Genomics tools provide clues to what causes 400 million cases of gastrointestinal disease each year

Jan 4 2005

In a study that could benefit medical and food-safety research, scientists have used comparative genomics tools to find 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.

The study, which appears in the January 2005 issue of PLoS Biology, compares the complete genome sequences of two strains of Campylobacter jejuni – the species most often associated with human illness – and supplements that analysis by contrasting those with the mostly-finished sequences of three other Campylobacters, including one species that may be an emerging pathogen in Africa.

In their analysis, the researchers found a set of genes that may be closely associated with the virulence of some Campylobacter strains as human pathogens. 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.

“Using comparative genomics, we have developed a blueprint for the analysis of this family of bacteria,” says Derrick Fouts, a scientist at The Institute for Genomic Research (TIGR) who is the first author of the PLoS paper. “This study lays the foundation for further research that may help scientists find new ways to detect and control the bacteria.”

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 adds.

TIGR’s genome sequencing and analysis of the Campylobacter bacteria – a project led by TIGR Associate Investigator Karen E. Nelson – was done in collaboration with scientists at the U.S. Department of Agriculture (USDA). The USDA was the overall project’s sponsor.

USDA scientists William Miller, Craig Parker and Robert Mandrell – who investigate ways to improve the molecular detection, differentiation, and measurements of virulence of Campylobacter at the Produce Safety and Microbiology Research Unit (PSMRU) at the USDA-ARS Western Regional Research Center in Albany, CA – provided the four Campylobacter strains to TIGR for sequencing and analysis. The selection was based on interesting features of the strains, such as virulence, resistance to drugs, or an association with a clinical illness.

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 colonizer of chicken digestive tracts.

The PLoS study also compared the two C. jejuni genomes to the not-quite-complete DNA sequences of a multidrug-resistant C. coli strain isolated from a chicken; a C. lari strain (clinical isolate) associated with human illness; and a C. upsaliensis strain isolated from an African child with Guillain-Barré Syndrome. The initial analysis of the comparative sequence data, which will be refined after scientists study how the gene sequences relate to gene function, revealed:

• Insertion elements that are remnants of phage or plasmids and putative lysogenic phage that are similar to Mu phage present in other bacteria;

• Megaplasmids (circular DNA structures outside of the chromosome) that contain novel genes;

• Housekeeping genes that can be used as markers to help identify emerging species;

• Numerous variable polynucleotide repeats in one of the emerging species of Campylobacter; and

• Novel genes encoding or modifying carbohydrate surface structures.

“The comparative genome sequences give scientists some new ideas to better control and detect these organisms,” says TIGR’s Nelson, the study’s senior author. She and Fouts also say the study has helped scientists better understand the evolutionary relationships among Campylobacter species. In addition, the phage and megaplasmids discovered by the genome analysis may yield clues to the intra- and inter-species lateral transfer of DNA among Campylobacter strains.

Campylobacter are the leading cause of bacterial gastrointestinal illness in the United States, where about 15 out of every 100,000 people are diagnosed with campylobacteriosis every year. Many other cases go unreported due to the sporadic nature of the disease. The illness lasts for a week to 10 days, with symptoms that include diarrhea, cramps, abdominal pain and fever. Infrequently, the infection can be more serious or even fatal when victims develop Guillain-Barré syndrome, which involves damage to the nerves that link the spinal cord and brain to the rest of the body.

Campylobacteriosis is usually caused by C. jejuni, a microbe normally found in cattle, swine and birds, where it causes no problems. But the illness can also be caused by C. coli (also found in cattle, swine and birds), C. upsaliensis (found in cats and dogs), and C. lari (present in seabirds in particular). People are often exposed to the disease-causing bacteria when they eat contaminated food – in many cases, undercooked or poorly handled poultry.

While C. jejuni colonizes the gastrointestinal tracts of many animals, it appears to be especially adapted to the enteric tracts of birds, including chickens and turkeys. That is why poultry is considered to be a source of human campylobacteriosis. The disease can also be transmitted via human contact with contaminated water, livestock or household pets.

USDA’s Mandrell says the new Campylobacter sequence data has allowed the PSMRU group in California to develop more comprehensive detection methods, including microarrays, for analyzing 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.

By identifying similar housekeeping genes among the non-jejuni species sequence data, the group has expanded its original fingerprinting method and initiated a study at several ARS locations to characterize differences among C. coli strains isolated from different animal and clinical sources.

The Institute for Genomic Research (TIGR) is a not-for-profit research institute based in Rockville, Maryland. TIGR, which sequenced the first complete genome of a free-living organism in 1995, has been at the forefront of the genomic revolution since the institute was founded in 1992. TIGR conducts research involving the structural, functional, and comparative analysis of genomes and gene products in viruses, bacteria, archaea, and eukaryotes.