Molecular basis of foodborne disease risk of variants of Salmonella Typhimurium DT193 and U288

The bacterium Salmonella accounts for about 125 million incidents of disease worldwide each year, and nearly a million deaths. The morbidity and mortality caused by this pathogen has a significant impact on the economies of both resource rich and resource poor countries. Most cases of non-typhoidal Salmonella are thought to result from fecal contamination of food and food products, either directly in the food chain or by cross contamination in the home or restaurants. A common and therefore critical step for this is the entry of the bacterium into the food chain from livestock and poultry in which this pathogen is commonly found. However, even though virtually all types of Salmonella have the potential to cause disease in man, not all are commonly associated with disease in man. Understanding how these processes work is critical to the detection of high risk types of Salmonella in livestock and the food chain, and efforts to decrease the likelihood of Salmonella entering these environments. We propose to study two common types of Salmonella that are both present in pig herds butter present distinct risk to food safety. We will study these bacteria at a genetic and behavioural level to understand how the different types circulate in pig populations in the UK and how they enter and survive in our food. First a collection of pig and food chain isolates of Salmonella Typhimurium will be whole genome sequenced and the variation in their genome used to define the how they spread into the food chain and into the human population. Then we will study important behavioural variations that may impact the threat posed by the variants in food. As the types of Salmonella to be studied are genetically closely related, the number of genetic differences are small, which makes it possible to identify candidate differences associated with altered behaviours of the variants. Genetic differences in types of Salmonella are potential candidates targets for surveillance to identify types more likely to represent a risk to food safety or for other intervention strategies aimed at decreasing the likelihood that they will enter the food chain.

The considerable economic and health impact of pathogens of the genus Salmonella is the result of their presence in livestock and poultry, entry into and survival within the food chain, and their ability to cause intestinal or systemic disease. However, not all variants of Salmonella are equally likely to cause disease in man and an understanding of the molecular basis of the likelihood that a particular variant will enter the food chain and cause disease in man is critical to food safety. Some variants of Salmonella are prevalent in food animals yet are not a predominant cause of human clinical infections. This research proposal seeks to address these questions using a molecular epidemiology and comparative whole genome sequence approach combined with classical molecular biology and infection models to compare two highly related variants of S. Typhimurium (DT193 and U288) that exhibit distinct risk profiles for foodborne disease in man, despite similar epidemiology in livestock. Little is known about the variation in genotype and phenotype of closely related variants of bacterial pathogens circulating in zoonotic reservoirs and the environment. Crucially, genotypic polymorphisms are not only potential candidate targets for intervention strategies aimed at decreasing the likelihood that these pathogens enter the food chain but also targets for distinguishing variants of pathogens that differ in their risk to food safety, useful for surveillance. This study will define the molecular epidemiology of common variants of Salmonella Typhimurium in the UK pig herds and those entering the food chain via abattoirs by analysis of whole genome sequence variation. Genotypic, transcriptomic and phenotypic variation will be determined and important genotypic differences understood in the context of their associated phenotype by whole genome recombination and mutagenesis approaches.

The beneficiaries of this research include research scientists, government agencies involved in surveillance activities, the food industry and the general public.
1. Research scientists will benefit from a greater understanding of the diversity of genotype and phenotype of the Salmonella pathogen. Salmonella is used as a model pathogen organism in thousands of research labs around the world. These labs tend to use a single or a limited number of strains in their studies. However, it is not known how generally applicable the conclusions are from experiments from a single strain. Our study will provide a baseline data for the diversity of genotype and phenotypes of closely related isolates of S. Typhimurium. These data may also provide insight for other bacterial pathogens in addition to Salmonella. Our work will also generate sequence data, phylogenetic information and genetically modified microorganisms that will be made freely available to the research community. As part of this project we will develop methodologies to construct chimeric strains of S. Typhimurium using high frequency recombination. The strains used for this methodology will be broadly applicable for many molecular genetic studies using S. Typhimurium and these will also be made freely available.
2. Government agencies (eg AHVLA and PHE) involved in surveillance of bacterial pathogens will benefit from the data and data analysis generated in this project. The Salmonella strains to be analysed are part of an on-going epidemic in the UK and new diagnostic methods to detect and differentiate these isolates are needed. The Dr Liljana Petrovska (AHVLA) and Dr Elizabeth de Pinna (PHE) are collaborators on this application and projects run internally within these organisations will benefit directly from the output of this project. The Principal Investigator is also an active member of the Global Microbial Identifier task force that is actively engaged in using the type of data generated in this project to identify pathogens and genes of interest in these pathogens for diagnostics and surveillance. The project will therefore have a potential global impact.
3. The food industry and in particular the pig rearing industry is interested in decreasing the incidence of Salmonella in the food chain. This is in part from the EC. The output from this project will provide the knowledge required to discriminate between pathogens of high and low risk to human disease.
4. In the longer term the general public will benefit from potential advances in diagnostic and surveillance methodologies that will become available with the knowledge generated from the proposed work. The network of scientists involved as collaborators on the research project have the expertise to deliver these improvements in parallel and as a direct result of the proposed work.
STRATEGIC RELEVANCE: The proposal addresses gaps in the fundamental knowledge impacting the ability of the UK food industry to deliver safe food with a reduced risk of contamination with food borne pathogens and in particular Salmonella. It is therefore directly relevant to the BBSRC strategic priorities 'Food, nutrition and Health'. The generation of a large amount of whole genome sequence data of Salmonella from food sources and the food chain is the starting point of this project. Integration of these data with existing whole genome sequence data to study the phylogenetics and molecular epidemiology of Salmonella in livestock and the food chain is an example of 'Exploiting New Ways of Working'. In addition the project benefits from working from this point back to mechanisms and classical molecular biology approaches. This work therefore in part fulfils the major responsive mode priorities 'Data driven biology'.