High-throughput identification of novel antimicrobial targets in Clostridium difficile

PhD available in Roy Chaudhuri‘s group, in collaboration with Rob Fagan.

Clostridium difficile is an important human pathogen and the primary cause of antibiotic-associated infections in UK hospitals. The bacteria that reside in the human gut (the microbiota) normally prevent colonisation with C. difficile. However, treatment with antibiotics causes severe disruption to this community allowing C. difficile to establish an infection. C. difficile itself is highly resistant to most commonly used antibiotics and our treatment options are limited. There is an urgent need for the development of new antibiotics, particularly species-specific antimicrobials that can kill C. difficile without causing further damage to the microbiota.

In this project we will employ a combination of bacterial genetics and bioinformatics to address the problem of antibiotic resistance in C. difficile. We will identify the core set of genes which are required for C. difficile to grow. These will represent attractive targets for future antibiotics. At the same time we will also dissect the mechanisms of resistance to existing antibiotics. This information may be used to breath new life into current therapies.

Traditionally, assigning a function to a given gene was extremely labour intensive. The development of random transposon mutagenesis allowed for the rapid generation of a large numbers of mutants but each mutant then had to be studied individually or in small pools. Recently, techniques such as transposon directed insertion site sequencing (TraDIS) (1), have allowed for the analysis of huge numbers of transposon mutants simultaneously using high-throughput Illumina sequencing. We have developed a highly efficient transposon mutagenesis system for C. difficile (2) and will combine this technology with cutting edge bioinformatics analysis (3) to identify novel antibiotic targets and characterise existing resistance mechanisms.

This is a cross-disciplinary project, and the successful applicant will receive training in both laboratory molecular microbiology techniques such as transposon mutagenesis, and computational methods, including the analysis of large-scale next generation sequencing datasets. There is considerable demand for such multi-skilled individuals from both academic and industrial employers.

For informal enquiries and further information please contact: Dr Roy Chaudhuri (r.chaudhuri@sheffield.ac.uk) or Dr Robert Fagan (r.fagan@sheffield.ac.uk).

Funding Notes:

The Department offers full time PhD research projects which are fully funded for 42 months. The funding will pay the UK/ EU tuition fees and a maintenance stipend at the RCUK standard rate (£13,863 in 2014/15).

How to apply: Complete an online application (http://www.shef.ac.uk/postgraduate/research/apply) form for admission as a postgraduate student.


1. Langridge, G. C., M. Phan, D. J. Turner, T. T. Perkins, L. Parts, J. Haase, I. Charles, D. J. Maskell, S. E. Peters, G. Dougan, J. Wain, J. Parkhill & A. K. Turner (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Research 19:2308-2316

2. Dembek, M., L. Barquist, C. J. Boinett, A. K. Cain, M. Mayho, T. D. Lawley, N. F. Fairweather and R. P. Fagan (2015) High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. mBio in press

3. Chaudhuri, R. R., E. Morgan, S. E. Peters, S. J. Pleasance, D. L. Hudson, H. M. Davies, J. Wang, P. M. van Dieman, A. M. Buckley, A. J. Bowen, G. D. Pullinger, D. J. Turner, G. C. Langridge, A. K. Turner, J. Parkhill, I. G. Charles, D. J. Maskell and M. P. Stevens (2013) Comprehensive assignment of roles for Salmonella Typhimurium genes in intestinal colonization of food-producing animals. PLoS Genetics e1003456

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