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From: The eUpdate, 6.28.11

E. Coli Outbreaks Point to Need for More Research, Expert Says

Pina Fratamico, PhD, calls for whole-genome sequencing

According to Dr. Fratamico, “sequencing the whole genome is the key to learning what virulence genes these organisms carry and how they may be evolving through horizontal gene transfer.”

Although they appear unrelated to each other and involve different strains of the bacteria, recent E. coli outbreaks in Germany and the U.S. underscore how much scientists still have to learn about this pathogen, said U.S. Department of Agriculture microbiologist Pina Fratamico, PhD.

As of June 20, the from European Centre for Disease Prevention and Control (ECDC) had logged 3,593 total cases in the outbreak, with 849 cases of hemolytic uremic syndrome and 40 deaths. On June 19, German officials confirmed that the infection has been transferred from person to person in the case of a Frankfurt kitchen worker who passed it on to 20 people she was cooking for after having eaten contaminated sprouts, the original source of the outbreak. The unusual “hybrid” strain of the bacterium has also been found in a Frankfurt stream.

Meanwhile, two states in the U.S. have their own E. coli puzzles to solve. Tennessee is tracking three different strains of E. coli in its outbreak of at least 11 cases, which involve the well-known O157:H7, as well as two other serogroups, O103 and O169.

The new cluster is puzzling, said Dr. Fratamico, an E. coli expert and lead researcher at the U.S. Department of Agriculture’s Center for Food Safety. “It doesn’t seem to be traceable to a single source, because the PFGE [pulsed-field gel electrophoresis] patterns don’t match,” she said. “Of course, O103 would not be the same strain as O169, nor as O157, but even the two O103 strains that they’ve isolated so far don’t seem to match. There doesn’t seem to be a common source.”

Nor is the O157 strain that has been isolated in Tennessee the same as one found in southwestern Virginia, where two children, a brother and sister, were rushed to the hospital after showing symptoms. The two-year-old girl later died.

Dr. Fratamico noted that while more attention is now being paid to other members of the so-called “Top Six” E. coli variants, beyond the behemoth O157:H7, those types are just the tip of the iceberg. “Based on [Centers for Disease Control and Prevention] data,” she said, “they only cause between 70% and 75% of the non-O157 infections, which leaves another 20-25% of E. coli illnesses in humans [that are] caused by other serogroups.”

One of those is the O169 variant found in Tennessee, which, Dr. Fratamico pointed out, has produced outbreaks on cruise ships. Another is the so-called “hybrid” E. coli that’s sickened thousands and killed dozens in Europe, which shows characteristics of both an enteroaggregative E. coli and a Shiga toxin-producing E. coli.

“Now that it’s become a lot less expensive to sequence whole genomes, I think that’s what we need to do with E. coli,” Dr. Fratamico said. “You can do PCR [polymerase chain reaction] and target specific virulence genes to see if the bacteria contains what you’re looking for, but that doesn’t help if you don’t know what you’re looking for. Sequencing the whole genome is the key to learning what virulence genes these organisms carry and how they may be evolving through horizontal gene transfer.”

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