Gene Probe Yields E. coli Clue

The culprit behind Europe’s deadly Escherichia coli outbreak appears to be an evolved and extremely toxic version of a bug first identified in Münster, Germany, in 2001, according to genetic analyses done by two separate teams of scientists.


virus1 Identifying the bug’s ancestor may help scientists identify the origin, spread and source of the disease. Such genetic comparisons could also help researchers explain the biological mechanism that makes the 2011 bacterium so virulent, while providing clues for future diagnostic tests or effective drugs.Researchers said the quick genetic analysis will help unlock the mystery. “Everything we know so far indicates it is an evolved strain,” said Alexander Mellmann of the University Hospital of Münster, who was involved in one of the genetic analyses. “If it was completely unknown, we’d struggle a lot more in our effort to fight it.”

In addition to Dr. Mellmann’s group, a separate team from BGI, formerly known as the Beijing Genomics Institute, and University Medical Center Hamburg-Eppendorf compared the genetic material of the 2001 and 2011 strains. They found that seven genes crucial to both bugs’ survival are identical, as are 12 virulence/fitness genes shared by both.


The 2001 strain caused fewer than five identified cases world-wide, and scientists never did identify its natural reservoir—where a new strain of the E. coli bug can originate, such as in cattle. But the genetic analysis showed that as the 2001 bug likely swapped genetic material with other bacterial strains, some big changes occurred.


The 2011 version turns out to be resistant to eight classes of antibiotics, including penicillin, streptomycin and sulfonamide. The likely reason is that rapid evolution “resulted in the gain of more genes during the last 10 years” that conferred immunity against many more antibiotics, according to BGI.


Three more deaths from the bug were reported in Germany on Wednesday. So far, at least 26 people have died and more than 2,700 have been sickened by the outbreak in at least 13 different countries. Nearly all the cases can be traced back to Germany. Public health officials in Germany haven’t yet succeeded in pinpointing the food source behind the outbreak; part of their investigation continues to focus on a bean sprout farm as a possible source of infection.


Regional authorities in Germany on Wednesday reported what could be a clue in the saga, saying they found the E. coli strain on some cucumber scraps in the town of Magdeburg, in Saxony-Anhalt, in north central Germany. This is the first time this strain has been isolated on a vegetable in Germany. Several members of a family fell ill on May 19, and one of them pointed to their eating cucumbers, according to reports.


case of e coli Authorities searched the family’s compost trash can and found the strain—though it is impossible to say how and when the bacteria were introduced to the waste, because it is two weeks old. Authorities can’t rule out that the family may have been sickened and then transferred the bacteria to the cucumber scraps.The discovery of the tainted cucumber scraps in Magdeburg is unlikely to be helpful in the search for a source, said Holger Paech, spokesman for the state of Saxony-Anhalt’s health ministry. The family members were the only ones in Magdeburg who fell ill, and all other clues in searching for the source of their sickness have resulted in dead ends, Mr. Paech said.The family had no connections to Hamburg or other areas which experienced more severe outbreaks. Authorities tested surface areas inside the family’s kitchen, as well as samples from supermarkets where they shopped—all with no other positive identifications of the strain.While the father in the family was only slightly ill, the mother and daughter were hospitalized. The mother has been released, but the daughter, a young adult, has complications and is still in the hospital. The state of Saxony-Anhalt has only reported 28 cases of E. coli infections in this outbreak, according to the Robert Koch Institute, which is funded by Germany’s Federal Ministry of Health.

Saxony-Anhalt officials passed along the information and samples to the federal government. They will test it to see if the 0104 strain found on the cucumber waste is an exact match to the 0104 strain found in humans.
“We have no information for people—this really leaves us with more question marks than answers,” added Mr. Paech.
Hamburg health authorities originally said the E. coli outbreak stemmed from a shipment of Spanish cucumbers, but later determined those were infected with a different strain of the bacteria. Authorities still don’t know where the cucumber scraps in the sickened family’s trash originated, and the Robert Koch Institute, has continued to point to cucumbers as one of the potential sources of the outbreak, along with tomatoes and lettuce.


The twin sets of genetic analysis of the 2011 bug were conducted at unprecedented speed thanks to a new kind of gene-sequencing machine used by both teams.Most DNA sequencers use light beams to read the code of an organism’s genome, and the process can take a week to complete. A newer machine, known as an ion torrent, does the job more quickly. For example, it took three days to complete the process of sequencing the 5.4 million letters of the latest bug’s genetic code. COUNTRY

“It’s a semiconductor device that senses chemistry, so it can directly read off the DNA,” said Jonathan Rothberg of Life Technologies Corp. of Carlsbad, Calif., which sells the ion torrent device.

The way that the genetic data of the 2011 E. coli strain were disseminated globally suggests a more effective approach for tackling public health problems. Both groups put their sequencing data on the Internet, so scientists the world over could immediately begin their own analysis of the bug’s makeup. BGI scientists also are using Twitter to communicate their latest findings.

Corrections and Amplifications

Jonathan Rothberg is an executive at Life Technologies Corp., which sells the ion torrent gene-sequencing machine. His last name was misspelled Rotheberg in an earlier version of this article.