Determination of the dynamics of antimicrobial resistance genes in the human and animal gut microbiome.

This research aims to develop a much deeper understanding of how antimicrobial resistance (AMR) resistance genes survive and spread within people and animals and to develop an understanding of how we might change the way we use antibiotics to reduce the amount and spread of AMR. AMR does not operate in an ecological vacuum and to understand the process properly, we need to obtain a much clearer appreciation of the underlying bacterial population and community dynamics of bacteria possessing AMR genes. The aims of this research are to measure the numbers and AMR genes in bacteria found in patients, farm animals and the environment and the way they change over time (the dynamic changes), and in response to the use of antibiotics with a particular emphasis on the clinical outcomes in cases of human and animal disease. The research will use state-of-the-art DNA sequencing technology and analytical techniques to look at mixed populations of bacteria on samples of bacteria obtained from experiments performed in the laboratory and samples taken from hospitals and farms. Many of the bacteria in the gut are impossible or very difficult to grow in the laboratory and are considered to be 'unculturable'. Previous research has ignored these. The overarching hypothesis to be tested is that the unculturable microbiome provides a reservoir of AMR genes that may both receive and donate AMR genes, in particular when the microbiome is under antimicrobial selective pressure. The specific objectives are: 1. To establish the accuracy and reproducibility of two novel DNA sequencing methods that enable the DNA from individual bacterial species containing AMR genes to be identified from within faecal microbiome samples. 2. To use these novel genomic techniques in experimental conditions (in mice and pigs) to investigate AMR gene transfer from E. coli expressing Extended Spectrum Beta-Lactamase (ESBL) and Salmonella enterica serovar Typhimurium with fluoroquinolone resistance within the gut microbiome both following the treatment with antibiotics that are effective and when an antibiotic is used to which the bacteria are resistant. 3. To perform studies of the gut bacteria over time in farmed pigs and humans receiving antibiotics for treatment of clinical disease. 4. To develop mathematical models that capture the flux of AMR genes in bacterial populations to identify factors that lead to the build-up or transmission of resistance.