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Clinical Gastroenterology: Investigation of Fidaxomicin Resistance Mechanisms in Clostridium difficile

PGR-P-393

Key facts

Type of research degree
4 year PhD
Application deadline
Ongoing deadline
Country eligibility
International (outside UK)
Funding
Non-funded
Supervisors
Professor Alex O'Neill and Professor Mark Wilcox
Additional supervisors
Dr Jane Freeman, Dr Ines Moura
Schools
School of Medicine
Research groups/institutes
Leeds Institute of Medical Research at St James's
<h2 class="heading hide-accessible">Summary</h2>

Clostridium difficile is a leading pathogen in healthcare-associated diarrheal infections. C. difficile has a plastic genome with multiple mobile genetic elements and recognized capacity to acquire genes involved in resistance and virulence. Antibiotic treatment is a major risk factor for C. difficile infection (CDI), with resistance to multiple antibiotics becoming frequent in newly emergent strains. CDI antibiotic treatment is currently limited to vancomycin and fidaxomicin, with the later showing high CDI resolution rates and reduced risk of recurrent infection1. Fidaxomicin is the first new antimicrobial agent licensed for use in CDI treatment for 30 years. This antibiotic can persist in the faeces for ~3 weeks following the cessation of dosing, and does not necessarily lead to eradication of C. difficile spores in patients. Furthermore, a recent novel extended dosage of fidaxomicin has been trialled, which involves a 25 day administration period (as opposed to the current standard 10 day regimen). Thus, there is a potential for C. difficile exposure to the antibiotic for ~9 weeks, increasing the risk of resistance emergence. We need to understand why resistance may develop in clinical C. difficile strains and what the potential implications are for clinical treatment of the disease.

<h2 class="heading hide-accessible">Full description</h2>

<p paraeid="{b4e1bbac-b927-40d0-9cf8-ba49febf3fb3}{44}" paraid="355252497">Clinical&nbsp;strains with increased minimum inhibitory concentration&nbsp;(MIC)&nbsp;consistent with&nbsp;in vitro&nbsp;resistance&nbsp;or reduced susceptibility&nbsp;to&nbsp;fidaxomicin&nbsp;are emerging.&nbsp;In a pan-European surveillance&nbsp;study1, we identified&nbsp;one&nbsp;isolate&nbsp;showing and MIC of&nbsp;&gt;4 mg/L&nbsp;to&nbsp;fidaxomicin,&nbsp;with one further isolate&nbsp;showing an&nbsp;MIC of 0.5 mg/L.&nbsp;Laboratory selection assays&nbsp;have implicated the&nbsp;RNA polymerase gene&nbsp;rpoB,&nbsp;and a&nbsp;transcriptional regulator gene&nbsp;marR,&nbsp;in&nbsp;fidaxomicin&nbsp;resistance&nbsp;in vitro2.&nbsp;However, it is unknown whether the same&nbsp;mechanisms&nbsp;occur&nbsp;in vivo, and their clinical implications in the treatment of CDI remain&nbsp;unclear.&nbsp;This project will&nbsp;investigate&nbsp;fidaxomicin&nbsp;resistance in clinical&nbsp;C. difficile&nbsp;isolates,&nbsp;assessing the stability of&nbsp;fidaxomicin&nbsp;resistance&nbsp;using&nbsp;MIC assays,&nbsp;and&nbsp;will use&nbsp;whole-genome sequencing to identify&nbsp;potential&nbsp;gene mutations&nbsp;associated with the high MIC phenotype.&nbsp;The student will&nbsp;also&nbsp;create mutants&nbsp;in&nbsp;fidaxomicin&nbsp;susceptible&nbsp;C. difficile&nbsp;strains&nbsp;for&nbsp;the genes of interest&nbsp;rpoB,&nbsp;marR&nbsp;and others possibly identified by&nbsp;the&nbsp;whole-genome sequencing&nbsp;analysis,&nbsp;and study the resulting phenotype.&nbsp;Mutations in multidrug efflux&nbsp;transporters can&nbsp;confer increased tolerance to macrocyclic antibiotics in other microorganisms. By&nbsp;over-expressing&nbsp;these systems in&nbsp;fidaxomicin&nbsp;susceptible strains,&nbsp;we will be able to infer other mechanisms or stress responses that may occur in&nbsp;C. difficile&nbsp;down the&nbsp;line.&nbsp;The fitness cost of these mutations&nbsp;regarding toxin production, sporulation and competitive growth&nbsp;will&nbsp;also&nbsp;be investigated.&nbsp;&nbsp;</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{43}" paraid="1373313647">In&nbsp;order to understand the clinical implications of&nbsp;fidaxomicin&nbsp;resistance, the student will use a clinically reflective&nbsp;chemostat&nbsp;model of the human colon,&nbsp;developed by the HCAI group3. This model accurately represents the human gut microbiota and has been used in multiple studies&nbsp;resulting&nbsp;in &gt;30 publications,&nbsp;helping&nbsp;define the UK prescribing&nbsp;regulations for CDI.&nbsp;Fidaxomicin&nbsp;resistant&nbsp;C. difficile&nbsp;strains&nbsp;will be inoculated in this model to investigate&nbsp;their&nbsp;potential to cause&nbsp;CDI&nbsp;in presence of&nbsp;drug&nbsp;concentrations&nbsp;equivalent to those found in the human colon.&nbsp;</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{43}" paraid="1373313647">Techniques associated with project</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{43}" paraid="1373313647">Bacterial culture and microbial identification,&nbsp;MIC determination, whole-genome sequencing analysis, genetic modification of class II microorganisms,&nbsp;assembly and&nbsp;use of&nbsp;a&nbsp;chemostat&nbsp;model.&nbsp;</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{43}" paraid="1373313647">References</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{161}" paraid="451320423">1.&nbsp;Freeman J, Vernon J, Pilling S, Clark E,&nbsp;Nicholson S, Morris K,&nbsp;Fabrega&nbsp;AP,&nbsp;Wilcox MH. 2018. Pan-European Longitudinal Surveillance of Antibiotic Resistance among Prevalent&nbsp;Clostridium difficile&nbsp;Ribotypes&nbsp;Study Group. The&nbsp;ClosER&nbsp;study: results from a three-year pan-European longitudinal surveillance of antibiotic resistance among prevalent&nbsp;Clostridium difficile&nbsp;ribotypes, 2011-2014.&nbsp;Clin&nbsp;Microbiol&nbsp;Infect 24:724&ndash;31.&nbsp;&nbsp;</p> <p paraeid="{1d77f8e1-c9f8-4f35-a904-fa2187f08c2b}{209}" paraid="1234391083">2.&nbsp;Leeds JA,&nbsp;Sachdeva&nbsp;M, Mullin S, Barnes SW,&nbsp;Ruzin&nbsp;A. 2013.?In vitro&nbsp;selection, via serial passage, of?Clostridium difficile?mutants with reduced susceptibility to&nbsp;fidaxomicin&nbsp;or vancomycin.?J&nbsp;Antimicrob&nbsp;Chemother?69:41&ndash;44.&nbsp;</p> <p paraeid="{f922a7c7-c502-40a4-96e4-d9a5db6534b0}{2}" paraid="319939329">3.&nbsp;Chilton CH, Crowther GS, Freeman J,&nbsp;Todhunter&nbsp;SL, Nicholson S,&nbsp;Longshaw&nbsp;CM, Wilcox MH. 2014. Successful treatment of simulated&nbsp;Clostridium difficile&nbsp;infection in a human gut model by&nbsp;fidaxomicin&nbsp;first line and after vancomycin or metronidazole failure. J&nbsp;Antimicrob&nbsp;Chemother. 69:451&ndash;62. &nbsp;</p> <p paraeid="{f922a7c7-c502-40a4-96e4-d9a5db6534b0}{2}" paraid="319939329">This project is part of the&nbsp;<a href="https://medicinehealth.leeds.ac.uk/leeds-institute-research-st-james/doc/international-phd-academy-medical-research">International PhD Academy: Medical Research</a></p> <p paraeid="{f922a7c7-c502-40a4-96e4-d9a5db6534b0}{2}" paraid="319939329"><strong>In line with the bespoke nature of our International PhD Academy a modified PhD project can be proposed dependent on students interests and background.</strong></p>

<h2 class="heading">How to apply</h2>

<p>Please note these are not standalone projects and applicants must apply to the PhD academy directly.</p> <p>Applications can be made at any time. To apply for this project applicants should complete an <a href="http://www.leeds.ac.uk/info/130206/applying/91/applying_for_research_degrees">online application form</a> and submit this&nbsp;alongside a full academic CV, degree transcripts (or marks so far if still studying) and degree certificates. Please make it clear in the research information section that you are applying for the International PhD Academy: Medical Research, as well as the title of the project you wish to be considered for.</p> <p>We also require 2 academic references to support your application. Please ask your referees to send these <a href="https://medicinehealth.leeds.ac.uk/downloads/download/130/faculty_graduate_school_-_scholarship_reference_form">references</a> on your behalf, directly to <a href="mailto:fmhpgradmissions@leeds.ac.uk">fmhpgradmissions@leeds.ac.uk</a></p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p>

<h2 class="heading heading--sm">Entry requirements</h2>

A degree in biological sciences, dentistry, medicine, midwifery, nursing, psychology or a good honours degree in a subject relevant to the research topic. A Masters degree in a relevant subject may also be required in some areas of the Faculty. For entry requirements for all other research degrees we offer, please contact us.

<h2 class="heading heading--sm">English language requirements</h2>

Applicants whose first language is not English must provide evidence that their English language is sufficient to meet the specific demands of their study. The Faculty of Medicine and Health minimum requirements in IELTS and TOEFL tests for PhD, MSc, MPhil, MD are: &bull; British Council IELTS - score of 7.0 overall, with no element less than 6.5 &bull; TOEFL iBT - overall score of 100 with the listening and reading element no less than 22, writing element no less than 23 and the speaking element no less than 24.

<h2 class="heading">Contact details</h2>

<p>Informal enquires about regarding the bespoke taught first year of the PhD programme and research projects can be made by contacting LIMRPhD@leeds.ac.uk.</p> <p>Enquiries regarding the application process should be directed to the Faculty of Medicine and Health Graduate School Office e: <a href="mailto:fmhpgradmissions@leeds.ac.uk">fmhpgradmissions@leeds.ac.uk</a>, t: +44 (0)113 343 8221.</p>


<h3 class="heading heading--sm">Linked research areas</h3>