Functional antimicrobial resistance during complex interactions of microbial cells with the human host (Complex Diseases: Cells to Systems)

Lead Research Organisation: University of Leicester
Department Name: Genetics


Aims: This project builds on our complimentary expertise on the three main bacterial pathogens involved in antimicrobial drug resistance (AMR) and the infections of otitis media (the most common reason for antibiotic prescription in children), meningitis and sepsis (pathologies with the highest mortality in children). The main aim of the project is to create a strong training program for a PhD student interlinking MRC projects on phase variation in Streptococcus and Neisseria in Leicester to on-going work at MRC Harwell on non-typeable Haemophilus influenzae; an ideal setup to investigate common underlying mechanisms that drive key events in multiple disease processes. The scientific aims would be to target common patterns in the infection models leading to functional antimicrobial resistance, a topic highlighted in the e IMPACT strategy document and also flagged up as a key involvement of the UK government in its effort to slow the growth of AMR (HMGovernment_2014).

Background: AMR is a world-wide health challenge and has been recently identified as one of the four Priority Challenges of the MRC. Across our groups we have generated detailed information on specific events during the pathogenesis of infection such as population bottlenecks, phase variation, biofilm formation and host immune responses. Not only do all of these processes impact the dynamics of infection but also on the development of functional resistance to antimicrobial therapy. AMR is a highly complex phenotype including host components and multiple aspects of microbial life including phase variation (Alamro_2014; Manso_2014; Oldfield_2013), population dynamics of selection (Gerlini_2014) and growth related phenotypes such as biofilm or intracellular growth (Trappetti_2015). All these aspects are largely ignored by normal in vitro testing but are reflected in the treatment failures associated with many bacterial infections. We now have models that give detailed insight into specific steps of the pathogenesis of infection and thus allow testing of specific hypotheses linked to potential treatment failures such as intracellular stages preceding sepsis or biofilm formation. The identification of the underlying mechanisms in the complexity in cause and consequences in infectious disease are predicted to give the project a strong case for producing innovation in treatment strategies.

Hypothesis: The central hypothesis of this proposal is that we will overcome functional AMR associated to treatment failure by targeting precise events in pathogenesis.

Experimental Methods: The student will test the hypothesis using experimental infection models of otitis media at Harwell (Jenkins_2010) and sepsis at Leicester (Gerlini_2014) and a large panel of complementary in vitro studies. Improved treatment strategies with antibiotics, peptides and bacteriophages will be investigated. Biofilms (Trappetti_2015) and intracellular replication (Gerlini_2014) will be the specific aspects addressed to solve functional AMR. The student will use multiple methodologies to complement the experimental infection work including; drug-susceptibility-testing, confocal microscopy and gene expression profiling (Oggioni_2015; Trappetti_2015; Manso_2014). The student will receive training in bioinformatics and programming to analyse high throughput sequencing data. The student will undertake interdisciplinary work as part of our on-going collaboration with the Leicester Mathematics department which aims to develop theoretical models of how the complex host-pathogen interactions may impact AMR (Manso_2014; Palmer_2013). Given the expertise, the details of the experimental plan and the precise nature of events to be tested, we envisage that the project will have a real impact on treatment strategies, potentially saving life and reducing health care costs.
The variety of cutting edge technologies ranging from phenotypes to genomics make this interdisciplinary project on the edge between


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Oldfield NJ (2017) Rise in Group W Meningococcal Carriage in University Students, United Kingdom. in Emerging infectious diseases

Description High Speed super-resolution confocal laser scanning microscope for sub-diffraction analysis at the multi-user Leicester Advanced Imaging Facility
Amount £283,824 (GBP)
Funding ID BB/S019510/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2019 
End 06/2020
Description Linking bacterial sugar metabolism and cell-to-cell signalling
Amount $399,000 (AUD)
Funding ID DP190102980 
Organisation Australian Research Council 
Sector Public
Country Australia
Start 04/2019 
End 03/2022
Description New correlates of protection for an Escherichia coli vaccine
Amount £50,000 (GBP)
Funding ID BVNCP3-05 
Organisation BactiVac Network 
Sector Academic/University
Country United Kingdom
Start 10/2019 
End 03/2020
Title HRA approved Trial: Pollution and Health: The allocation of resources dilemma. Evidence from the University Hospitals of Leicester NHS Trust. 
Description Study Title Pollution and Health: The allocation of resources dilemma. Evidence from the University Hospitals of Leicester NHS Trust. (Acronym PHN) Trial Design Study limited to working with data Planned Sample Size Convenience sample based on the data available from UHL NHS trust Planned Trial Period 1 years 11 months 31 days Primary Objective This project aims to analyse the impact of pollution on the economic costs of public healthcare in Leicester. Secondary Objectives (1) How much of the cost of operating emergency rooms is explained by air pollution? (2) How much of the cost of attending emergency rooms per individual is attributable to air pollution? 
Type Health and Social Care Services
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2019
Development Status Under active development/distribution
Clinical Trial? Yes
UKCRN/ISCTN Identifier REC reference: 19/LO/1465
Impact we are still in the process of data analysis