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Genome tools help explain food pathogen

05-Jan-2005

Genomic tools help scientists gain an insight into the roots of foodborne disease and to identify clues about why some strains of the bacterium campylobacter - which each year cause more than 400 million cases of gastrointestinal disease - are more virulent than others.

A constant threat to the food chain, in the US alone foodborne illness annually costs the country $7.69 billion. And as global food production, processing and distribution rises, so grows in parallel demand for food safety research to ensure the food supply remains secure.

Campylobacters are prevalent in food animals such as poultry, cattle, pigs, sheep, ostriches and shellfish. The main route of transmission is generally believed to be foodborne, via undercooked meats and meat products, as well as raw or contaminated milk. The ingestion of contaminated water or ice is also a recognised source of infection.

But one of the major gaps in scientific knowledge at present is the contribution of the sources to the overall burden of disease.

Since common-source outbreaks account for a rather small proportion of cases, the vast majority of reports are made sporadically, with no easily discernible pattern.

This latest US study may help to close the gap, with researchers identifying a set of genes that could be closely associated with the virulence of some campylobacter strains as human pathogens.

"This study lays the foundation for further research that may help scientists find new ways to detect and control the bacteria," said Derrick Fouts, a scientist at The Institute for Genomic Research (TIGR) and lead author of the study.

They also found sequence variations among the four campylobacter isolates, including major structural differences related to the insertion of new stretches of DNA in the genome sequences. Those "insertions" and other gene variations may help scientists understand why there are major differences in the biology of various campylobacter strains.

For the research, scientists compared the complete genome sequences of two strains of Campylobacter jejuni - the species most often associated with human illness.

They supplemented the analysis by contrasting those with the mostly-finished sequences of three other campylobacters, including one species that may be an emerging pathogen in Africa.

"Using comparative genomics, we have developed a blueprint for the analysis of this family of bacteria," added Fouts.

Fouts, who studies bacteriophages (viruses that infect bacteria), says the genome comparison identified novel phages in the campylobacters. One of those phages has the potential to be developed as a tool for genetic manipulation of the microbe in ways that would benefit food safety or health, he commented.

Scientists at the US departement of agriculture, William Miller, Craig Parker and Robert Mandrell, provided the four campylobacter strains to TIGR for sequencing and analysis. The selection was based on features of the strains, such as virulence, resistance to drugs, or an association with a clinical illness.

USDA's Mandrell says the new Campylobacter sequence data will allow scientists to develop more comprehensive detection methods, including microarrays, for analysing human and environmental isolates of the bacteria. The goal is to be able to 'fingerprint' strains, an important aspect of determining their source, fitness and epidemiology.

In 2000, scientists had published the first genome of a campylobacter species - C. jejuni - which is used as a model to study pathogenic forms of the bacteria, but which may have lost some of its virulence genes during years of propagation in laboratories.

In the new study, TIGR and collaborators compared that lab strain to the sequence of the C. jejuni RM1221 strain, which was isolated from chicken skin and was found by the USDA-ARS lab to be an efficient coloniser of chicken digestive tracts.

Full findings of the study appear in the January 2005 issue of PLoS Biology.

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