Persisters, persistent infections and the Yin–Yang model

Figures & data

Figure 1 The Yin–Yang model of persisters and latent infections.^5,8,19 In a growing population of bacteria (Yang, red), there is a small population of non-growing or slowly growing persisters (Yin, black). In the persister population, there is a small number of growing bacteria (reverters). The persister population (Yin) or the growing population (Yang) is again heterogeneous and composed of various subpopulations with varying metabolic or dormant states in continuum in varying hierarchy (expressed by color from light to dark). The black spot in Yang (red) is connected to and the root of the Yin half (black), and the red spot in Yin, reverters, is connected to the Yang half (red). In the case of TB, INH kills growing bacteria (Yang) and RIF kills some growing bacteria, as well as slowly growing persisters, whereas PZA kills only persisters. Persisters not killed by antibiotics could revert to replicating forms (reverters) and cause relapse. The Yin–Yang model can be used to better describe latent infections (Yin) and active disease (Yang) at the host level and their respective interconversions.^8,19 As drug treatment and immune responses inhibit or kill the growing bacteria (Yang) and some of the persisters, some persisters (Yin) still remain and the infection becomes latent (Yin), but may revert and cause relapse or sustained chronic infections with symptoms. In a hierarchical manner and among heterogeneous persister cell populations, there are a few true ‘stem’ persister cells or mother cells (black spot in Yang) that have the capacity to derive other persisters (Yin) and initiate disease or cause reactivation. The Yin–Yang model proposes use of drugs targeting both replicating and non-replicating cells in combination or sequentially in a dynamic fashion and in cycles for better treatment of persistent bacterial infections. This Yin–Yang model can also be applied to other microbes, such as fungi, parasites, viruses, and their infections and even cancer and the respective treatments of infections and cancer.¹⁹

Table 1 Studies and observations that support or are consistent with the Yin–Yang model (see Figure 1)

Setting	Organisms	References
Inclusion of pyrazinamide that kills persisters with other drugs that kill growing bacilli shortens TB treatment in mice and humans	M. tuberculosis	78,106,107,108
Two phases of TB therapy where the first phase involves a combination of INH, RIF, EMB and PZA followed by the second phase of only INH and RIF. INH is a drug that only kills growing bacteria and its inclusion in the second phase of treatment is to kill the ‘reverters’ from the persisters not killed by the first phase treatment	M. tuberculosis	8,109
Use of isoniazid, a drug that is only active for growing bacteria, for treatment of LTBI; during LTBI, there are growing TB bacteria (reverters) that are susceptible to INH	M. tuberculosis	8,109
Spectrum or varying levels of persistence during latent TB infection and treatment	M. tuberculosis	51,106
Rapidly growing bacteria can give rise to persisters, whereas stationary phase bacteria can have cryptic growth	E. coli	12,110
Heterogeneity of persisters as demonstrated by varying antibiotic exposure times: ‘shallow’ persisters and ‘deep’ persisters	E. coli	4,9
Cancer stem cell drug candidates used in combination with current cancer drugs improve cancer treatment in mice	Breast cancer	111,112,113

Abbreviations: EMB, ethambutol; LTBI, latent TB infection.

Table 2 Diseases with known bacterial persistence problems

Disease	Pathogen	Treatment
Tuberculosis	M. tuberculosis	Isoniazid, rifampin, pyrazinamide, ethambutol
Syphilis	Treponema pallidum	Penicillins, doxycycline, macrolide
Lyme disease	Borrelia burgdorferi	Doxycycline, amoxicillin
Urinary tract infections	E. coli, Enterococcus, Pseudomonas aeruginosa, Chlamydia, Mycoplasma genitalium	Trimethoprim, amoxicillin, nitrofurantoin, quinolones, doxycycline, macrolide
Peptic ulcer	Helicobacter pylori	Amoxicillin, clarithromycin, metronidazole, omeprazole, doxycycline, bismuth
Bacteremia/sepsis	Staphylococcus aureus, Group B Streptococcus	Various antibiotics
Endocarditis	Streptococcus, Staphylococcus, Enterococcus	Penicillins, vancomycin
Otitis media	S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis	Amoxicillin, azithromycin
Brucellosis	Brucella abortus	Doxycycline, rifampin
Biofilm infections, periodontitis, prosthetic device infections	Various pathogens	Refractory to antibiotic treatment

Table 3 Persister mechanisms in bacteria

Persister pathways	Genes involved	Mechanisms/features	References
Toxin–antitoxin modules	hipBA, relBE, mazEF, tisAB, mqsR, hhA, hokA, cspD, pasT	Toxin–antitoxin modules inhibit protein or nucleic acid synthesis; Lon protease can degrade the antitoxin to regulate persister formation	3,12,37,40,69,114,115
Alternative energy production	sucB, ubiF, glpD, plsB, tgs1	Provision of energy under stress conditions	9,63,116
Stringent response	relA, dksA	ppGpp synthesized by RelA inhibits RNA synthesis	31,34,68,117
SOS response/DNA repair and protection of DNA	lexA, recA, recB, xerC, xerD, dps	Repair of DNA damage caused by ROS	29,118,119,120
Antioxidant defense H2S, NO	Superoxide dismutase, catalase	Removal of ROS and hydroxyl radical	24,33,35,36
Enhanced efflux or transporter activity	Various	Removal of toxic substances or antibiotic buildup, underlying tolerance to antibiotics and stresses	33,121,122
Phosphate metabolism	phoU	PhoU is a negative regulator of phosphate uptake, mutant has dramatic defect in persister phenotype; shutdown of metabolic activity	4,67,123
Trans-translation	ssrA, smpB, rpsA	Degradation of toxic proteins and mRNA and recycling of ribosomes	27,81
Signaling pathways	comE/comC; tnaA, oxyR, flu, pspBC	Quorum sensing peptide or homoserine lactone or indole, acting through TA or antioxidant defense OxyR and phage-shock pathways	32,124,125

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