(Meta)genomics of bacteria and antimicrobial resistance from different food production systems


During the COVID-19 pandemic, sales of organic foods had the biggest year-on-year increase in 15 years. Claims that organic or free-range food is better and healthier for people and the planet may have helped drive this trend, despite sometimes contradictory evidence. Many food production systems, such as organic and free-range, variously include practices to improve animal welfare and reduce or avoid the use of artificial fertilisers, pesticides and antibiotics but what is the underlying evidence? This studentship will further understanding of the microbial pathogens and antimicrobial resistance (AMR) burden in both conventional and non-conventional food production systems.

This multidisciplinary project will utilise comprehensive microbiological and (meta)genomic approaches to understand the microbial pathogens and antimicrobial resistance (AMR) burden, and thus the food safety, of foods produced through organic, free-range and conventional systems. This project will include both wet lab and dry lab components, including study design, culture-based microbiology and both short-read and long-read genome and metagenome sequencing. You will benefit from existing links with policymakers, including the Food Standards Agency, who will have an interest in the results of this work, and from the experience of generating and communicating data for public health action. You will develop skills in state-of-the-art bioinformatics, microbiology, molecular biology and genomic epidemiology.

You will join an interdisciplinary team that will support your training and development. Quadram Institute Bioscience provides a stimulating and supportive environment for research on bacterial genomics, microbiology, and the microbiome, and you will also work with collaborators at the Royal Veterinary College and the Wellcome Sanger Institute. You will have intellectual input into shaping the project and there will be opportunities to collaborate with partners both within and outside the institute to develop further skills and impact of the project.

This project is a Joint-Studentship with the Food Standards Agency.


Janecko, N.†, Bloomfield, S.J.†, Palau, R. and Mather, A.E. (2021) Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail. Microb. Genom. doi: 10.1099/mgen.0.000647.

†authors contributed equally

de Oliveira Martins, L., Bloomfield, S.J., Stoakes, E., Grant, A.J., Page, A.J. and Mather, A.E. (2021) Tatajuba – exploring the distribution of homopolymer tracts (preprint). https://biorxiv.org/cgi/content/short/2021.06.02.446710v1.

Mellor, K.C., Petrovska, L., Thomson, N.R., Harris, K., Reid, S.W.J. and Mather, A.E. (2019) Antimicrobial resistance diversity suggestive of distinct Salmonella Typhimurium sources or selective pressures in food-production animals. Front Microbiol. doi: 10.3389/fmicb.2019.00708.