A Queensland group have developed an efficient method of identifying strains of bacteria, which will help to manage outbreaks of diseases such as meningococcal disease. The Cooperative Research Centre for Diagnostics, based at Queensland University of Technology (QUT) has taken advantage of two new technologies that have emerged in the area of DNA sequencing recently - DNA chip technology and comparative gene sequence databases.
The Queensland team saw an opportunity. "All this comparative sequence data emerging at the same time as the emergence of the DNA chip technology meant that is was a superb opportunity to be able to make use of this explosion of data," said Dr Paul Giffard, a microbiologist and senior research fellow at the CRC for Diagnostics.
When DNA chip technology is combined with the vast amount of comparative gene sequences that are held on databases such as the Multi Locus Sequence Typing, there is a potential for fast, cheap bacteria strain identification.
DNA chips work in a similar way to microarrays. "ItĶs just a way of putting lots and lots of different bits of DNA onto a solid support and then subjecting that to some sort of reaction," explained Dr Giffard. They allow researchers to look at individual bases in a sample.
The group hypothesised that instead of doing sequencing to get a reliable genetic fingerprint, it was possible to 'mine' the data in multi-locus-sequence databases to find single bases or locations within genes - called single nucleotide polymorphisms - that are variable. Those bases or polymorphisms can then be interrogated using emerging DNA chip technology to obtain a genetic fingerprint.
The group focused on the meningococcal bacteria because it is a significant public health problem, and it is already routinely subjected to genetic fingerprinting by different methods by public authorities. It also happened to be the first multi-locus-sequence database put up on the web. There is an enormous amount of interest in tracking this organism.
When there is an outbreak of a disease like meningococcal disease, it is useful to know if people in different locations have been infected by the same strain or by two different strains coincidentally.
Comparative techniques that are currently being used for fingerprinting such as Pulse Field Gel Electrophoresis or Multi Locus Enzyme Electrophoresis have problems with replication between laboratories. The new system is not only fast, but highly replicable. While the team is currently looking at bacteria only, they anticipate extending the research to viruses in the future.