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Cholera Sequencing Study Uncovers Genetic Diversity Present in Haitian Outbreak Isolates

NEW YORK (GenomeWeb News) – Researchers from the US and Bangladesh used whole-genome sequencing to reveal the genetic variation present in Vibrio cholerae isolates collected during the Haitian cholera outbreak.

In a study appearing online last night in the Proceedings of the National Academy of Sciences, the team reported that it has sequenced 76 V. cholerae isolates collected from cholera patients in 18 Haitian towns in November 2010, not long after the first of many cholera cases was diagnosed in that country.

By comparing these genomes to one another and eight V. cholerae reference strains that they sequenced and to genomic information in public databases, investigators were able to look at relationships between the Haitian isolates — which included bugs from two different V. cholerae populations — relative to strains found in other parts of the world.

Their phylogenetic analyses also highlighted the extensive genetic diversity that can exist within isolates from the same outbreak collected over a relatively short time. Indeed, given the extent of the diversity they saw, those involved in the study argued that more comprehensive V. cholerae sequence databases are needed to prevent and track cholera in the future.

"[Q]uite quickly, i.e., within a [three-week] period early in the cholera epidemic, substantial genomic diversity accumulated in the circulating population," corresponding author Rita Colwell and colleagues explained. Colwell, a University of Maryland researcher who is also affiliated with Johns Hopkins University, is the founder of the Maryland-based pathogen detection software company CosmosID.

"Our study speaks to the critical need for an up-to-date, properly curated, and publicly available reference genomic database … if investigations of future V. cholerae epidemics are to be effective and useful for public health applications," study authors wrote.

Haiti's cholera outbreak began in the fall of 2010 as the country continued to recover from a massive earthquake early that year. The disease spread quickly, researchers explained, affecting around a half a million people and killing more than 6,500 individuals — an outbreak that was exacerbated by heavy rains and flooding that occurred not long after the first cholera cases were diagnosed in late October.

Subsequent sequence typing and phylogenetic studies uncovered some genetic insights into the V. cholerae strains contributing to the outbreak, the study authors added, but the source of the original outbreak strain is still a contentious issue, with some arguing the it arrived with peacekeepers from Nepal after the Haitian earthquake and others pointing to a potential South Asian origin.

"Although the molecular and genomic data in the previous reports … have been interpreted as being consistent with V. cholerae being introduced to Haiti by outside visitors, a definitive statement of source attribution cannot yet be made," they wrote.

For their own study, the team used Illumina whole-genome sequencing alone or in combination with Roche 454 sequencing to sequence eight reference strains isolated in Thailand, Bangladesh, and elsewhere during other cholera epidemics, along with 76 strains isolated during the Haitian outbreak. The latter included 47 isolates from the V. cholerae serogroup O1, which has been implicated in other cholera epidemics, and 27 isolates from the non-O1/O139 serogroup.

When they brought data on these newly sequenced strains together with information on 27 publicly available V. cholerae genome sequences, researchers uncovered the extent of the genetic diversity present within the Haitian isolates.

They also found evidence suggesting the Haitian O1 strains shared genetic features with so-called "El Tor" strains from Zimbabwe, Zambia, Thailand, and Bangladesh.

Meanwhile, phylogenetic analyses indicated that almost all of the non-O1/O139 V. cholerae serogroup isolates tested from Haiti clustered closer than expected with some O1 strains described in the past, hinting that these strains share a genetic backbone with strains from another V. cholerae lineage.

"Results of comprehensive genomic analysis showed that V. cholerae O1 populations were clonal, resembling epidemic isolates from South Asia and Africa," the researchers reported. "V. cholerae non-O1/O139 populations were not clonal, but most probably serve as a reservoir for genomic and pathogenicity islands."