‘HYPERVIRULENT’ THE ATTACK
C. difficile detectives tackle a global menace with roots in Canada
Trevor Lawley keeps hundreds of samples of C. difficile in his freezer, each identified by the country in which the bacterium unleashed its unique brand of misery and death.
He tracked down Aus001 in Melbourne, Australia; collected Gla010 in Glasgow, Scotland; and picked up Lei017 in the Netherlands as part of an international hunt for the origin of “epidemic” C. difficile — a global menace that pumps toxins into the guts of its victims. It has spread around the world’s hospitals in the last decade, killing thousands.
Lawley, a Canadian with a flair for microbial forensics who now works at a leading British research centre, spent two years travelling the globe collecting hundreds of samples of C. difficile.
Then, in his lab at the Wellcome Trust Sanger Institute, near Cambridge, England, Lawley and his colleagues extracted the bacteria’s secrets.
Two strains of antibiotic resistant C. difficile that emerged in North America caused the global epidemic, the sleuths report.
One emerged in the northeast U.S. a decade ago; the second, which they call FQR2, surfaced in Quebec.
And it was FQR2 — the Quebec bug — that took off globally, becoming a scourge in the U.K., continental Europe and Australia, the team reports. “It was the biggie,” says Lawley.
He and his colleagues say the emergence of the potentially lethal pathogen was fuelled by antibiotics — wonder drugs that are increasingly the source of very big problems.
“They were the secret ingredient,” says Lawley, pointing specifically to fluoroquinolones, a class of antibiotics widely used in North American hospitals when the epidemic C. difficile strains appeared.
It is impossible to know exactly where FQR2 morphed into existence, but the intestines of a patient in a Quebec hospital is one scenario. Another is that it emerged unnoticed in the northeast U.S., then spread north.
It’s an odd fate for C. difficile, an ancient and formerly innocuous bacterium that can’t even grow in the presence of oxygen. It has coexisted with humans for eons and spends most of its time as dormant and almost indestructible spores. C. difficile can, however, come to life in the gut, and when conditions are right, it begins to multiply.
Doctors used to think of C. difficile and its spores, found in dirt, on food and animals, simply as a nuisance that could cause diarrhea.
“It was a low-grade problem,” says Dr. Mark Miller, former head of infectious diseases at the Jewish General Hospital in Montreal, who witnessed and helped document C. difficile’s transformation.
In 2000, doctors in Pittsburgh began to see patients with severely inflamed colons. Eighteen patients died. An investigation pointed to a new virulent strain of C. difficile.
An eerily similar C. difficile surfaced in 2002 in Quebec. People undergoing hip replacements or heart bypasses started developing severe diarrhea and inflamed colons. Many ended up having their “toxic megacolons” removed, in a desperate bid to save their lives.
“We had never seen people getting so bad that you needed to take their colon out, or so bad that they had to go to intensive care unit, and certainly so bad that they would die of C. diff,” recalls Miller.
Miller and other infectious disease doctors in Montreal and Sherbrooke, anxious to figure out what they were dealing with, came up with a plan to track the cases and rates of complications.
They isolated and grew the microbes in the lab and soon realized the virulent C. difficile had also acquired the ability to live in the presence of fluoroquinolones, the potent antibiotic that doctors in Canada and the U.S. had begun heavily prescribing in the mid-1990s.
Fluoroquinolones, which prevent bacteria from replicating, were used to treat everything from urinary to respiratory infections. By 2002, they had become the most common antibiotic given to adults in the U.S. Almost one-quarter of all patients in one Quebec teaching hospital in 2003-04 were on fluoroquinolones.
Like many broad-spectrum antibiotics, fluoroquinolones disrupt the elaborate community of microbes living in people’s intestines by killing off beneficial as well as harmful bacteria.
But microbes with resistance, such as the new C. difficile, can continue to grow and multiply even when people take fluoroquinolones.
Making the situation even worse, the resistant C. difficile could pump out extraordinary amounts of toxin: 16 to 23 times more toxin than garden variety C. difficile, according to one Quebec study.
This new “hypervirulent” C. difficile, as the doctors soon described it, can have a devastating impact, especially in people over age 60.
Once it takes hold in someone’s gut, the bacterium can invade the lining of the colon and pump out its extra-strength toxins with lethal impact. Cells in the colon start to disintegrate, and the colon begins to leak and ooze pus.
There is also relentless diarrhea, with each episode releasing millions of C. difficile spores that can cling to toilets, bedpans and ambulances. The Quebec hospitals could not get rid of them.
The outbreak defied cleaning and infection control and the microbe moved from one hospital to the next. C. difficile spores, researchers later found, are so hardy, alcohol does not kill them. They can be carried on shoes, clothes, people and animals, which helps explain how FQR2 skipped across continents.
Miller, who has co-authored several studies on the newly evolved C. difficile and the toll it has taken, says more than 2,000 people died because of C. difficile infections during the two-year peak of the Quebec epidemic. “That’s conservative.”
People started cancelling elective surgery and stayed away from the hospitals. “It was really quite a catastrophe,” says Miller.
The hypervirulent C. difficile, which Canadian microbe trackers classify as NAP1, was also on the move. It spread to Ontario hospitals and then across the country, infecting thousands of people in hospitals and nursing homes and causing an untold number of deaths. Across the Atlantic, C. difficile also became a scourge, triggering unprecedented outbreaks in hospitals across the U.K. and Europe. The British government reports 7,916 deaths related to C. difficile at the peak of the epidemic in England in 2007.
But Lawley and his colleagues at the Sanger Institute, home to powerful genome sequencing machines, had the forensic tools to find out where NAP1, or “epidemic” C. difficile, emerged.
Lawley literally followed the trail of the NAP1’s “rapid transcontinental dissemination.” He collected samples of NAP1 from hospitals in the U.K., Europe, Asia, Australia and North America, amassing more than 300 strains isolated from infected patients.
Back in the lab, Lawley and his colleagues coaxed the bacteria to grow in oxygen-free cabinets, extracting enough DNA to sequence the organisms’ genomes and make a family tree showing how the microbes are genetically related.
The analysis not only confirmed “epidemic” NAP1 C. difficile originated in North America, but showed it had evolved twice. The C. difficile lineage, or strain, they call FQR1, first seen in the Pittsburgh area in 2000, spread across the U.S. and later showed up in Switzerland and South Korea. “The second strain of C. difficile, FQR2, originated in Canada and spread rapidly over a much wider area, throughout North America, Australia and Europe,” the Sanger Institute reports.
The analysis did not pinpoint where FQR2 originated, but Lawley says the bacterium likely emerged in either Quebec or the northeast U.S.
And it show FQR2’s “descendants” were circulating in Birmingham, England, within months of the outbreak in Quebec and there were two other “transatlantic transmission events” from North America into the U.K., two more into continental Europe and a more recent introduction into Australia.
Miller, who is now chief medical officer at bioMerieux, an infectious diseases diagnostic company, and who does research at McGill University and the Jewish General Hospital, describes the findings as “obviously fascinating.”
“Everyone has been pointing fingers at one another,” Miller says of a long-running debate over whether the epidemic C. difficile should be called the Pittsburgh or Quebec strain. “In fact they are different.”
Michael Mulvey, who tracks C. difficile and other superbugs in Canada at the National Microbiology Laboratory in Winnipeg, says the findings show the power of new genetic mapping tools that can detect tiny changes that occur when bacteria multiply and spread.
Mulvey’s team is taking a close look at 150 C. difficile samples collected by hospitals across Canada since 2004. They’re now feeding DNA from the organisms into their sequencing machines, which can spit out the genetic blueprint of a bacterium in less than 24 hours.
The 100 bacteria analyzed so far are all related to the FQR2.
Lawley says FQR1 and FQR2 appear to share a common ancestor, a virulent form of C. difficile that existed in nature. But it was when the virulent organism mutated and became resistant to fluoroquinolones antibiotics that the bacteria acquired the competitive advantage to take hold and thrive in hospitals, he says.
He adds it’s not surprising that the resistant, virulent C. difficile evolved twice, considering the way fluoroquinolones were so widely used. C. difficile needed just one small change in its genome to become resistant to the antibiotics. “So it was just a matter of time,” says Lawley.
The FQR1 and FQR2 strains continue to cause much misery, but the scientists say new C. difficile strains are now on the rise.
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