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DNA Sequencing Matches Cholera Strain in Haiti with Bacteria from South Asia

A team of researchers from Harvard Medical School, Brigham and Women's Hospital, and Massachusetts General Hospital, with others from the United States and Haiti, has determined that the strain of cholera erupting in Haiti matches bacterial samples from South Asia and not those from Latin America. These findings, which appeared in the New England Journal of Medicine, conclude that the cholera bacterial strain introduced into Haiti probably came from an infected human, contaminated food or other item from outside of Latin America.

To identify the probable origin of the cholera strain in Haiti, scientists used a third-generation, single-molecule DNA sequencing method developed by Pacific Biosciences. They determined the genome sequences of two Haitian cholera samples and three cholera samples from elsewhere around the world. Based on advanced imaging technology, the method enables researchers to observe a natural enzyme synthesizing a strand of DNA in real time. As such, the technology actually tracks and documents nature at work, a rapid approach compared to other sequencing technologies. The method allowed a comprehensive analysis and comparison of critical DNA features among the various cholera samples, which included single nucleotide variations, insertions and deletions of particular portions of the genome, and structural variations. The analysis showed a close relationship between the Haitian samples and the seventh pandemic variant strains isolated in Bangladesh in 2002 and 2008.

Genetic changes occur quickly, within hours in the lab and probably weeks within the environment, through natural modes of DNA swapping and mutation among bacteria. Their evolution is based, in part, on the acquisition, loss, and alteration of mobile genetic elements, including DNA from the CTX bacterial virus, which bears the genes encoding the cholera toxin, and other genetic sequences that may make a particular strain more adapted to a given ecosystem. The resulting heterogeneity has been used to categorize strains of the seventh pandemic and to understand their transmission around the globe.

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