Thanks to traditional DNA sequencing technologies, researchers have succeeded in sequencing the genomes of over 450 species of bacteria, including representative strains of all major human pathogens. However, this process is extremely slow, and in the case of an outbreak or terrorist attack, scientists need to determine the pathogen's genome as soon as possible so that they can determine which virulence genes or drug resistance genes the bacteria has.
Recently, techniques have been developed which enable scientists to sequence an entire bacterial genome in a matter of hours. However, the finishing steps required to obtain the complete sequence are still very time consuming. In this latest study, scientists in France and Sweden investigated whether enough information to mount a response to an outbreak could be obtained by using a rapidly sequenced, incomplete genome and comparing it to existing genomes for the same species. Their results are published online by the journal Genome Research.
They tested their theory on a strain of Francisella tularensis, a highly infectious bacterium that causes a disease called tularaemia. People catch the disease from the bite of an infected tick, while handling infected animal carcasses or by eating or drinking contaminated food or water. Symptoms include fever, chills, headaches, diarrhoea, muscle and joint pain and progressive weakness. If left untreated, it can be fatal. The scientists chose it for their study because there are strong concerns that it could be genetically manipulated for use as a biological weapon.
"In the context of an outbreak, a quick approach may help to identify immediately the genetic determinants responsible for modified virulence or transmission," explained Dr Bernard La Scola of the University of the Mediterranean in France.
Dr La Scola and his colleagues used rapid sequencing technology to obtain the genome of a strain of F. tularensis taken from a patient suffering from tularaemia. They were able to identify a number of genes linked to virulence as well as a mutation associated with quinolone resistance. The researchers were also able to distinguish their strain from 80 other strains of F. tularensis.
"We demonstrated that this strategy was efficient to detect gene polymorphisms such as a gene modification responsible for antibiotic resistance, and loss of genetic material," commented Dr La Scola.
According to the team, with enough researchers working on the project, the time from DNA extraction to complete genome analysis can be cut to just six weeks. Dr Scola believes that future advances in the software used to analyse and compare genome sequences could cut this time still further.
EU support for the research came from the EU-funded EuroPathoGenomics Network of Excellence, which is funded under the 'Life sciences, genomics and biotechnology for health' thematic area of the Sixth Framework Programme (FP6).
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