First PhD student cohort – 2018-19

The first cohort of PhD students funded by the Medical Research Foundation. Sixteen students undertaking multidisciplinary PhD projects are based in UKRI cross-council funded AMR consortia in 13 universities and institutions across the UK.

Our first cohort are:

Simone Arienti (SHIELD consortium)

Supervised by Professor Sarah Walmsley and Professor Adriano Rossi, University of Edinburgh

Metabolic Plasticity of Inflammatory Neutrophils During Infection
Neutrophils play an important role in antimicrobial responses, yet uncontrolled neutrophilic inflammation is implicated in many disease states including chronic obstructive pulmonary disease (COPD). We are investigating the metabolic plasticity of neutrophils during acute infection and in chronic obstructive pulmonary disease (COPD) where impaired bacterial clearance is seen. This will enable us to better understand the processes regulating effective host pathogen responses and develop strategies for optimising antimicrobial outcomes.

SHIELD consortium

Daniel Buhl (CAMBRIDGE consortium)

Supervised by Professor Mark Holmes, University of Cambridge

Application of novel mass spectrometry methods to enable the rapid identification of bacteria and antimicrobial resistance directly from clinical samples
Using diagnostic microbiology, we are developing a new mass spectrometry technique to identify different species of bacteria and their antibiotic susceptibility directly from clinical samples.

Kevin Chau (REHAB consortium)

Supervised by Dr Daniel Read, UK Centre for Ecology & Hydrology and Prof Derrick Crook & Dr Nicole Stoesser, Nuffield Dept. Medicine, University of Oxford

Wastewater influent and population-level surveillance of antimicrobial resistance in Enterobacteriaceae in Oxfordshire using whole genome sequencing
AMR in species such as Escherichia and Klebsiella spp.  is a major health concern. These bacteria can colonise human, animal and environmental niches and are a major cause of disease. Our research will monitor population dynamics and human AMR gene loads in sewage treatment works’ influent and the impact of wastewater processes on AMR gene dissemination into the environment.

REHAB consortium

Ryan Cook (EVAL FARMS consortium) 

Supervised by Dr Michael Jones, University of Nottingham

Assessment of role and risk of phage in AMR transfer between agricultural and clinical organisms
Bacteriophage are involved in horizontal gene transfer between bacteria and pose a risk of AMR and virulence genes transferring between agricultural and human clinical bacteria. Our research combines metagenomics, phage-isolation and characterisation to understand the risk from phage on the spread of AMR between medically important organisms on dairy farms.

EVAL FARMS consortium

Sarah Dodd (SILENT PHARMACY consortium)

Supervised by Dr Andy Bailey, University of Bristol

Exploring fungal genomes for hidden antibiotics
Genome sequencing has revealed that there are far more gene clusters in a typical fungal genome than has been realised suggesting that there is a plethora of chemical entities yet to be discovered. Given that the metabolic pathways have been maintained in the face of natural selection, it is likely that these pathways will make bioactive molecules, some of which are likely to have antibiotic properties. Our team are looking at metabolic pathways in fungi to screen for antibiotic properties. 

SILENT PHARMACY consortium

Rebecca Hull (SHIELD consortium)

Supervised by Professor Alison Condliffe, University of Sheffield

How do bacteria evolve resistance to cellular immunity?
Our research will determine how conditions at sites of infection encourage bacteria to evolve and evade immune responses, and how such adaptations might be overcome. We are studying Staphylococcus aureus, which causes a range of severe (potentially lethal) infections, and readily develops antimicrobial resistance (Methicillin-Resistant Staphylococcus aureus – MRSA, a ‘superbug’). Bacteria will be grown in a medium that mimics the human lung environment, but results will be applicable to other infection settings. Genetic sequencing of evolved bacteria and interactions with immune cells will identify how resistance is occurring, and how it might be stopped. 

SHIELD consortium

William Hutton (CHICKEN or the EGG consortium) 

Supervised by Dr Adam Roberts, Liverpool School of Tropical Medicine and Dr Andrew Singer, UK Centre for Ecology & Hydrology

Characterising the natural drivers of antimicrobial resistance genes in the environment
Our research explores the natural drivers of resistance, such as geology (e.g. metals) and plants, to offer insight into what are ‘normal’ levels of AMR, and how these levels vary over space and time. This evidence base will be needed to rationalise environmental targets for AMR and any future regulatory measures on emissions, e.g. wastewater effluent and landspreading. Our work will feed into a national risk assessment model for environmental AMR. 

Nidhee Jadeja (ASPIRES consortium) 

Supervised by Professor Alison Holmes, Imperial College London

Systems Thinking Based Evaluation of Patients and Doctors Behavioural Drivers of Antimicrobial Resistance
We know that individual and organisational behaviours impact on AMR. When introducing new policy interventions to limit AMR we need to be able to capture positive and unintended impacts on patient health, healthcare professional behaviours and economic outcomes. By using System Dynamics to evaluate policies, we hope to model behaviours and provide policy makers and managers with the ability to predict future outcomes.

ASPIRES consortium

Declan Kohl (RID AMR@LEEDS consortium)

Supervised by Professor Lars Jeuken, University of Leeds                     

Active Biosensor Modules for Infection Diagnostics
The lack of instant and accurate tools to diagnose infection leads to inappropriate or unnecessary antibiotic prescribing and contributes directly and significantly to AMR in primary and secondary care settings. We hope to address this challenge by developing innovative approaches for next generation biosensors, with improvedaccuracy and sensitivity. Successful devices will enable rapid diagnosis of infectious diseases, informing treatment and reducing the spread of AMR.

Pauline Lang (SWON ALLIANCE consortium)

Supervised by Professor Christopher Schofield, University of Oxford

Biophysical studies on Class D β-lactamases
The Class D beta-lactamases currently represent the greatest threat to beta-lactam antibiotics worldwide. Our research aims to enable the design and synthesis of new types of beta-lactamase inhibitor based on mechanistic studies, including involving time resolved crystallography, employing use of both conventional and X-ray laser synchrotron X-ray sources.

SWON ALLIANCE consortium

Becky McCall (PASS consortium)

Supervised by Dr Laura Shallcross and Professor Andrew Hayward, University College London and Professor Michael Wilson, University of Loughborough

Storytelling to communicate the concept of AMR to the public
As the nature of communication and public debate changes, we need new tools to help the public engage with important but inaccessible issues such as AMR. Storytelling is a fundamental and universal form of expression that allows people to process information and give meaning and value to their experiences. Stories offer insight into how individuals and groups of people understand themselves, others, and the world around them. In this project we will work with patients and their families to understand people’s experiences of infection and antibiotic use and explore the use of storytelling to communicate an understanding of AMR to the public.

Chloe Morrison (UMOYA OMUHLE consortium) 

Supervised by Dr John Manton, London School of Hygiene and Tropical Medicine

Historical and bioethical dimensions of infection prevention & control for drug-resistant TB in contemporary South Africa
We are investigating the historical and bioethical dimensions of dynamic interactions shaping infection prevention and control for drug resistant tuberculosis (TB) in South Africa. By looking at questions relating to racially politicised social and economic inequalities that permeate clinic organisation and working cultures, our research complements and informs on-going work to develop ‘whole systems’ interventions to strengthen measures to reduce nosocomial transmission of drug-resistant TB.

UMOYA OMUHLE consortium

Ahmed Raza (ARCH consortium)

Supervised by Dr Charis Marwick, University of Dundee

Characterising Antimicrobial Resistance in Care Homes using Whole Genome Sequencing
Older people living in care homes are at higher than average risk of contracting drug resistant infections. To identify potential transmissions of, and quantify specific resident risk factors for, AMR infections, we will analyse the DNA of bacteria from samples (e.g. urine and sputum) from care home residents and link this bacterial genomic data to anonymised information about the individual resident and the care home they live in.
ARCH consortium

Esther Rottenburg (AMIS consortium) 

Supervised by Dr John Manton, London School of Hygiene and Tropical Medicine

Whose rationality is it?  Following Antibiotic and AMR Facts in Uganda
Our research takes an interdisciplinary approach, combining history and anthropology, to document various knowledge practices relevant to antibiotics and AMR in Uganda and explore the contexts of ‘rational’ antibiotic use. We will investigate how different ‘facts’, scientific or popular, come to be produced and travel across disciplines, spaces and groups, as well as exploring various relevant processes and reactions.

AMIS consortium

Jordan Sealey (OH-STAR consortium)

Supervised by Professor Matthew Avison, University of Bristol

Chasing the transmission of AMR plasmids between farms and local communities
Transmission of resistant bacteria from animals to humans has a potentially important impact on human health, and is one of the main reasons why farmers and veterinary surgeons are urged to reduce antibiotic use. AMR can be spread by the mobilisation of resistance genes on plasmids from one bacterium to another.  We are using a variety of disciplines to identify interventions to reduce antibiotic resistance on UK farms and its impact on the surrounding environment and population.

OH STAR consortium

Daniela Sordillo (SWON ALLIANCE consortium)

Supervised by Professor Chris Dowson, University of Warwick

Cell Wall Biosynthesis in ESKAPE Pathogens – a mechanistic characterization of Class B penicillin-binding-protein activity and its Inhibitors
Bacterial cell survival is dependent on an intact cell wall made from peptidoglycan, which is produced by enzymes called penicillin-binding proteins. As their name suggests, penicillin-binding proteins (PBP) are the target of penicillin and related antibiotics. Bacteria have become resistant to these antibiotics by developing ways of eliminating the antibiotic from the cell (not by changes to the PBPs themselves). By gaining insight into the structural and biochemical substrate specificity of PBPs we aim to aid the development of new antibiotics.

SWON ALLIANCE consortium