DOI: http://doi.org/10.3389/fmicb.2017.01264

8. Kysela D.T., Randich A.M., Caccamo P.D., Brun Y.V. Diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology. PLoS Biol. 2016; 14(10): e1002565. DOI: http://doi.org/10.1371/journal.pbio.1002565

9. Kawai Y., Mercier R., Errington J. Bacterial cell morphogenesis does not require a preexisting template structure. Curr. Biol. 2014; 24(8): 863-7. DOI: http://doi.org/10.1016/j.cub.2014.02.053

10. Harms A., Maisonneuve E., Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science. 2016; 354(6318): aaf4268. DOI: http://doi.org/10.1126/science.aaf4268

11. Maisonneuve E., Gerdes K. Molecular mechanisms underlying bacterial persisters. Cell. 2014; 157(3): 539-48. DOI: http://doi.org/10.1016/j.cell.2014.02.050

12. Orman M.A., Brynildsen M.P. Inhibition of stationary phase respiration impairs persister formation in E. coli. Nat. Commun. 2015; 6: 7983. DOI: http://doi.org/10.1038/ncomms8983

13. Randich A.M., Brun Y.V. Molecular mechanisms for the evolution of bacterial morphologies and growth modes. Front. Microbiol. 2015; 6: 580. DOI: http://doi.org/10.3389/fmicb.2015.00580

14. Stubbendieck R.M., Straight P.D. Multifaceted interfaces of bacterial competition. J. Bacteriol. 2016; 198(16): 2145-55. DOI: http://doi.org/10.1128/JB.00275-16

15. Gaivão M., Dionisio F., Gjini E. Transmission fitness in cocolonization and the persistence of bacterial pathogens. Bull. Math. Biol. 2017; 79(9): 2068-87. DOI: http://doi.org/10.1007/s11538-017-0320-3

16. Dorosky R.J., Pierson L.S., Pierson E.A. Pseudomonas chlororaphis produces multiple R-Tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities. Appl. Environ. Microbiol. 2018; 84(18): e01230- 18. DOI: http://doi.org/10.1128/AEM.01230-18

17. Fisher R.A., Gollan B., Helaine S. Persistent bacterial infections and persister cells. Nat. Rev. Microbiol. 2017; 15(8): 453-64. DOI: http://doi.org/10.1038/nrmicro.2017.42

18. Grant S.S., Hung D.T. Persistent bacterial infections, antibiotic tolerance, and the oxidative stress response. Virulence. 2013; 4(4): 273-83. DOI: http://doi.org/10.4161/viru.23987

19. Randall R.E., Griffin D.E. Within host RNA virus persistence: mechanisms and consequences. Curr. Opin. Virol. 2017; 23: 35- 42. DOI: http://doi.org/10.1016/j.coviro.2017.03.001

20. Böhm L., Torsin S., Tint S.H., Eckstein M.T., Ludwig T., Pérez J.C. The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice. PLoS Pathog. 2017; 13(10): e1006699. DOI: http://doi.org/10.1371/journal.ppat.1006699

21. Codony F., Miranda A.M., Mas J. Persistence and proliferation of some unicellular algae in drinking water systems as result of their heterotrophic metabolism: short communication. Water SA. 2003; 29(1): 113-6. DOI: http://doi.org/10.4314/wsa.v29i1.4953

22. Pearl Mizrahi S., Gefen O., Simon I., Balaban N.Q. Persistence to anti-cancer treatments in the stationary to proliferating transition. Cell Cycle. 2016; 15(24): 3442-53. DOI: http://doi.org/10.1080/15384101.2016.1248006

23. Long R.L., Gorecki M.J., Renton M., Scott J.K., Colville L., Goggin D.E., et al. The ecophysiology of seed persistence: a mechanistic view of the journey to germination or demise. Biol. Rev. Camb. Philos. Soc. 2015; 90(1): 31-59. DOI: http://doi.org/10.1111/brv.12095

24. Yafremava L.S., Wielgos M., Thomas S., Nasir A., Wang M., Mittenthal J.E., et al. A general framework of persistence strategies for biological systems helps explain domains of life. Front. Genet. 2013; 4: 16. DOI: http://doi.org/10.3389/fgene.2013.00016

25. van Boxtel C., van Heerden J.H., Nordholt N., Schmidt P., Bruggeman F.J. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J. R. Soc. Interface. 2017; 14(132): 20170141. DOI: http://doi.org/10.1098/rsif.2017.0141

26. Smith S.E. Organisms as persisters. Theor. Pract. Biol. 2017; 9(14). DOI: http://doi.org/10.3998/ptb.6959004.0009.014

27. Pu Y., Ke Y., Bai F. Active efflux in dormant bacterial cells — new insights into antibiotic persistence. Drug. Resist. Updat. 2017; 30: 7-14. DOI: http://doi.org/10.1016/j.drup.2016.11.002

28. Kim J.S., Wood T.K. Tolerant, growing cells from nutrient shifts are not persister cells. mBio. 2017; 8(2): e00354-17. DOI: http://doi.org/10.1128/mBio.00354-1718. Available at: http://mbio.asm.org/content/8/2/e00354-17.long

29. Ayrapetyan M., Williams T.C., Baxter R., Oliver J.D. Viable but non-culturable and persister cells coexist stochastically and are induced by human serum. Infect. Immun. 2015; 83(11): 4194- 03. DOI: http://doi.org/10.1128/IAI.00404-15

30. Ayrapetyan M., Williams T., Oliver J.D. Relationship between the viable but nonculturable state and antibiotic persister cells. J. Bacteriol. 2018; 200(20): e00249-18. DOI: http://doi.org/10.1128/JB.00249-18

31. Amato S.M., Fazen C.H., Henry T.C., Mok W.W., Orman M.A., Sandvik E.L., et al. The role of metabolism in bacterial persistence. Front. Microbiol. 2014; 5: 70. DOI: http://doi.org/10.3389/fmicb.2014.00070

32. Ishii S., Tago K., Senoo K. Single-cell analysis and isolation for microbiology and biotechnology: Methods and applications. Appl. Microbiol. Biotechnol. 2010; 86(5): 1281-92. DOI: http://doi.org/10.1007/s00253-010-2524-4.

33. Li M., Xu J., Romero-Gonzalez M., Banwart S.A., Huang W.E. Single cell Raman spectroscopy for cell sorting and imaging. Curr. Opin. Biotechnol. 2012; 23(1): 56-63. DOI: http://doi.org/10.1016/j.copbio.2011.11.019

34. Mazutis L., Gilbert J., Ung W.L., Weitz D.A., Griffiths A.D., Heyman J.A. Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protoc. 2013; 8(5): 870-91. DOI: http://doi.org/10.1038/nprot.2013.046

35. Stuart T., Satija R. Integrative single-cell analysis. Nat. Rev. Genet. 2019; 20(5): 257-72. DOI: http://doi.org/10.1038/s41576-019-0093-7

36. Peterson V.M., Zhang K.X., Kumar N., Wong J., Li L., Wilson D.C., Moore R., et al. Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 2017; 35(10): 936-9. DOI: http://doi.org/10.1038/nbt.3973

37. Ramani V., Deng X., Qiu R., Gunderson K.L., Steemers F.J., Disteche C.M., et al. Massively multiplex single-cell Hi-C. Nat. Methods. 2017; 14(3): 263-6. DOI: http://doi.org/10.1038/nmeth.4155

38. Tóth E.N., Lohith A., Mondal M., Guo J., Fukamizu A., Pourmand N. Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. J. Biol. Chem. 2018; 293(13): 4940-51. DOI: http://doi.org/10.1074/jbc.M117.800763

39. Hong-Geller E., Micheva-Viteva S.N. Targeting bacterial persistence to develop therapeutics against infectious disease. DOI: http://doi.org/10.5772/59404 Available at: https:// www.intechopen.com/books/drug-discovery-and-development-from-molecules-to-medicine/targeting-bacterial-persistence-to-develop-therapeutics-against-infectious-disease

40. Lin J.M., eds. Microfluidics for Single-Cell Analysis. Beijing, China: Springer Singapore; 2019. DOI: http://doi.org/10.1007/978-981-32-9729-6

41. Michiels J.E., van den Bergh B., Verstraeten N., Michiels J. Molecular mechanisms and clinical implications of bacterial persistence. Drug. Resist. Updat. 2016; 29: 76-89. DOI: http://doi.org/10.1016/j.drup.2016.10.002

42. Tian C., Semsey S., Mitarai N. Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation. Nucleic. Acids. Res. 2017; 45(14): 8180-9. DOI: http://doi.org/10.1093/nar/gkx552

43. Svenningsen M.S., Veress A., Harms A., Mitarai N., Semsey S. Birth and resuscitation of (p)ppGpp induced antibiotic tolerant persister cells. Sci. Rep. 2019; 9(1): 6056. DOI: http://doi.org/10.1038/s41598-019-42403-7

44. Wood T.K. Combatting bacterial persister cells. Biotechnol. Bioeng. 2016; 113(3): 476-83. DOI: http://doi.org/10.1002/bit.25721

45. Maisonneuve E., Castro-Camargo M., Gerdes K. (p)ppGpp controls bacterial persistence by stochastic induction of toxin-antitoxin activity. Cell. 2013; 154(5): 1140-50. DOI: http://doi.org/10.1016/j.cell.2013.07.048

46. Manav M.C., Beljantseva J., Bojer M.S., Tenson T., Ingmer H., Hauryliuk V., et al. Structural basis for (p)ppGpp synthesis by the Staphylococcus aureus small alarmone synthetase RelP. J. Biol. Chem. 2018; 293(9): 3254-64. DOI: http://doi.org/10.1074/jbc.RA117.001374

47. Syal K., Flentie K., Bhardwaj N., Maiti K., Jayaraman N., Stallings C.L., et al. Synthetic (p)ppGpp analogue is an inhibitor of stringent response in mycobacteria. Antimicrob. Agents. Chemother. 2017; 61(6): e00443-17. DOI: http://doi.org/10.1128/AAC.00443-17

48. Hauryliuk V., Atkinson G.C., Murakami K.S., Tenson T., Gerdes K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat. Rev. Microbiol. 2015; 13(5): 298- 09. DOI: http://doi.org/10.1038/nrmicro3448

49. Ogura T., Hiraga S. Mini-F plasmid genes that couples host cell division to plasmid proliferation. Proc. Natl. Acad. Sci. USA. 1983; 80(15): 4784-8. DOI: http://doi.org/10.1073/pnas.80.15.4784

50. Page R., Peti W. Toxin-antitoxin systems in bacterial growth arrest and persistence. Nat. Chem. Biol. 2016; 12(4): 208-14. DOI: http://doi.org/10.1038/nchembio.2044

51. van Melderen L. Toxin-antitoxin systems: why so many, what for? Curr. Opin. Microbiol. 2010; 13(6): 781-5. DOI: http://doi.org/10.1016/j.mib.2010.10.006

52. Lee K.Y., Lee B.J. Structure, biology, and therapeutic application of toxin-antitoxin systems in pathogenic bacteria. Toxins. 2016; 8(10): 305. DOI: http://doi.org/10.3390/toxins8100305

53. Maleki A., Ghafourian S., Pakzad I., Badakhsh B., Sadeghifard N. MazE antitoxin of toxin-antitoxin system and fbpA as reliable targets to eradication of Neisseria meningitidis. Curr. Pharm. Des. 2018; 24(11): 1204‐10. DOI: http://doi.org/10.2174/1381612824666171213094730

54. Cui P., Xu T., Zhang W.H., Zhang Y. Molecular mechanisms of bacterial persistence and phenotypic antibiotic resistance. Yi Chuan. 2016; 38(10): 859-71. DOI: http://doi.org/10.16288/j.yczz.16-213

55. Chowdhury N., Wood T.L., Martínez-Vázquez M., García-Contreras R., Wood T.K. DNA-crosslinker cisplatin eradicates bacterial persister cells. Biotechnol. Bioeng. 2016; 113(9): 1984- 92. DOI: http://doi.org/10.1002/bit.25963

56. Conlon B.P., Nakayasu E.S., Fleck L.E., LaFleur M.D., Isabella V.M., Coleman K., et al. Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature. 2013; 503(7476): 365-70. DOI: http://doi.org/10.1038/nature12790

57. Równicki M., Pieńko T., Czarnecki J., Kolanowska M., Bartosik D., Trylska J. Artificial activation of Escherichia coli mazEF and hipBA toxin-antitoxin systems by antisense peptide nucleic acids as an antibacterial strategy. Front. Microbiol. 2018; 9: 2870. DOI: http://doi.org/10.3389/fmicb.2018.02870

Journal of microbiology, epidemiology and immunobiology. 2020; 97: 271-279

Molecular Mechanisms оf Persistence оf Bacteria

Andryukov Boris G., Lyapun Irina N.

https://doi.org/10.36233/0372-9311-2020-97-3-10

Abstract

A significant mortality rate from infectious diseases is largely mediated by the widespread and uncontrolled use of antibiotics, which has led to the emergence of drug-resistant strains of bacteria. The rapid evolution of bacterial resistance to antimicrobials is a serious challenge for modern health care, mediates the need to create new antibiotic agents, as well as to intensify the study of molecular mechanisms underlying the formation of microorganism resistance. One of these mechanisms is bacterial persistence, manifested by the formation of persistent cells in the culture, which are a phenotypic variant of the isogenic population. The persistence of bacteria can occur spontaneously, regardless of exposure to antimicrobials or environmental reasons, such as lack of nutrients, oxidative stress or hypoxia. This small cell subpopulation is able to maintain viability even in the presence of antimicrobial agents at concentrations many times higher than therapeutic. The presence of persistent cells of pathogenic bacteria in the host organism reduces the effectiveness of antibiotic treatment, not due to the genotypic drug resistance of the microorganism, but due to the presence of phenotypic resistance of persister cells. The difference is fundamental, since cell-persisters are insensitive to any antibiotics and the development of fundamentally new antimicrobial strategies is necessary for their eradication. Persister cells are phenotypic variants of the maternal culture of bacteria that are present in all populations of microorganisms, and after the onset of favorable conditions, they are able to reclaim and form a new generation of vegetative bacteria. This review discusses modern concepts of the molecular genetic mechanisms of bacterial persistence with an emphasis on their clinical significance for the occurrence of persistent infections, and discusses innovative technologies for the eradication of resistant cell forms of microorganisms.
References

1. Hobby G.L., Meyer K., Chaffee E. Observations on the mechanism of action of penicillin. Proc. Soc. Exp. Biol. NY. 1942; 50(2): 281-5. DOI: http://doi.org/10.3181/00379727-50-13773

2. Bigger J.W. Treatment of staphylococcal infections with penicillin by intermittent sterilization. Lancet. 1944; 244(6320): 497-500. DOI: http://doi.org/10.1016/S0140-6736(00)74210-3

3. van den Bergh B., Michiels J.E., Fauvart M., Michiels J. Should we develop screens for multi-drug antibiotic tolerance? Expert. Rev. Anti. Infect. Ther. 2016; 14(7): 613-16. DOI: http://doi.org/10.1080/14787210.2016.1194754

4. Rehab Mahmoud abd El-Baky. The future challenges facing antimicrobial therapy: resistance and persistence. Am. J. Microbiol. Res. 2016; 4(1): 1-15. DOI: http://doi.org/10.12691/ajmr-4-1-1

5. Balaban N.Q., Merrin J., Chait R., Kowalik L., Leibler S. Bacterial persistence as a phenotypic switch. Science. 2004; 305(5690): 1622-5. DOI: http://doi.org/10.1126/science.1099390

6. Lewis K. Persister cells. Annu. Rev. Microbiol. 2010; 64: 357- 72. DOI: http://doi.org/10.1146/annurev.micro.112408.134306

7. van Teeseling M.C.F., de Pedro M.A., Cava F. Determinants of bacterial morphology: from fundamentals to possibilities for antimicrobial targeting. Front. Microbiol. 2017; 8: 1264. DOI: http://doi.org/10.3389/fmicb.2017.01264

8. Kysela D.T., Randich A.M., Caccamo P.D., Brun Y.V. Diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology. PLoS Biol. 2016; 14(10): e1002565. DOI: http://doi.org/10.1371/journal.pbio.1002565

9. Kawai Y., Mercier R., Errington J. Bacterial cell morphogenesis does not require a preexisting template structure. Curr. Biol. 2014; 24(8): 863-7. DOI: http://doi.org/10.1016/j.cub.2014.02.053

10. Harms A., Maisonneuve E., Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science. 2016; 354(6318): aaf4268. DOI: http://doi.org/10.1126/science.aaf4268

11. Maisonneuve E., Gerdes K. Molecular mechanisms underlying bacterial persisters. Cell. 2014; 157(3): 539-48. DOI: http://doi.org/10.1016/j.cell.2014.02.050

12. Orman M.A., Brynildsen M.P. Inhibition of stationary phase respiration impairs persister formation in E. coli. Nat. Commun. 2015; 6: 7983. DOI: http://doi.org/10.1038/ncomms8983

13. Randich A.M., Brun Y.V. Molecular mechanisms for the evolution of bacterial morphologies and growth modes. Front. Microbiol. 2015; 6: 580. DOI: http://doi.org/10.3389/fmicb.2015.00580

14. Stubbendieck R.M., Straight P.D. Multifaceted interfaces of bacterial competition. J. Bacteriol. 2016; 198(16): 2145-55. DOI: http://doi.org/10.1128/JB.00275-16

15. Gaivão M., Dionisio F., Gjini E. Transmission fitness in cocolonization and the persistence of bacterial pathogens. Bull. Math. Biol. 2017; 79(9): 2068-87. DOI: http://doi.org/10.1007/s11538-017-0320-3

16. Dorosky R.J., Pierson L.S., Pierson E.A. Pseudomonas chlororaphis produces multiple R-Tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities. Appl. Environ. Microbiol. 2018; 84(18): e01230- 18. DOI: http://doi.org/10.1128/AEM.01230-18

17. Fisher R.A., Gollan B., Helaine S. Persistent bacterial infections and persister cells. Nat. Rev. Microbiol. 2017; 15(8): 453-64. DOI: http://doi.org/10.1038/nrmicro.2017.42

18. Grant S.S., Hung D.T. Persistent bacterial infections, antibiotic tolerance, and the oxidative stress response. Virulence. 2013; 4(4): 273-83. DOI: http://doi.org/10.4161/viru.23987

19. Randall R.E., Griffin D.E. Within host RNA virus persistence: mechanisms and consequences. Curr. Opin. Virol. 2017; 23: 35- 42. DOI: http://doi.org/10.1016/j.coviro.2017.03.001

20. Böhm L., Torsin S., Tint S.H., Eckstein M.T., Ludwig T., Pérez J.C. The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice. PLoS Pathog. 2017; 13(10): e1006699. DOI: http://doi.org/10.1371/journal.ppat.1006699

21. Codony F., Miranda A.M., Mas J. Persistence and proliferation of some unicellular algae in drinking water systems as result of their heterotrophic metabolism: short communication. Water SA. 2003; 29(1): 113-6. DOI: http://doi.org/10.4314/wsa.v29i1.4953

22. Pearl Mizrahi S., Gefen O., Simon I., Balaban N.Q. Persistence to anti-cancer treatments in the stationary to proliferating transition. Cell Cycle. 2016; 15(24): 3442-53. DOI: http://doi.org/10.1080/15384101.2016.1248006

23. Long R.L., Gorecki M.J., Renton M., Scott J.K., Colville L., Goggin D.E., et al. The ecophysiology of seed persistence: a mechanistic view of the journey to germination or demise. Biol. Rev. Camb. Philos. Soc. 2015; 90(1): 31-59. DOI: http://doi.org/10.1111/brv.12095

24. Yafremava L.S., Wielgos M., Thomas S., Nasir A., Wang M., Mittenthal J.E., et al. A general framework of persistence strategies for biological systems helps explain domains of life. Front. Genet. 2013; 4: 16. DOI: http://doi.org/10.3389/fgene.2013.00016

25. van Boxtel C., van Heerden J.H., Nordholt N., Schmidt P., Bruggeman F.J. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J. R. Soc. Interface. 2017; 14(132): 20170141. DOI: http://doi.org/10.1098/rsif.2017.0141

26. Smith S.E. Organisms as persisters. Theor. Pract. Biol. 2017; 9(14). DOI: http://doi.org/10.3998/ptb.6959004.0009.014

27. Pu Y., Ke Y., Bai F. Active efflux in dormant bacterial cells — new insights into antibiotic persistence. Drug. Resist. Updat. 2017; 30: 7-14. DOI: http://doi.org/10.1016/j.drup.2016.11.002

28. Kim J.S., Wood T.K. Tolerant, growing cells from nutrient shifts are not persister cells. mBio. 2017; 8(2): e00354-17. DOI: http://doi.org/10.1128/mBio.00354-1718. Available at: http://mbio.asm.org/content/8/2/e00354-17.long

29. Ayrapetyan M., Williams T.C., Baxter R., Oliver J.D. Viable but non-culturable and persister cells coexist stochastically and are induced by human serum. Infect. Immun. 2015; 83(11): 4194- 03. DOI: http://doi.org/10.1128/IAI.00404-15

30. Ayrapetyan M., Williams T., Oliver J.D. Relationship between the viable but nonculturable state and antibiotic persister cells. J. Bacteriol. 2018; 200(20): e00249-18. DOI: http://doi.org/10.1128/JB.00249-18

31. Amato S.M., Fazen C.H., Henry T.C., Mok W.W., Orman M.A., Sandvik E.L., et al. The role of metabolism in bacterial persistence. Front. Microbiol. 2014; 5: 70. DOI: http://doi.org/10.3389/fmicb.2014.00070

32. Ishii S., Tago K., Senoo K. Single-cell analysis and isolation for microbiology and biotechnology: Methods and applications. Appl. Microbiol. Biotechnol. 2010; 86(5): 1281-92. DOI: http://doi.org/10.1007/s00253-010-2524-4.

33. Li M., Xu J., Romero-Gonzalez M., Banwart S.A., Huang W.E. Single cell Raman spectroscopy for cell sorting and imaging. Curr. Opin. Biotechnol. 2012; 23(1): 56-63. DOI: http://doi.org/10.1016/j.copbio.2011.11.019

34. Mazutis L., Gilbert J., Ung W.L., Weitz D.A., Griffiths A.D., Heyman J.A. Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protoc. 2013; 8(5): 870-91. DOI: http://doi.org/10.1038/nprot.2013.046

35. Stuart T., Satija R. Integrative single-cell analysis. Nat. Rev. Genet. 2019; 20(5): 257-72. DOI: http://doi.org/10.1038/s41576-019-0093-7

36. Peterson V.M., Zhang K.X., Kumar N., Wong J., Li L., Wilson D.C., Moore R., et al. Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 2017; 35(10): 936-9. DOI: http://doi.org/10.1038/nbt.3973

37. Ramani V., Deng X., Qiu R., Gunderson K.L., Steemers F.J., Disteche C.M., et al. Massively multiplex single-cell Hi-C. Nat. Methods. 2017; 14(3): 263-6. DOI: http://doi.org/10.1038/nmeth.4155

38. Tóth E.N., Lohith A., Mondal M., Guo J., Fukamizu A., Pourmand N. Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. J. Biol. Chem. 2018; 293(13): 4940-51. DOI: http://doi.org/10.1074/jbc.M117.800763

39. Hong-Geller E., Micheva-Viteva S.N. Targeting bacterial persistence to develop therapeutics against infectious disease. DOI: http://doi.org/10.5772/59404 Available at: https:// www.intechopen.com/books/drug-discovery-and-development-from-molecules-to-medicine/targeting-bacterial-persistence-to-develop-therapeutics-against-infectious-disease

40. Lin J.M., eds. Microfluidics for Single-Cell Analysis. Beijing, China: Springer Singapore; 2019. DOI: http://doi.org/10.1007/978-981-32-9729-6

41. Michiels J.E., van den Bergh B., Verstraeten N., Michiels J. Molecular mechanisms and clinical implications of bacterial persistence. Drug. Resist. Updat. 2016; 29: 76-89. DOI: http://doi.org/10.1016/j.drup.2016.10.002

42. Tian C., Semsey S., Mitarai N. Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation. Nucleic. Acids. Res. 2017; 45(14): 8180-9. DOI: http://doi.org/10.1093/nar/gkx552

43. Svenningsen M.S., Veress A., Harms A., Mitarai N., Semsey S. Birth and resuscitation of (p)ppGpp induced antibiotic tolerant persister cells. Sci. Rep. 2019; 9(1): 6056. DOI: http://doi.org/10.1038/s41598-019-42403-7

44. Wood T.K. Combatting bacterial persister cells. Biotechnol. Bioeng. 2016; 113(3): 476-83. DOI: http://doi.org/10.1002/bit.25721

45. Maisonneuve E., Castro-Camargo M., Gerdes K. (p)ppGpp controls bacterial persistence by stochastic induction of toxin-antitoxin activity. Cell. 2013; 154(5): 1140-50. DOI: http://doi.org/10.1016/j.cell.2013.07.048

46. Manav M.C., Beljantseva J., Bojer M.S., Tenson T., Ingmer H., Hauryliuk V., et al. Structural basis for (p)ppGpp synthesis by the Staphylococcus aureus small alarmone synthetase RelP. J. Biol. Chem. 2018; 293(9): 3254-64. DOI: http://doi.org/10.1074/jbc.RA117.001374

47. Syal K., Flentie K., Bhardwaj N., Maiti K., Jayaraman N., Stallings C.L., et al. Synthetic (p)ppGpp analogue is an inhibitor of stringent response in mycobacteria. Antimicrob. Agents. Chemother. 2017; 61(6): e00443-17. DOI: http://doi.org/10.1128/AAC.00443-17

48. Hauryliuk V., Atkinson G.C., Murakami K.S., Tenson T., Gerdes K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat. Rev. Microbiol. 2015; 13(5): 298- 09. DOI: http://doi.org/10.1038/nrmicro3448

49. Ogura T., Hiraga S. Mini-F plasmid genes that couples host cell division to plasmid proliferation. Proc. Natl. Acad. Sci. USA. 1983; 80(15): 4784-8. DOI: http://doi.org/10.1073/pnas.80.15.4784

50. Page R., Peti W. Toxin-antitoxin systems in bacterial growth arrest and persistence. Nat. Chem. Biol. 2016; 12(4): 208-14. DOI: http://doi.org/10.1038/nchembio.2044

51. van Melderen L. Toxin-antitoxin systems: why so many, what for? Curr. Opin. Microbiol. 2010; 13(6): 781-5. DOI: http://doi.org/10.1016/j.mib.2010.10.006

52. Lee K.Y., Lee B.J. Structure, biology, and therapeutic application of toxin-antitoxin systems in pathogenic bacteria. Toxins. 2016; 8(10): 305. DOI: http://doi.org/10.3390/toxins8100305

53. Maleki A., Ghafourian S., Pakzad I., Badakhsh B., Sadeghifard N. MazE antitoxin of toxin-antitoxin system and fbpA as reliable targets to eradication of Neisseria meningitidis. Curr. Pharm. Des. 2018; 24(11): 1204‐10. DOI: http://doi.org/10.2174/1381612824666171213094730

54. Cui P., Xu T., Zhang W.H., Zhang Y. Molecular mechanisms of bacterial persistence and phenotypic antibiotic resistance. Yi Chuan. 2016; 38(10): 859-71. DOI: http://doi.org/10.16288/j.yczz.16-213

55. Chowdhury N., Wood T.L., Martínez-Vázquez M., García-Contreras R., Wood T.K. DNA-crosslinker cisplatin eradicates bacterial persister cells. Biotechnol. Bioeng. 2016; 113(9): 1984- 92. DOI: http://doi.org/10.1002/bit.25963

56. Conlon B.P., Nakayasu E.S., Fleck L.E., LaFleur M.D., Isabella V.M., Coleman K., et al. Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature. 2013; 503(7476): 365-70. DOI: http://doi.org/10.1038/nature12790

57. Równicki M., Pieńko T., Czarnecki J., Kolanowska M., Bartosik D., Trylska J. Artificial activation of Escherichia coli mazEF and hipBA toxin-antitoxin systems by antisense peptide nucleic acids as an antibacterial strategy. Front. Microbiol. 2018; 9: 2870. DOI: http://doi.org/10.3389/fmicb.2018.02870