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Cholera patients in a clinic in Harare, Zimbabwe, in January 2009. Photo: Tsvangirayi Mukwazhi / AP

The planet is in the midst of its seventh cholera pandemic — one that affects about 3 million people each year and, unlike past pandemics that faded away, persists. Stopping its spread hinges on tracking its movements.

By analyzing the genomes of bacteria isolated from samples collected during cholera outbreaks over the past half-century, scientists have now determined that outbreaks in Africa and the Americas were sparked by strains that arrived from Asia. Tracing the paths into and around these regions offers new targets for efforts to control the disease.

The back story: The seventh pandemic began in Indonesia in 1961, then spread to South Asia (1963), Africa (1970), Latin America (1991) and then Haiti (2010). A current outbreak in Yemen just surpassed that in Haiti, and is nearing 1 million cases in the war-torn country.

The challenge: "When cholera was imported into Africa in 1970, it was easy to spot introduction routes and propagation routes because it was a new disease. At some point, the signal was lost because it was everywhere and you weren't able to link the outbreaks to each other," says Francois-Xavier Weill from the Institut Pasteur in Paris, who was involved in both studies.

The bacteria responsible for cholera, Vibrio cholerae, doesn't change much over time, so differences in the DNA of one strain compared to another are hard to spot. So the researchers turned to whole genome sequencing to analyze 714 samples collected on the three continents.

What they found: In Africa, cholera epidemics were traced to at least 11 different introductions from Asia since 1970. (The last five were multi-drug resistant strains.) And, it tended to enter through East/Southern Africa and West Africa.

"All the action should be taken there first," Weill says of public health surveillance efforts. Knowing the genetic fingerprint of the pandemic-producing strain could also inform decisions about when and where to use a global stockpile of cholera vaccine.

The researchers also found that one strain caused an outbreak in Africa that lasted 28 years. Both papers indicate that there's no local reservoir for cholera, meaning if a strain disappears at some point and another isn't introduced, cholera could be eliminated from the region, says Weill.

What's next: Until now, models of cholera's pathways were based on tens of samples. "Not only does the analysis provide more insight into how cholera moves but it also adds samples for others to make inferences so more researchers will be able to study its movement," says Andrew Azman from Johns Hopkins University, who was not involved in the research but studies cholera's epidemiology in East Africa. He says by adding the whole genome sequences of hundreds of strains to the public domain researchers can further understand the dynamics of how cholera is transmitted. Azman plans to pair Weill's results with detailed analysis of cases of cholera in Africa.

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