Year 1 mini research projects

Students undertake 2 mini project rotations in different research groups during their first year (one at UoB and one at UoN) and a third ‘informatics’ project.  For the 2018 cohort, a total of 39 mini projects were available for the students to choose from across both institutions. Here are summaries of some of these projects:

Magic balloons - delivering antibiotics directly to infected cells via targeted liposomes

Supervisors:  Alan Huett and Snow Stolnik 

Background and relevance to AMR: Antibiotic resistance is an inevitable consequence of antibiotic use. Whilst the speed of resistance development and its spread can be limited by good practice, the exposure of the patient microbiome to large doses of antibiotics directly selects for resistance throughout all body sites. In addition, the removal of susceptible organisms and resultant disruption of the normal microbiota leaves patients more prone to other infections, particularly in the hospital setting. Finally, some drugs or drug combinations are poorly bioavailable, or toxic to certain tissues (typically the kidneys and cells in the inner ear), and this limits their use.

Rationale for the project: In this project we are developing a new generation of drug delivery methods to reduce all three of these problems. By encapsulating drugs within lipid nanospheres, coated with tissue-specific ligands, we aim to deliver antibiotics directly to desired tissues. This will reduce whole-body exposure to selective drugs, reducing resistance development and limiting collateral damage to the patient microbiome. Similarly, by directed delivery, and avoiding susceptible tissues, we hope to generate high local concentrations of antibiotics, reducing overall dosage and enhancing drug performance.

Why this research is important: This research will enable us to understand how to reformulate new and existing antibiotics, or antibiotic combinations, to yield more potent treatments whilst increasing the effective clinical lifespan of these drugs.

Smart adsorbent materials for mitigating anti-microbial resistance in dairy farm wastewater (SAMs for Farm)

Supervisors: Andrea Laybourn and Rachel Gomes

The University Dairy Farm currently disposes 4-6 tonnes of metal-containing cattle footbath waste (used to protect against lameness caused by bacteria) into slurry wastewater per annum. The waste also contains antibiotic-contaminated milk, urine and faeces. Both metal ions and antibiotics are co-selection drivers for antimicrobial-resistant bacteria. As the slurry tank mixture is eventually spread onto land, the environment becomes contaminated with toxic metals and resistant bacteria.

This project will develop smart sorbent materials to treat cattle waste for the reduction of antimicrobial resistance (AMR) and recovery of metal and antibiotic contaminants. Removal of contaminants from cattle waste will enable safe re-use as a fertiliser for crops.

This exciting multidisciplinary project offers the unique opportunity to prepare novel smart materials for AMR mitigation with real-world impact in the Dairy Farm. The project addresses concerns/challenges in AMR and security and safety of UK and global food industries owing to uptake of metal and antibiotic contaminants by livestock and crops as a result of waste valorisation. The project has significant potential to deliver economic and societal impact in UK and global agriculture. 

Enzyme-responsive Particles for the delivery of Last Resort Antimicrobial Peptides

Supervisors:  Francisco Fernandez-Trillo and Miguel Cámara

Background and relevance to AMR: Antimicrobial resistance is an increasing medical problem, worsened by the lack of new antibiotics reaching the market. This dry antimicrobial pipeline has prompted the resurgence of “old” antibiotics such as polymyxins. Despite their toxicity, polymyxins are now increasingly being prescribed as last-resort antibiotics against multi-resistant strains of gram-negative bacteria. However with the emergence of transmissible colistin resistance,3,4 uncontrolled release of polymyxins should be avoided. Thus, targeted strategies that selectively deliver these antibiotics at the site of infection should be investigated.

Rationale for the project: Activity and toxicity in polymyxins is associated with their polycationic and amphiphilic nature, which facilitates their interaction with the gram-negative cellular envelope, but also with other biological membranes.5-7 To address this toxicity, we have recently reported the preparation of polyion complex (PIC) nanoparticles for the delivery of polymyxin.8 These PIC nanoparticles are formed by the interaction between cationic polymyxin and negatively charged polymers, and this way the toxicity of polymyxin is minimised. In this project, we will develop novel pseudolysin-degradable polymers and particles for the targeted delivery of polymyxin B.

Why this research is important: Identifying new ways of using “old” antibiotics is a much needed approach in the fight against antimicrobial resistance. Moreover, being able to deliver these antibiotics in a targeted way, will minimise the off-target development of resistance.

How do β-lactams kill Mycobacterium tuberculosis?

Supervisors:  Patrick Moynihan and Gurdyal Besra

The UN and WHO have both recognised tuberculosis (TB) as a major driver of poverty with drug-resistant forms of TB causing high mortality rates. Poor treatment options contributed to TB killing approximately 1.8 million people last year. Despite global efforts, this problem is only getting worse. The percentage of TB cases reported to be resistant to rifampicin, a frontline antibiotic, rose from 31% in 2015 to 41% in 2016. This is an antibiotic resistance crisis and new therapeutic options are urgently needed.

One of the most efficient ways to address this crisis is to rehabilitate existing medicines. For years β-lactam antibiotics have not been used in TB treatment due to its endogenous broad-spectrum β-lactamase. Recent studies including a clinical trial, have changed this view. Indeed, when combined with a β-lactamase inhibitor, β-lactam antibiotics perform as well as existing therapeutics providing a safe alternative treatment for this terrible disease. Despite this, we know very little about how these antibiotics kill mycobacteria at the molecular level, or if we are even using the best possible β-lactams for treatment. In general, the β-lactam antibiotics target a large class of proteins collectively called penicillin binding proteins (PBPs) which are typically involved in cell wall biosynthesis. There is no available structural data for the majority of PBPs in M. tuberculosis and the inhibition landscape for this important class of antibiotics is completely unknown. This project will address this gap in knowledge by interrogating the molecular basis of β-lactam inhibition of PBPs in M. tuberculosis using a combination of biochemistry and structural biology. 


Energy variability in bacterial persister cells

Supervisors: Sara Jabbari and Iain Johnston

One approach to tackling antimicrobial resistance is to seek novel treatment types. Alternative therapies to conventional antibiotics may involve inhibiting the virulence and/or resistance systems of bacteria, for example preventing bacteria from binding to host cells (a crucial early step in infection) or controlling regulation of efflux pumps (a key resistance mechanism). The nonlinear reactions involved in host-pathogen-drug interactions render it challenging to predict optimal strategies, and can often result in counter-intuitive outcomes. Computational models, where our biological knowledge is translated into mathematical equations, can be an extremely useful tool to represent these interactions. By integrating experimental data wherever possible, we maximise model reliability. Resulting in silico predictions can then be used to identify and refine experimental programmes. By adopting a cyclical approach, whereby experiments inform models that inform experiments, we can accelerate the development of these novel treatment types.  

'The APH(3′)-IIb aminoglycoside 3’-phosphotransferase gene conferring antibiotic resistance in Pseudomonas aeruginosa: unravelling its true biological function

Supervisors: Stephan Heeb and Steve Atkinson

Background & relevance to AMR: Pseudomonas aeruginosa is naturally resistant to several aminoglycoside antibiotics due to the presence of a long-known aph locus in its chromosome, a single gene encoding aminoglycoside phosphotransferase.  This has always prevented the use of these antibiotics to treat P. aeruginosa infections, but despite this, little has been published on the regulation of aph, on the specific characteristics of the enzyme it encodes, or on the biological function of this gene embedded in what appears to be a metabolic operon.  Unravelling this knowledge is relevant to AMR research as it has the potential to enable the use of a variety of classic aminoglycoside antibiotics that have been long neglected in the treatment of P. aeruginosa infections.

Rationale for the project: Pangenome sequencing has revealed that the aph gene is part of the core genome of P. aeruginosa and that it is always located next to the pha operon involved in hydroxyphenylacetic acid catabolism.  This raises questions about the true biological roles of the aph gene and its association with the hpa operon, which will be addressed by constructing new reporter plasmids and strains to study their biology.

 Why this research is important: AMR has become a top priority of the public health agenda of OECD countries and beyond, with rates already high and projected to grow further.  One way to consider novel antimicrobial strategies is to reconsider long-known but somewhat neglected resistance mechanisms such as the one addressed in this project on the intrinsic resistance of P. aeruginosa against aminoglycosides.

Structural refinement of teixobactin for treating Cutibacterium acnes infection

Supervisors:  Weng Chan and Sarah Kuehne

Cutibacterium acnes (formerly Propionibacterium acnes), an aerotolerant, anaerobic Gram-positive organism, is part of the normal microbiota of the oral cavity, skin, and gastrointestinal and genitourinary tracts.[1] The organism is a skin commensal due to its capacity to colonise the sebaceous glands and hair follicles of the human skin. However, over-colonisation by C. acnes leads to the chronic skin disease, acne vulgaris. Significantly, C. acnes can act as an opportunistic pathogen to cause invasive infections, particularly those associated with medical implants. Until recently, C. acnes has been susceptible to a wide range of antibiotics. However, over the past 2 decades, resistance to metronidazole, macrolides, clindamycin, tetracycline and trimethoprim-sulfamethoxazole has been observed with increasing frequency. Unsurprisingly, macrolide resistance is attributed to their widespread topical and oral use for clinical management of acne vulgaris.

Teixobactin, isolated from Eleftheria terrae, is a peptide antibiotic comprising of a highly constrained 13-membered tetradepsipeptide and a tethered linear heptapeptide.[2] Mechanistically, teixobactin appeared to make strong interactions with the pyrophosphate and adjacent N-acetylmuramic acid components of lipid II. In our recent campaign to identify novel synthetic analogues of teixobactin through the installation of unnatural amino acids, we have discovered a potent analogue, VNTXB-69. When tested against Staphylococcus aureus USA300, the MIC was established to be 4 µg/mL. Significantly, VNTXB 69 is 2-fold more potent against C. acnes ATCC 11828, with MIC = 2 µg/mL.[3]

Thus, this mini-project will entail the chemical synthesis and microbiological evaluation of novel teixobactin analogues as potential antimicrobials for the treatment of C. acnes infections especially those caused by multi-drug resistant C. acnes.

[1] Grice, EA, Kong, HH, Conlan, S, Deming, CB, Davis, J, et al. (2009) Science, 324, 1190.
[2] Ling, LL, Schneider, T, Peoples, AJ, Spoering, AL, Engels, I, et al. (2015) Nature, 517, 455.
[3] Ng, V, Kuehne, SA and Chan, WC (2018) Chem – Eur. J., 24, 9136.

Functional genomics of multi-drug resistant Enterococcus faecium

Supervisors:  Willem van Schaik and Alan McNally

 Enterococcus faecium is a Gram-positive bacterium that colonises the gut of humans and animals. Recently, a specific subpopulation of E. faecium has emerged that has adapted to thrive in the hospital environment, by acquiring genes and mutations that contribute to biofilm formation, tolerance to disinfectants and resistance to antibiotics. Multi-drug resistant E. faecium has recently become a major cause  of hospital-acquired infections. The ability of E. faecium to acquire resistance to vancomycin is of particular concern. Vancomycin resistance is located on mobile genetic elements (plasmids and conjugative transposons) that can easily spread between enterococci and other bacteria.

In this mini-project, we developed a new tool to detect and quantify horizontal gene transfer of vancomycin resistance plasmids and transposons in E. faecium. We have designed a codon-optimised fluorescent reporter gene of which the expression is controlled by a chromosomally encoded repressor. Thus the donor strain will not be fluorescent but upon transfer of the antibiotic resistance plasmid the recipient strain will start to fluoresce (see figure). We can use this tool to study the factors that induce or repress vancomycin resistance gene transfer (e.g. exposure to disinfectants or sub-inhibitory concentrations of antibiotics) among E. faecium strains. In addition, we can study to what extent vancomycin resistance genes can spread to other members of the gut microbiome, by incubating the donor strains in faecal suspensions. Cells that have started to fluoresce can be isolated using a Cell Sorter and characterised by whole-genome sequencing. 

Our studies will lead to important new insights into the factors that influence transfer of vancomycin resistance genes among Enterococcus faecium strains and other members of the gut microbiota and can contribute to the development of strategies to minimise the spread of this important resistance determinant.    

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