Cholera Imported to Haiti by accident (by NGO workers infected from S. Asia)

http://www.nytimes.com/2011/08/30/science/30microbe.html?pagewanted=2&_r=1&ref=science#

Dr. Waldor and his colleagues asked a slightly different question when Haiti was swept by cholera after last year’s earthquake. Cholera had not been seen in Haiti for more than a century. Why the sudden epidemic?

The scientists quickly sequenced the genome of the bacteria in Haiti and compared them with known cholera strains from around the world. It turned out that the Haitian strain was different from cholera bacteria in Latin America and Africa, but was identical to those in South Asia.

So the researchers concluded that the earthquake was indirectly responsible for the epidemic. Many relief workers who came to Haiti lived in South Asia, where cholera was endemic. “One or more of these individuals likely brought cholera to Haiti,” Dr. Waldor said.

Charting Disease Maps

One of Dr. Waldor’s collaborators in that study, Eric Schadt, wants to take the idea of molecular forensics one step further. Dr. Schadt, the chairman of genetics at Mount Sinai School of Medicine and chief scientific officer of Pacific Biosciences, wants to make disease weather maps.

He began with pilot studies, first in his company’s offices. For several months, the company analyzed the genomes of microbes on surfaces, like desks and computers and handles on toilets. As the flu season began, the surfaces began containing more and more of the predominant flu strain until, at the height of the flu season, every surface had the flu viruses. The most contaminated surface? The control switches for projectors in the conference rooms. “Everybody touches them and they never get cleaned,” Dr. Schadt said.

He also swabbed his own house and discovered, to his dismay, that his refrigerator handle was always contaminated with microbes that live on poultry and pork. The reason, he realized, is that people take meats out of the refrigerator, make sandwiches, and then open the refrigerator door to return the meat without washing their hands.

“I’ve been washing my hands a lot more now,” Dr. Schadt said.

The most interesting pilot study, he says, was the analyses of sewage.

“If you want to cast as broad a net as possible, sewage is pretty great,” Dr. Schadt said. “Everybody contributes to it every day.”

To his surprise, he saw not only disease-causing microbes but also microbes that live in specific foods, like chicken or peppers or tomatoes.

“I said, ‘Wow, this is like public health epidemiology,’ ” he said. “We could start assessing the dietary composition of a region and correlate it with health.”

Dr. Relman, meanwhile, is focusing on the vast bulk of microbes that live peacefully in or on the human body. There are far more bacterial genes than human genes in the body, he notes. One study that looked at stool samples from 124 healthy Europeans found an average of 536,122 unique genes in each sample, and 99.1 percent were from bacteria.

Bacterial genes help with digestion, sometimes in unexpected ways. One recent studyfound that bacteria in the guts of many Japanese people — but not in the North Americans tested as control — have a gene for an enzyme to break down a type of seaweed that wraps sushi. The gut bacteria apparently picked up the gene from marine bacteria that live on this red algae seaweed in the ocean.

But if these vast communities of microbes are as important as researchers think they are for maintaining health, Dr. Relman asked, what happens when people take antibiotics? Do the microbial communities that were in the gut recover?

Using rapid genome sequencing of all the microbes in fecal samples, he found that they did return, but that the microbial community was not exactly as it was before antibiotics disturbed it. And if a person takes the same antibiotic a second time, as late as six months after the first dose, the microbes take longer to come back and the community is deranged even more.

Now he and his colleagues are looking at babies, taking skin, saliva and tooth swabs at birth and during the first two years of life, a time when the structure of the microbe communities in the body is being established.

“We wait for the babies to be exposed to antibiotics — it doesn’t take that long,” Dr. Relman said. The goal, he says, is to assess the effects on the babies’ microbes, especially when babies get repeated doses of antibiotics that are not really necessary.

“Everything comes with a cost,” he said. “The problem is finding the right balance. As clinicians, we have not been looking at the cost to the health of our microbial ecosystems.”