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DNA sequencing traces Haiti cholera epidemic to South Asia

cholera _SM.jpgThe strain of cholera bacterium responsible for the epidemic currently raging in Haiti came from South Asia, and was most likely carried to Haiti by an infected human or some form of human activity, researchers report in the New England Journal of Medicine today.

A report obtained by the Associated Press earlier this week had suggested the likely source of the epidemic to a group of United Nations peace-keepers from Nepal – a conclusion supported by the current study.

According to the most recent data by the US Centers for Disease Control and Prevention, the cholera epidemic in the earthquake-devastated country has already infected over 91,000 people and caused at least 2,000 deaths.

“We really wanted to ask the question, how did cholera get to Haiti? It hasn’t been there more for than a century,” says Matthew Waldor, an infectious disease biologist at the Brigham and Women’s Hospital in Boston, Massachusetts, the study’s lead author.


Several of Waldor’s clinical colleagues had traveled to the country to provide medical treatment after the outbreak began in October and returned with isolates of the bacterium. The group sent the samples off to Pacific Biosciences, a DNA sequencing company in Menlo Park, California, because its real time sequencing technology – currently in beta-testing and due to hit the market next year – was able to turn the samples around quickly.

The five samples – two Haitian isolates, a Latin American strain, and two Bangladeshi strains from different epidemics – were sequenced in just two and a half days. (Using older technology, each strain would have taken about 10 days to sequence, Waldor estimates.)

The researchers compared single-base differences and structural variation in the 5 genome sequences to 23 other partial or complete sequences available in the public database GenBank, and found the Haitian sequences to be nearly identical to South Asian isolates. Such a close similarity strongly suggests that the bug was most likely carried to Haiti by humans, rather than longer-acting environmental forces like ocean currents, Waldor says.

That knowledge brings power, he explains: it allows the global health community “to think about how we can alter our policies in the future to alter the spread of cholera by human activities.” For example, those coming to help with relief efforts from regions where cholera is highly endemic could be screened for the bacterium and treated if they are carriers.

Also, he says, the technology on which the group’s analysis relied “allows for a new era” in the way outbreaks are analyzed.

That’s not just because of its speed, says Eric Schadt, Pacific Biosciences’ chief scientific officer, but because many of the variants the researchers identified were found in repetitive, hard-to-read elements of the genome. Those sections are best sequenced with technologies such as this, which can read 1000 or more bases of a genome at a stretch, rather than chunks of 250 or so bases like most currently used technologies, he said.

“This is right in line with where the sweet-spot of the technology is,” Schadt says.

Image: Adult cholera patient, via Wikipedia

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    Reeta Clare said:

    It is too bad Waldor et al could not sample sequences from any of the Nepalese soldiers at the base.

    The UN claims no soldiers at the base were tested for cholera. (see link and excerpt below)

    http://www.cbsnews.com/stories/2010/10/29/world/main7005281.shtml

    >None of the Nepalese soldiers based there have been tested for cholera because none presented symptoms, mission spokesman Vincenzo Pugliese said Friday. He said media reports published elsewhere saying that all soldiers had tested negative for the disease were incorrect.

    >"By none of them presenting the symptom of the cholera there was no need to do another test," Pugliese told AP. “It’s not the same as saying they were all tested negative because none of them had to be tested.” The soldiers have not been tested for cholera since the outbreak, he said.

    >But about 75 percent of people infected with cholera do not exhibit symptoms and can still shed them into the environment and infect others for two weeks, Pan American Health Organization deputy director Jon Andrus told reporters at a press briefing on Oct. 25.

    >None of the Nepalese soldiers based there have been tested for cholera because none presented symptoms, mission spokesman Vincenzo Pugliese said Friday. He said media reports published elsewhere saying that all soldiers had tested negative for the disease were incorrect.

    >"By none of them presenting the symptom of the cholera there was no need to do another test," Pugliese told AP. “It’s not the same as saying they were all tested negative because none of them had to be tested.” The soldiers have not been tested for cholera since the outbreak, he said.

    >But about 75 percent of people infected with cholera do not exhibit symptoms and can still shed them into the environment and infect others for two weeks, Pan American Health Organization deputy director Jon Andrus told reporters at a press briefing on Oct. 25.< (end of excerpt)

    Absence of evidence is not evidence of absence, but apparently the UN thinks absence of evidence is a good talking point. It certainly helps them rationalize their faux-indignation about the “rumors” that the troops brought the cholera.

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