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Clostridium Difficile Genetic Patterns in Europe Point to Possible Infection Sources Beyond Hospital

NEW YORK (GenomeWeb) – New research suggests a proportion of Clostridium difficile cases in Europe involve not only hospital-acquired infections but also infections associated with other sources, such as food.

As part of a multicenter study, investigators from the University of Oxford, the University of Leeds, Astellas Pharma Europe, and elsewhere used a combination of ribotyping, sequencing, phylogenetics, and geographic analyses to retrace the genetic diversity and potential sources of C. difficile isolates involved in infections in European hospitals.

Some of the strains clustered by locale, consistent with spread from one individual to the next, for example in a healthcare setting. But more unexpectedly, the team also saw strains smattered across seemingly unconnected sites. And because at least one of those strains had previously been linked to pig farming, the researchers speculated that some infections may have been transmitted through food sources.

David Eyre, a clinical lecturer at the University of Oxford, was slated to present the work at the European Congress of Clinical Microbiology and Infectious Diseases annual meeting in Vienna this past weekend. The study was funded by Astellas Pharma's Europe, Middle East, and Africa (EMEA) program.

"We don't know much about how C. difficile might be spread in the food chain, but this research suggests it may be very widespread," Eyre said in a statement. "If that turns out to be the case, then we need to focus on some new preventative strategies such as vaccination in humans once this is possible, or we might need to look at our use of animal fertilizers on crops."

"This study doesn't give us any definitive answers," he explained, "but it does suggest other factors [than hospital infections] are at play in the spread of C. difficile and more research is urgently needed to pin them down."

For their analyses, the researchers attempted to culture C. difficile isolates from stool samples collected at 482 hospitals in 20 European countries on two days in 2012 and 2013. They then used a molecular technique called ribotyping to differentiate between C. difficile strains in the cultured isolates.

From there, the team selected representatives from 10 common, toxigenic European ribotypes for whole-genome sequencing with the Illumina HiSeq 2500 platform, using these sequences to track C. difficile diversity and to highlight country-by-country differences in the ribotypes that predominated in the sampled isolates.

With phylogenetic analyses and comparisons of within- and between-country SNP sharing patterns, the researchers uncovered five C. difficile strain types that clustered by location to one extent or another. But other strains were less concentrated, including a form of the microbe linked to pig farming in past studies.

"We know that C. difficile infection can spread within hospitals," Eyre said. "If this was the only route of transmission, we would expect to see each type of the bacteria concentrated within one area. However, because we also saw some types that were spread around several countries, this suggests the bacteria are moving around by other means."

From their C. difficile  data, the investigators also got a glimpse at C. difficile ribotypes that were more often associated with resistance to antimicrobial drugs. Based on the way these strains clustered by country, they proposed ties between healthcare-associated C. difficile isolates and resistant to fluoroquinolone drugs.

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