Whole genome sequencing was first used in 2015 after 37 people became infected with a rare form of salmonellosis Salmonella Agona in Western Sydney. It was linked to two sushi shops. Credit:Georgia Willis A growing number of disease control agencies around the world are using whole genome sequencing, which reveals the complete DNA make-up of an organism, to contain and control outbreaks. In Australia, rates of food-borne salmonella poisoning have climbed from 38 per 100,000 people in 2004 to 76 per 100,000 in 2016, with a record-breaking 18,170 cases last year, according to the National Notifiable Diseases Surveillance System. Dr Shadbolt said whole genome sequencing allowed their investigators to see the genetic sequence of a bacteria, for example, in infected patients and match it to bacteria found during an investigation. He said any delay in being able to definitively identify the cause of an outbreak increased the chances of more people becoming ill.

Salmonella was rampant in NSW in 2016. Credit:Rocky Mountain Laboratories,NIAID,NIH "Prior to the adoption of whole genome sequencing, which is the most significant advancement in this field in a generation, we were unable to confirm related cases as quickly as we can now," he said. "Where in the past cases may have appeared random and unrelated we now have the ability to see the genetic sequence of bacteria found in infected patients and match them, allowing us to more quickly connect an outbreak back to its source." Dr Vicky Sheppeard, Director Communicable Diseases at NSW Health. Credit:Edwina Pickles The technology was first used in 2015 after 37 people became infected with a rare form of salmonellosis Salmonella Agona in Western Sydney.

Using traditional methods, the investigators concluded a tuna sushi product at a particular sushi shop was to blame and the shop was ordered to stop selling the product. However, whole genome sequencing of several samples revealed the first cases occurred earlier than thought and the source may have been raw chicken meat, which was supplied to two sushi shops in the one shopping centre. Since then, the tool has been further refined and used in the salmonella outbreak linked to rockmelons and a multi-jurisdictional outbreak of listeriosis last year. NSW Health's communicable diseases director Dr Vicky Sheppeard said the technology was part of a two-year trial, and they would compare the cost and timeliness of new and existing methods. "It did take a little time to ramp up but over the past couple of months the timelines has been getting quite similar to our existing methods and the increased sensitivity has allowed us to find outbreaks that we weren't finding before," she said.

Dr Sheppeard said one of the challenges was the large amounts of data processing and storage required. "Our 2016 annual report is just about to go up and we have seen a downturn in salmonella in NSW, so we are seeing promising early signs the actions that have been implemented are showing results," she said. Minister for Primary Industries Niall Blair said the results so far were "exciting". "The use of this technology essentially means we are now looking at organisms with a microscope now instead of a magnifying glass," he said. "The adoption of this technology will help reduce future outbreaks because we can see more, act faster and control them better."