Study level

  • Master of Philosophy
  • Honours


Topic status

We're looking for students to study this topic.

Research centre


Associate Professor Makrina Totsika
Principal Research Fellow
Division / Faculty
Faculty of Health


The last fifteen years have witnessed an unprecedented rise in the rates of antimicrobial resistance among Gram-negative bacteria, described by the World Health organisation as a global health crisis (1). Escherichia coli sequence type 131 (E. coli ST131) is a ‘high-risk’ group of Gram-negative pathogens that have emerged rapidly and spread worldwide in the period of the last 10 years (2). E. coli ST131 strains are typically resistant to multiple classes of antibiotics and cause bloodstream and urinary tract infections (UTI) that are extremely difficult to treat.

My lab has recently shown that ST131 strains are proficient colonizers of the gut allowing them to persist for long periods of time with the possibility of new hybrid strains emerging (3). This project will investigate newly emerged sub-lineages of ST131 with enhanced pathogenic potential.


  • Comparative genomics of diverse E. coli ST131 clinical isolates.
  • Identification and characterisation of key virulence factors in newly emerged ST131 isolates.

References/key papers

  1. World Health Organization, Antimicrobial Resistance: Global Report on Surveillance (2014).
  2. Nicolas-Chanoine M-H, Bertrand X, Madec J-Y. Escherichia coli ST131, an Intriguing Clonal Group. Clinical Microbiology Reviews. 2014;27(3):543-574.
  3. Sarkar S, Hutton ML, Vagenas D, Ruter R, Schüller S, Lyras D, Schembri MA, Totsika M. (2018) Intestinal colonisation traits of pandemic multidrug resistant Escherichia coli ST131. Journal of Infectious Diseases, 218(6):979-990.

Approaches, skills and techniques

  • Comparative bacterial genomics and bioinformatics.
  • Culture of human cell lines.
  • Handling/culturing multidrug resistant bacterial pathogens and GMOs.
  • Gene expression analysis (including DNA/RNA isolation, genetic engineering, protein preparation, PCR, qRT-PCR, DNA/protein gel-electrophoresis).
  • in vitrocell infection assays.

You will also receive training in conducting literature searches and critical literature review, research design and methodology, data analysis and presentation in lab meetings.


Enhanced understanding of E. coliST131 diversity in mechanisms of antibiotic resistance, virulence and host colonisation and disease.

Required skills and experience

An ideal candidate will have an active interest in microbiology, infectious diseases and/or pathogen genomics. Prior study in these areas would be desirable.



Contact Associate Professor Makrina Totsika for more information.