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Researchers Use Third Generation Sequencing to Characterize Haitian Cholera Strains

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – The strain of cholera-causing bacteria currently circulating in Haiti likely originated somewhere in South Asia, according to a genome sequencing study appearing online last night in the New England Journal of Medicine.

Researchers from the US and Haiti sequenced the genomes of five Vibrio cholerae isolates using Pacific Biosciences' single molecule, real-time sequencing platform. Two of the samples tested were from the current Haitian outbreak, while the remaining isolates came from South Asia and Latin America.

By comparing the sequences with one another — and with nearly two dozen V. cholerae sequences from public databases — the team was able to determine the bug's origin within a matter of days, showing that it was most similar to a strain found in Bangladesh and other parts of South Asia.

"Now armed with a more complete characterization of this pathogen, the scientific community is empowered with information that can be used to inform public health policy decisions such as the appropriate use of vaccines to quell this epidemic," corresponding author Eric Schadt, chief scientific officer of Pacific Biosciences, said in a statement.

The cholera outbreak in Haiti was first detected this fall and has rampaged through the country, affecting more than 93,000 individuals and killing more than 2,100. The first cholera case in the country was confirmed on October 19th, the researchers explained, but cholera has now been detected in every Haitian province and, to a lesser extent, in the neighboring Dominican Republic.

To try to track down the source of the outbreak, Schadt and his colleagues used the PacBio RS sequencing system to sequence two V. cholerae genomes from DNA in Haitian clinical samples. In less than 24 hours, the team generated enough sequence to cover the genomes of the Haitian strains 60 and 32 times, respectively.

"Third generation single-molecule, real-time sequencing involves direct observation of the DNA polymerase while it synthesizes a strand of DNA," the authors explained, "thus, it is much faster than previously developed methods and provides a comparatively long read length."

Similarly, the researchers used the PacBio system to sequence two strains from Bangladesh — one isolated in 2002 and a second isolated in 2008 — and a single strain isolated in Peru in 1991, which were sequenced to an average coverage of between 28 and 36 times.

The team then compared the newly sequenced V. cholerae genomes with reference genomes for three other V. cholerae strains and with 23 other previously sequenced V. cholerae strains.

In the process, the team tracked down 1,588 conserved orthologous genes in the five newly sequenced strains.

Overall, the SNP, copy number variant, and hyper-variable sequence patterns in the Haitian strains were most similar to those found in South Asian strain known as El Tor O1, marking the first time that strain has been detected in the Caribbean.

"Collectively, our data strongly suggest that the Haitian epidemic began with introduction of a V. cholerae strain into Haiti by human activity from a distant geographic source," the researchers wrote. "It is therefore unlikely that climatic events led to the Haitian epidemic, as has been suggested in the case of other cholera epidemics."

Based on their findings so far, those involved in the study suggest that such sequencing strategies hold potential for not only characterizing strains during an outbreak but also for preventing and treating such outbreaks — for instance, by predicting where outbreaks might occur and/or helping to determine which vaccines are most appropriate in a given region.

"The ability to quickly and easily perform real-time monitoring of pathogens also opens the door to using this technology as a routine surveillance method, for public health protection in addition to pandemic prevention and response," Schadt said in a statement.

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