Gene sequencing of cholera bacterium from Haiti points to U.N. source


The United Nations sent Nepalese peacekeeping troops to bring relief to Haiti after it was devastated by a 7.0 earthquake in 2010. A new study concludes the peacekeepers brought something else, as well -- cholera, triggering an epidemic that has sickened hundreds of thousands of Haitians and killed more than 8,000, according to the Centers for Disease Control and Prevention.

After sequencing the DNA of 23 samples of the cholera-causing bacterium from Haiti and comparing them to the DNA of strains found elsewhere, researchers said the outbreak could be traced to Nepal, where the disease is endemic. They also concluded that the outbreak in Haiti could be traced to a single source, undermining the hypothesis that the strain was repeatedly introduced to the country over the past three years.

Cholera is a disease caused by a bacterium called Vibrio cholerae. It’s typically spread through contaminated food or water, and symptoms include diarrhea, vomiting and dehydration. The disease spreads quickly in areas with inadequately treated sewage and drinking water, as is often the case in places that have been hit with a natural disaster. The World Health Organization estimates that 3 million to 5 million people are sickened with cholera annually, causing 100,000 to 120,000 deaths each year. Oral rehydration salts, intravenous fluids and antibiotics can be used to treat the disease.


Cholera first emerged in Haiti about nine months after the January 2010 quake that killed hundreds of thousands of Haitians. The outbreak was a surprise, since the disease had never before been documented in the small island nation.

At first, circumstantial evidence reported by French epidemiologist Renaud Piarroux indicated that poor sanitary conditions at a U.N. camp about 40 miles outside the capital, Port-Au-Prince, resulted in contamination of local water supplies. But that didn’t explain how V. cholerae wound up in the camp in the first place.

About 1,300 Nepalese peacekeepers arrived in Haiti in October 2010 to help with earthquake recovery efforts. The first indication that they might be responsible for the cholera outbreak was a December 2010 study that examined bacterial DNA and concluded that the cholera epidemic was caused by a strain most likely introduced to Haiti from South Asia, not some strain that traveled from neighboring Latin America.

A 2011 study found that V. cholerae samples from Haiti were almost genetically indistinguishable from Nepalese samples. Those results were published in mBio, the journal of the American Society for Microbiology. But some people remained unconvinced because most of the samples analyzed in that study came from Nepal.

The study published Tuesday, which also appears in mBio, considered more than 100 samples from recent cholera outbreaks in 16 different countries. Even with more candidates in the mix, the Haiti and Nepal samples were strikingly similar, perched on the same branch of the evolutionary tree that researchers constructed based on their data.

“They’re very closely related,” said William Hanage, a study author and infectious disease expert at Harvard University’s School of Public Health. But he cautioned that just because the Haiti samples bore the most resemblance to the Nepal samples out of the genomes studied, that doesn’t rule out the existence of even more closely related samples elsewhere.

The data are “consistent with a hypothesis of an introduction from Nepal, but not definitive,” Hanage said, adding that they underscore the importance of seeking “bigger, better data sets.”


Hanage and his colleagues had set out to study how V. cholerae had evolved since it arrived in Haiti -- in particular, whether it gained genes that allowed it to adapt to its new environment. They found that the Haitian V. cholerae strain had a limited ability to “pick up” genes from other bacteria or the environment through a process called horizontal gene transfer, Hanage said. However, it’s still possible that the strain could acquire genetic material through other means -- for example, if a virus injects its genetic material into a bacterium.

The study authors saw DNA sequence changes, or mutations, in the Haiti strain, but they appeared to be random, rather than helpful for surviving in its new environment.

The Haiti and Nepal samples belong to a type of V. cholerae called “atypical El Tor” strains, which, in locations in Asia and Africa, has become more virulent, resulting in higher infection rates and worse symptoms. It’s also become resistant to several cholera drugs.

The strain’s uniform lineage and geographic isolation offer “an unprecedented natural experiment” for understanding the deadly pathogen’s evolution, the study authors wrote.

“The study brings up a great new light into the epidemic that’s been occurring in Haiti,” said Pardis Sabeti, a computational geneticist at Harvard University’s Center for Systems Biology, who was not part of the study. “It provides an opportunity to watch how bacteria evolve over time and
hopefully provide an opportunity to think of interventions.”

The study also revealed another problem: When analyzed with a testing technique called pulse-field gel electrophoresis, or PFGE, the Haiti samples appeared diverse, as if they had originated from several outbreaks. But when the researchers used whole genome sequencing, which allowed them to piece together long DNA fragments rather than several short fragments, they found that the strains were all part of the same outbreak.

“PFGE is like watching hockey on a fuzzy 14-inch black-and-white TV around 1970, and genomics is watching it on a 60-inch set in HD,” Hanage explained.


PFGE is the method most often used to investigate outbreaks in the U.S., but this study revealed that it leaves something to be desired, Hanage said. Luckily, whole genome sequencing is getting cheaper, which means it will be easier for public health experts to track sources of disease.

The results come just shy of the 60-day deadline the Institute for Justice and Democracy, a Boston-based human rights group, set for the U.N. to compensate Haitian cholera victims or face a lawsuit in a U.S. court.

Hanage said the legal threat underscores the importance of making the right conclusions about outbreaks, which depends on gathering as much data as possible. “Our ability to reconstruct these events have legal and ethical implications,” he said. “The scientific community should be taking those seriously.”

Sabeti thinks the battle should be waged against the microbes, not their unwitting carriers. While she agrees that the Haitian epidemic is devastating, she worries that litigation could chill genetic-based epidemiological research when our understanding of outbreaks is still poor.

“The attention should be on the microbes themselves,” she said. “As the world becomes more global, this kind of thing is going to happen all the time. We can’t just have a lawsuit every time this happens.”

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