• 2.53 Bob Champion Research & Education Bldg

Accepting PhD Students

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Personal profile

Key Research Interests

  • The biology of the bacterial pathogen Acinetobacter baumannii
  • Evolution of bacterial drug resistance mechanisms
  • Transmission of drug resistance in bacterial populations
  • Population dynamics of bacterial pathogens

The evolution and spread of antibiotic resistance

Bacteria can become resistant to antibiotics through a number of different mechanisms. These include intrinsic mechanism that all members of the bacterial species posses and that they switch on or ‘ramp up’ when exposed to antibiotics, and mechanisms that the bacteria acquire from external sources that can then be exchanged between bacteria.
 
My work centres on understanding which mechanisms bacteria are using to become resistant to antibiotics, and how these are evolving and being transferred in bacterial populations. An example of current work is investigating the effect of non-antibiotic drugs, such as cancer chemotherapies, on promoting antibiotic resistance. Many drugs used in healthcare coincidently have antibacterial properties, and therefore bacteria develop resistance against these. However, in doing so, some bacteria can become more resistant to antibiotics at the same time, even without having been exposed to any antibiotics. This ‘cross-resistance’, where exposure to one drug (e.g. a cancer chemotherapy) causes resistance to a different drug (e.g. an antibiotic) is not well understood despite its potential to have a major impact on the evolution and spread of antibiotic resistance. By understanding how different drugs cause cross-resistance to antibiotics we will gain a more holistic view of antibiotic resistance that can be exploited in the design and development of new drugs, and in the management and use of existing drugs.

Postgraduate Research Opportunities

If you have obtained or have the option to obtain funding to complete a PhD, I would be interested to hear from you. Please email me to discuss further.

Current Opportunity!

Superpowers of a superbug: genomic signatures of pathogen evolution in antibiotic resistant Acinetobacter

Background                                           

Antibiotic resistant superbugs are highlighted by the World Health Organization as a critical healthcare challenge. Species of Acinetobacter bacteria cause serious infections in hospital patients that are very difficult to treat due to antibiotic resistance. We have a limited understanding of how these superbugs manage to adapt and evolve to evade our attempts to treat them. In this project you will fill this gap in our knowledge, which is essential for successful new treatments in the future. Bacteria have the amazing ability to flip around massive sections of their genome, changing the expression of hundreds of genes, adapting immediately to new threats. You will examine this phenomenon for the first time in Acinetobacter. Furthermore, bacteria can evolve very rapidly. You will conduct the largest ever study on the evolution of Acinetobacter and identify the genes that have been evolving in response to antibiotic treatment.

Methods

Using our unique collection of Acinetobacter genomes, combined with publicly available genomes, you will identify patterns of genome rearrangements and recombination, and identify genes impacted by rearrangement, devising a metric to assess transcriptional impact. You will assess evidence for positive selection using dN/dS ratios, codon usage and McDonald-Kreitman tests. You will have the opportunity to study gene families of particular interest in more detail, such as antimicrobial drug resistance or virulence.

Training

Your supervisory team (Dr Ben Evans, UEA, UK; Dr Gemma Langridge, Quadram Institute, UK; Dr Santiago Castillo-Ramirez, UNAM, Mexico; Dr Louis-Patrick Hararoui, Sherbrooke, Canada) provide expertise in Acinetobacter, evolutionary genomics, bioinformatics, and medicine. You will have the opportunity to attend internal and external training courses, such as in microbial genomics, evolution and programming, and to present your work at lab meetings, and conferences. You will develop skills in programming (e.g., Python), data analyses and presentation (e.g., using R), and scientific communication. You will have the opportunity to apply for funds from the Turing Scheme to visit the members of the supervisory team based outside of the UK.

Person specification

Minimum 2:1 undergraduate degree with experience of bioinformatics or computer science.  Knowledge in microbiology or evolutionary biology, and programming skills, would be beneficial.

To apply please find the project on the UEA webpages and use the application link.

Career

Sept 2006 – Nov 2009: PhD in Medical Microbiology, University of Edinburgh, UK

Nov 2009 – Jul 2011: Post-doctoral Research Associate, University of Manchester, UK

Aug 2011 – Sep 2012: Post-doctoral Research Associate, University of Liverpool, UK

Oct 2012 – Sep 2013: Lecturer in Microbiology and Medical Biotechnology, Anglia Ruskin University, Cambridge, UK

Sep 2013 – Jul 2016: Senior Lecturer in Microbiology and Medical Biotechnology, Anglia Ruskin University, Cambridge, UK

Sep 2015 – Jul 2016: Deputy Head of Department (Acting), Biomedical and Forensic Sciences, Anglia Ruskin University, UK

Jul 2016 – Present: Lecturer in Medical Microbiology, University of East Anglia, UK

Academic Background

  • The biology of Acinetobacter baumannii
  • Antibiotic resistance in Gram-negative bacterial pathogens
  • Natural transformation in Streptococcus pneumoniae
  • Population evolution in Pseudomonas aeruginosa
  • Bacterial genomics

Teaching Interests

  • Lecturing on the Gateway to Medicine course
  • Tutor for 1st Year Student Selected Studies (SSS) Genetics
  • Supervisor for SSS Research
  • Gateway to Medicine Problem-Based Learning (PBL) and SSS tutor
  • Advisor to medical students

Administrative Posts

  • Director of the MRC Doctoral Antimicrobial Research Training (DART) iCASE programme
  • UEA Microbiological Safety Officer
  • UEA Genetic Modification Safety Officer
  • Chair, UEA Biological Hazards and Genetic Modification Review Committee

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being

Education/Academic qualification

Doctor of Philosophy, University of Edinburgh

20062009

Bachelor of Science, University of Edinburgh

20012005

Keywords

  • Medicine (general)
  • Bacteriology
  • Antibiotic resistance
  • Genomics
  • Evolution

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