BioWorld International Correspondent

LONDON - The bacterium Clostridium difficile has a "pick and mix" approach to its genes, analysis of its genome sequence has shown.

A multitude of genes that help the bacterium cause disease and resist treatment with many antibiotics have hitched a ride on its genome, some of them arriving only recently in its evolution.

Details of the sequence could boost research efforts aimed at developing new antibiotics and studies that try to determine how the bacterium interacts with its host and how it causes its unpleasant symptoms.

Julian Parkhill, head of the pathogen sequencing unit at the Wellcome Trust Sanger Institute at Hinxton, UK, told BioWorld International, "The genome sequence does not give you the answers straight away, but clearly there are going to be new drug targets in there. What the sequence does is give researchers the opportunity to look at all the possible targets of the organism in a holistic way. It also will accelerate and enhance existing work aimed at understanding the pathogenicity of this bacterium."

Clostridium difficile is a cause of infectious diarrhea, commonly acquired in hospitals. It can thrive when patients are given broad-spectrum antibiotics, which kill protective gut bacteria and allow C. difficile to multiply. It also can cause a life-threatening disease of the colon, called pseudomembranous colitis.

C. difficile is more prevalent and causes more deaths in the UK than multidrug resistant Staphylococcus aureus (MRSA). It caused more than 44,000 cases of disease in the UK in 2004, mostly in people older than 65, and is the leading cause of hospital-acquired infections in the developed world.

C. difficile already is resistant to many antibiotics and is treatable only with metronidazole and vancomycin. Researchers fear it is only a matter of time before those drugs, too, fail to work on C. difficile infections.

The team from the Wellcome Trust Sanger Institute published their findings on the C. difficile sequence in the June 25, 2006, online publication of Nature Genetics in a paper titled "The multi-drug resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome." The first author is Mohammed Sebaihia.

The strain chosen for the sequencing project was a virulent and multidrug resistant strain of the bacterium isolated from a hospital patient in Zurich, Switzerland, with severe pseudomembranous colitis, which had spread to several other patients on the same ward.

Analysis of the genome sequence showed it contained many mobile "islands" of DNA, many of them carrying genes involved in drug resistance or pathogenicity. Sebaihia, who led the analysis at the institute, said, "The genome of C. difficile is in a state of flux. More than 10 percent of its genome consists of mobile elements - sequences that can move from one organism to another - and this is how it has acquired genes that make it such an effective pathogen."

Parkhill said, "In the gut, where this bacterium lives, there are huge numbers of different organisms, all exchanging DNA, and C. difficile seems to be very adept at acquiring DNA and exchanging DNA."

Often, genes for drug resistance in bacteria are found on plasmids, but in this case, Parkhill explained, the mobile DNA is integrated into the chromosomes. "These elements have the ability to excise themselves from the chromosome and to move from cell to cell," he added.

The researchers found that half of the genes found in C. difficile are absent from four of its closest relatives - including the bacteria that cause botulism, gas gangrene and tetanus.

Brendan Wren, professor of microbial pathogenesis at the London School of Hygiene and Tropic Medicine, said, "When we compared eight different strains of C. difficile, we were surprised to find that they shared only 40 percent of the genes between them. More than 10 percent of the C. difficile genome is derived from self-mobile DNA elements, and its overall variation is remarkable. The genetic comparison of those strains will help us understand how C. difficile ticks and help to explain how the hypervirulent strains emerged and spread so rapidly."

Other findings from the sequence analysis included the discovery that C. difficile can produce a chemical called paracresol, allowing it to kill its competitors, and that it can pump out bile acids, which normally kill many bacteria.

Writing in Nature Genetics, the authors concluded, "The apparent ease with which C. difficile can acquire antibiotic resistance determinants serves as a timely reminder on restricting the use of antibiotics given orally."

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