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Department of Genetics


The role of biofilms and persisters in bacterial infections


Antibiotic, biofilm, persisters, UTIs

Research Interests

Research in the Zarkan laboratory is focused on understanding and combatting bacterial biofilms and antibiotic persisters, using E. coli as a model organism. Biofilms and persisters are two important aspects of antibiotic resistance. Biofilms provide structural protection for bacteria and other microorganisms against antimicrobials and the host immune system, while persistence refer to the ability of subpopulation of genetically sensitive bacteria to survive antibiotic treatment by virtue of their dormancy. Biofilms and persisters are associated clinically with treatment failure and recurrent infections. In the case of E. coli, biofilms and persisters are common in patients with urinary tract infections (UTIs) leading to recurrent UTIs. We aim to address the following questions:

  • What is the role of the bacterial enzyme tryptophanase in the formation of biofilms and persisters?
  • What is the relation between bacterial membrane potential and antibiotic persistence? 
  • How do urinary extracellular vesicles contribute to combatting biofilms and persisters in UTIs?

Key publications

  • Shi, X & Zarkan, A (2022). Bacterial Survivors: Evaluating the Mechanisms of Antibiotic Persistence. Microbiol168:001266.  
  • Goode, O., Smith, A., Zarkan, A, et al (2021). Persister E. coli have a lower intracellular pH than susceptible cells but maintain their pH in response to antibiotic treatment. mBio12:e00909-21. 
  • Zarkan, A, et al (2020). Inhibiting indole signalling offers a potential strategy for combatting antibiotic persisters. Behind the Paper: Nature Microbiology Community 
  • Zarkan, A, et al (2020). Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters. Scientific Reports 10:11741.  
  • Zarkan, A., et al (2020). Local and Universal Action: The Paradoxes of Indole Signalling in Bacteria. Trends in Microbiology 28:566-577. 
  • Zarkan, A., et al (2019). Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner. Scientific Reports 9:3868. 
  • Zarkan, A., et al (2017). Zn(II) mediates vancomycin polymerization and potentiates its antibiotic activity against resistant bacteria. Scientific Reports 7:4893. 
  • Zarkan, A., et al (2016). The frontline antibiotic vancomycin induces a zinc starvation response in bacteria by binding to Zn(II). Scientific Reports 6:19602. 

Contact details

Group Leader: Ash Zarkan


Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge CB2 3EH,
United Kingdom