Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters

Abstract

Persisters are a sub-population of genetically sensitive bacteria that survive antibiotic treatment by entering a dormant state. The emergence of persisters from dormancy after antibiotic withdrawal leads to recurrent infection. Indole is an aromatic molecule with diverse signalling roles, including a role in persister formation. Here we demonstrate that indole stimulates the formation of Escherichia coli persisters against quinolone antibiotics which target the GyrA subunit of DNA gyrase. However, indole has no effect on the formation of E. coli persisters against an aminocoumarin, novobiocin, which targets the GyrB subunit of DNA gyrase. Two modes of indole signalling have been described: persistent and pulse. The latter refers to the brief but intense elevation of intracellular indole during stationary phase entry. We show that the stimulation of quinolone persisters is due to indole pulse, rather than persistent, signalling. In silico docking of indole on DNA gyrase predicts that indole docks perfectly to the ATP binding site of the GyrB subunit. We propose that the inhibition of indole production offers a potential route to enhance the activity of quinolones against E. coli persisters. The decreasing effectiveness of antibiotic therapy represents an unprecedented, worldwide threat to human and animal health. The most widely publicised, and best understood, aspect of this problem is antibiotic resistance. This involves genetic change, through mutation or horizontal gene transfer. The target organism is rendered immune to the antibiotic by inactivation of the drug, alteration of its target or export from the cell 1. A less well studied but increasingly important aspect of the anti-bacterial problem is the ability of small sub-populations (< 1%) of genetically sensitive bacteria to survive high concentrations of antibiotic by entering a dormant or partially-dormant state. These cells are known as antibiotic persisters 2-4. When treated with a bactericidal concentration of an antibiotic, persisters display a temporary, non-heritable phenotype where they survive but do not replicate. When the antibiotic therapy is withdrawn, persisters revert to the growing state, giving rise to a population characterised by the same antibiotic sensitivity as the original population. In contrast, resistant cells continue to grow and divide in the presence of the antibiotic and the resistance phenotype is heritable 5-7. The mechanisms by which persister cells enter a dormant state are not well understood. It has been suggested that the activation of chromosome-encoded toxin-antitoxin systems is an important mechanism 8 although this has recently been questioned 9. Links have also been made to the stringent response and carbon source transitions 10. A few reports 11,12 have suggested a role for the signalling molecule indole and this seems plausible because indole has been known for several years to induce reversible E. coli dormancy 13. Indole is an aromatic signalling molecule produced by over 85 species of bacteria encompassing ...

Persister Escherichia coli Cells Have a Lower Intracellular pH than Susceptible Cells but Maintain Their pH in Response to Antibiotic Treatment

“…However, in stationary phase, this phenomenon was reversed, with a higher proportion of persisters found in the Δ tnaA than in the parental strain, but mimics of persistent indole signaling restored the persister levels measured for the parental strain. Therefore, the Δ tnaA strain appears to be a high-persister-level mutant ( 21 ), exhibiting high persister levels in stationary but not in exponential phase, suggesting that persistent indole signaling increases the level of triggered persisters but not of spontaneous persisters ( 89 ). Surprisingly, we found that the abundance of VBNC cells within the E. coli population was not affected by the removal of either tryptophanase activity or indole signaling.…”

Indole Inhibits IncP-1 Conjugation System Mainly Through Promoting korA and korB Expression

“…The reason behind this phenomenon may be that E. coli may utilize indole to compete against other microorganisms that could produce antibiotics ( Han et al, 2011 ). However, CIP is a member of synthetic quinolone antibiotics, and indole is reported to stimulate the formation of E. coli persisters against quinolone antibiotics ( Zarkan et al, 2020 ). We referred that CIP may in turn play a role through inhibiting indole production.…”

Biological Effects of Quinolones: A Family of Broad-Spectrum Antimicrobial Agents

“…The authors conclude that although concentrations are below any toxic effect in humans, the presence of these agents has to be screened for safety issues [ 335 ]. Zarkan et al, found that inhibition of indole production increases the activity of quinolones against persisters of E. coli [ 336 ], probably by binding to the ATP binding site of GyrB subunit of DNA gyrase. The use of anti-virulence factors have been proposed as an antimicrobial therapy alternative to antibiotics [ 337 ].…”