Whole-genome sequencing of 2011 E. coli outbreaks in Europe provides new insight

Study revealed small differences among the 
E. coli O104:H4 strains.
 

The outbreak in Germany, which was caused by the strain E. coli O104:H4, led to around 4,000 cases of bloody diarrhea, 850 cases of hemolytic uremic syndrome (HUS), which can lead to kidney failure, and over 50 deaths. The source of the outbreak was traced to sprouts from an organic farm in Germany. In France, where 15 people were sickened with bloody diarrhea that progressed to HUS in nine people, the source of the outbreak was sprouts, germinated from seeds purchased at a garden retailer, that were served at a children's community center buffet. European investigators, using traditional epidemiological methods, traced the outbreaks to a shipment of seeds from Egypt that arrived in Germany in December 2009.

The researchers analyzed isolates of E. coli from both the German and French outbreaks. Based on conventional molecular epidemiological analysis, the E. coli strains from the outbreaks in Germany and France appear identical. However, by the whole-genome sequencing and analysis allow to determine that there were small, but measurable, differences among the isolates. They found two surprising findings: All the strains connected to the larger German outbreak were found to be nearly identical, while the strains in France showed greater diversity; and the German isolates appeared to be a subset of the diversity seen in the French isolates.
 

If genomes have fewer differences than we expect, like the German outbreak, it suggests that the outbreak might have passed through a single bottleneck. A bottleneck might be something like disinfection procedures that killed most but not all of the bugs, or maybe passage through a single infected individual.

Another hypothesis offered by the researchers is that there was uneven distribution of diversity in the original shipment of contaminated seeds.

As costs for genomic sequencing decline, these tools, combined with traditional epidemiological techniques, can provide greater insight into the emergence and spread of infectious diseases and will help guide preventive public health measures in the future.
 

Source: http://www.eurekalert.org/pub_releases/2012-02/hsop-wso020612.php