Outbreak Detection and Response

Program Summary

Public health surveillance is a critically important activity that enables accurate outbreak detection and effective epidemic control. Surveillance depends on rapid and accurate identification and characterisation of pathogens and typically involves the use of numerous culture based and molecular techniques such as serotyping and pulse field gel electrophoresis (PFGE). Many of these techniques offer poor resolution, meaning that it is often necessary to perform multiple different tests in order to obtain sufficient accuracy to determine epidemiologically relevant links. As such, it is often labour intensive, time-consuming, and expensive to perform typing that is adequate for surveillance and outbreak detection, particularly during larger outbreaks.

The dramatic reduction in the cost of next generation sequencing and the advent of benchtop sequencers that facilitate rapid and high throughput analysis means that it is now cost effective to use genomic techniques to enhance current surveillance and outbreak detection protocols. The exquisite resolution afforded by this technology also means that epidemiological linkage of isolates can be perfomed with a much higher degree of accuracy than is possible when using current techniques.

The objectives of this research priority are therefore to demonstrate the utility of using next generation sequencing technology to enhance current surveillance practices In Australia.  This technology has the potential to allow more rapid identification of disease outbreaks, which should result in a more rapid response and more timely implementation of infection control measures leading to a reduction in the burden of outbreak-associated disease.