Title of project: Epigenetic control and the development of antimicrobial resistance and
cross-resistance to antibiotics.
Director of Studies: Dr Donna Johnson
Second Supervisor: Dr Margarita Gomez Escalada
Overview of project
Triclosan is a widely used antimicrobial that has been associated with resistance development and
development of antibiotic cross-resistance, following the discovery of its competitive inhibition of enoyl
reductase, which is involved in fatty acid biosynthesis[1]. This issue is timely as the US Food and
Drug Administration recently published an announcement that it will review Triclosan’s licence
because of these concerns which may be applicable to a range of other antimicrobial agents. A
number of publications[2, 3] have reported the development of antibiotic resistance (ABR), and in
some cases multiple antibiotic resistances (MARs), following exposure to sub-inhibitory
concentrations of Triclosan. While it is thought that the mechanisms of resistance may be acquired
through efflux[4], the mechanisms of this acquired ABR/MAR have never been fully elucidated.
In order to maximise survival, clonal bacterial populations exhibit cell-cell variation. While it has been
generally assumed that mutation is the cause of such variation, it is becoming increasingly apparent
that mechanisms such as DNA methylation can also result in such[5, 6]. DNA methylation is the most
common epigenetic change in prokaryotes[7] and in Gram negative bacteria, it is primarily mediated
by Dam and Dcm (adenine and cytosine methyltransferase enzymes respectively)[7, 8]. DNA
methylation has been shown to affect a range of processes including: regulation of secretion systems
in Ps. aeruginosa and enteroaggressive E. coli, and phase regulation in uropathogenic E. coli. In
addition, the methyltransferases have been linked to virulence and pathogenesis in a range of
bacteria including Y. pestis and P. multocida[9]. It has been suggested that DNA methylation may
also impact resistance development[6]. Militelo et al. found that lack of methylation was linked to
ethidium bromide resistance through relieved repression of the small multidrug resistance protein
SugE [9]. Adam et al. also saw increased antibiotic resistance in E. coli as a result of epigeneticallyinduced changes in the expression of resistance-associated genes[6].
Currently, robust and user-friendly assays are available for the assessment of cytosine methylation,
largely due to the widespread study of such in humans. Although not specifically designed for
bacteria, these are easily transferable for the study of bacterial cytosine methylation. There are,
however, no equivalent methods available for the study of adenine methylation. In bacteria, the ability
to assess adenine methylation is vitally important given the range of roles it is implicated in and thus
its analysis represents an area of unmet need.
In the short term we would make available a new tool for the study of epigenetic control in bacteria
which would be of benefit in a range of areas outside of AMR. In the medium term the application of
the techniques piloted here could be applied to a more inclusive range of important, clinically relevant
Gram negative pathogens such as Pseudomonas, Klebsiella and Acinetobacter. The ultimate long
term goal of this work is the identification of novel pathways for the development of antimicrobial
sensitising agents or circumventing strategies and policies to the epigenetic adaptive mechanisms.
Overall this project adds knowledge to the pathways involved in AMR, with epigenetic control being of
particular importance due to its potential to produce short term resistance that could lead to stable
resistance mutations.
The ultimate long term goal of this work is the identification of novel pathways for the development of
antimicrobial sensitising agents or circumventing strategies and policies to the epigenetic adaptive
mechanisms. In the short term we would make available a new tool for the study of epigenetic control
in bacteria which would be of benefit in a range of areas outside of AMR. In the medium term the
application of the techniques piloted here could be applied to a more inclusive range of important,
clinically relevant Gram negative pathogens such as Pseudomonas, Klebsiella and Acinetobacter.
Overall this project adds knowledge to the pathways involved in AMR, with epigenetic control being of
particular importance due to its potential to produce short term resistance that could lead to stable
resistance mutations.
The outputs of this project will also facilitate funding applications to utilise cutting edge single
molecule real time sequencing and gene expression analysis in order to more fully elucidate the
mechanisms and key pathways involved in AMR.
Link to Faculty Research Themes
Centre for Biomedical Research. Panel A, predominantly A5 (Biological Sciences) but with significant
relevance to A2 (Public Health, Health Services and Primary Care), A3 (Allied Health Professions,
Dentistry, Nursing and Pharmacy)
Outline of project including proposed timescales
The PhD student will work alongside to develop and validate assays for non-E.coli species and take
advantage of the sequencing data to more fully investigate the mechanisms and key pathways
involved in the development of AMR in E. coli using gene expression analysis. Regardless of the
success of the submitted bid, this project remains feasible, either taking advantage of the cutting edge
sequencing data and adaptation to a larger range of bacteria or producing novel tools for the study of
bacterial epigenetics.
References
Escalada, M.G., et al., Journal of Antimicrobial Chemotherapy, 2005. 55(6): p. 879-882.
Braoudaki, M. and A. Hilton, Journal of Clinical Microbiology, 2004. 42(1): p. 73-78.
Braoudaki, M. and A.C. Hilton, FEMS microbiology letters, 2004. 235(2): p. 305-309.
Piddock, L.J., Clinical microbiology reviews, 2006. 19(2): p. 382-402.
Ni, M., et al., PLoS genetics, 2012. 8(12): p. e1003148.
Adam, M., et al., BMC evolutionary biology, 2008. 8(1): p. 52.
Casadesús, J. and J. Torreblanca, Cold Spring Harbor Monograph Archive, 1996. 32: p. 141-153.
Casadesús, J. and D. Low, Microbiology and molecular biology reviews, 2006. 70(3): p. 830-856.
Zautner, A.E. and H. Frickmann, Introduction to Genetics: DNA Methylation, Histone Modification and
Gene Regulation, 2013.
Further information
To apply you must be eligible for NHS Continuing Professional Development (CPD) funding and have
the support of your line manager in writing. General enquiries should be directed by email to the
Faculty Research Director r.hogston@leedsbeckett.ac.uk to discuss the project further please contact
the Director of Studies Donna.Johnson@leedsbeckett.ac.uk
Applications should be made on line here
http://www.leedsbeckett.ac.uk/research/research-degrees/research-studentships-andfees-only-bursaries/