Monday, June 17, 2013

Diarrhea, international politics and genome sequencing

At this time two years ago, European countries were in the grip of a severe outbreak of foodborne illness. From May to July 2011, over 4,000 people were sickened, and at least 50 people died. The culprit was a bacterium called Escherichia coli. You might find this name familiar. We have E. coli living inside us as part of our gut microbial community. These E. coli quietly exist in symbiosis with us, processing some of the food we eat and possibly protecting us from pathogens. However, some strains of E. coli are not so mild-mannered. 

The strain of E. coli responsible for the 2011 European outbreak was equipped with the genetic weaponry to cause not only gastrointestinal illness, which includes bloody diarrhea, but also a potentially fatal condition called hemolytic-uremic syndrome, which can lead to kidney failure. Investigations of this outbreak impacted international politics and deployed cutting-edge technologies, ultimately demonstrating just how much these little microbes can disrupt our carefully constructed human lives.

Electron micrograph of E. coli bacteria, magnified 10,000X.

German health officials first observed an increase in cases of E. coli infection in early May 2011. Although the outbreak centered in Germany, cases were reported across Europe and as far away as the United States, mostly due to people who travelled to Germany, ate contaminated food and then returned home. The graphic below shows the distribution of cases across Europe at the mid-point of the outbreak.

It's not that unusual for health agencies to deal with outbreaks of foodborne illness. For example, E. coli infections in the United States account for about 265,000 illnesses and 100 deaths each year. But from the beginning, there was clearly something unusual about this outbreak. For starters, most E. coli infections affect children, elderly people and others whose immune systems aren't as strong as healthy, middle-aged adults. With this outbreak, investigators noticed that more adults were affected than usual. Also, the percentage of patients developing the dangerous hemolytic-uremic syndrome was higher with this outbreak. Obviously, this was not a run-of-the-mill E. coli outbreak.

Investigating a disease outbreak involves identifying the culprit, determining how that culprit is spreading through communities and tracking it back to its original source. This field of science is called infectious disease epidemiology. Once the E. coli outbreak was detected, epidemiologists and other scientists got to work collecting data from patients and testing possible sources of the bacterium, which is typically contaminated food. This is where microbiology gets political.

German health officials initially implicated cucumbers from a handful of Spanish farms as the source of the pathogenic E. coli. In response, the European Commission issued a warning to consumers to avoid Spanish vegetables. Russia went so far as to completely ban all produce imports from Spain and Germany. As it turned out, Spanish cucumbers were unjustly accused. After further testing, German officials determined that Spanish farms were not the source of the outbreak. Instead, a shipment of fenugreek seeds from Egypt, which were then used by farms in Germany to produce sprouts, was identified as the source. 

This was small consolation to Spanish agriculture, which projected losses of $290 million a week as a result of the warnings and bans. Spain furiously accused Germany of incompetence at best and irreparable damage to a rival agricultural industry at worst. All this over a microbe! But the health and economic impacts of microbes are serious business, as this outbreak showed.

On the positive side of things, the 2011 European E. coli outbreak marked a leap forward in how new sequencing technologies can enhance investigations of disease outbreaks. Over the past few years, tremendous advances have been made in DNA sequencing. Sequencing an organism's genome essentially gives you the ultimate information manual for that organism. In 1997, researchers released the very first DNA sequence for a strain of E. coli. It took these scientists 15 years to produce that information manual. During the 2011 outbreak, researchers completed a draft of the DNA sequence for the strain of E. coli involved in the outbreak in three days. Three days! This information, made possible by new sequencing technologies, allowed real-time outbreak analysis, including accurate patient diagnosis and strain tracking. Researchers and companies are continuing to improve methods of DNA sequencing and analysis, and these technologies will become important tools in infectious disease epidemiology.

So there it is! The tale of a humble microbe that wreaked havoc across Europe, sickening thousands and throwing a wrench in international diplomacy but at the same time providing a testing ground for some of science's greatest new achievements. All in a day's work for E. coli.


E. coli micrograph is available through Wikimedia Commons. Credit: Eric Erbe and Christopher Pooley of USDA ARS.
Map of outbreak cases uses data from the World Health Organization and was made by Smart Draw, LLC to demonstrate their software ( 


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