Optimisation of Salmonella genotyping and epidemiological data analysis for detection and investigation of outbreaks

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Bacteria known as salmonella are the most important causes of food-borne diarrhoeal disease. They occasionally cause potentially fatal septicaemia, especially in young children and people with underlying disease. We estimate that more than 80,000 cases of salmonella infection occur in Australia, each year, at a cost to the community of $37 million. Salmonella are divided into more than 2000 different types, but one - called Typhimurium - causes about 40% of infections and a few others cause most of the rest. This means that is difficult to distinguish cases of salmonella infection that have originated from one source (an outbreak) from cases that have originated from another. Without this information, is it hard to track the source, which is usually inadequately cooked meat or chicken another food that has been contaminated with salmonella after preparation. There are several existing methods for fingerprinting salmonella, but they are quite slow or do not distinguish different strains well enough to identify outbreaks quickly. This means that sources of contaminated food are often not identified in time to prevent more cases occurring. We aim to develop a faster and more discriminatory system for fingerprinting salmonella, based on novel technology that can identify many small genetic sequences that occur in different combinations in different strains. As well, we will develop electronic scanning tools that will link the fingerprints of the salmonella strains with information about the people infected with them, such as the types of food and places where they have eaten, to identify patterns or clusters that indicate a common source. The more rapidly this can be done the sooner the source of contaminated food can be found and eliminated and additional cases can be prevented. This has important implications for public health - it will increase food safety and reduce illness and economic loss.