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Genomic Analysis of Haiti Cholera Strains Indicate Limited Ability to Acquire New Genes

NEW YORK (GenomeWeb News) – The cholera strain behind the outbreak that emerged in Haiti in 2010 has a limited ability to acquire new genes, according to an evolutionary analysis of isolate genomes conducted by Cheryl Tarr at the US Centers for Disease Control and Prevention and her colleagues.

By sequencing a number of Vibrio cholerae isolates obtained from different locales and at different stages of the outbreak in Haiti, Tarr and her colleagues found that the strain did not appear to acquire new genes from the environment, and it seemed to have an impaired ability to undergo horizontal gene transfer, which typically allows bacteria to adapt quickly. The researchers reported their findings today in mBio.

The cholera outbreak in Haiti began in October 2010, following the January 2010 earthquake there. Earlier sequencing-based characterizations of the outbreak strain traced it back to Southeast Asia and the Bay of Bengal. Consequently, UN peacekeepers from Nepal who had been dispatched to Haiti after the earthquake were identified as a likely source of the disease.

In this study, Tarr and her colleagues developed a phylogenetic tree based on both Haitian and other isolates, and that, too, grouped the Haitian isolates with Nepalese ones, indicating a single source for the V. cholera O1 epidemic in Haiti.

"The single-source introduction and geographic isolation of the Haiti epidemic, along with the extended duration of the outbreak, provide an unprecedented natural experiment for characterizing in detail the intrinsic tempo and mode of genome evolution in this deadly pathogen," Tarr and her colleagues wrote.

To determine how the pathogen changed over time, the investigators sequenced 23 cholera samples from geographically disperse areas of Haiti using the Illumina GAIIx platform and downloaded the Illumina runs of 87 publicly available cholera genomes from the Sequence Read Archive. They also sequenced nine of those 23 isolates — as well as resequenced the reference genome — using the Pacific Biosciences platform.

For the Haiti isolates they sequenced, Tarr and her colleagues selected ones that had different fingerprints by pulse-field gel electrophoresis or antibiotic susceptibility patterns.

A molecular clock analysis of the isolates dated the most recent common ancestor of the Haiti and Nepal groups to Sept. 28, 2010, with a credibility interval ranging from the end of July to the middle of October; the Nepalese peacekeepers arrived on Oct. 9, the researchers noted.

While all the genes found in the Haiti isolates were also contained in the reference genome, they did contain a few substitutions or deletions. The 2012EL-1410 isolate, for example, contained a GAA to TAA substitution in the wbeT gene —involved in O antigen modification —that introduced a premature stop codon, leading to a truncated protein. In addition, the nonagglutinating isolate, 2012V-1069, had an approximately 10 kilobase deletion in the rfb region, which is also involved in O antigen production. This isolate, the researchers added, appears to belong to serogroup O1, though it cannot synthesize or transport that antigen to its cell surface.

A number of isolates had deletions in the SXT region, which is an area of high genetic diversity. A few isolates that had altered susceptibility to antibiotics lost the floR, strA, strB, and sul2 resistance genes in the SXT region.

Still, by a Blast analysis, the Haiti isolates appeared to not have gained any genes or genome islands. "It is well accepted that [horizontal gene transfer] is a major force driving evolution in bacteria, including Vibrio; thus, the lack of HGT observed in our study might be surprising," the researchers wrote. They added that previous studies — including of a different serotype of cholera — indicated that gene acquisition may occur early on in an outbreak.

DNA uptake assays of 12 isolates indicated, rather, that compared to a control cholera strain, the Haiti strains were not able to take up environmental DNA, though the strains did appear to be able to undergo the necessary quorum-sensing step. "Our study indicates that transformation by unrelated environmental strains of V. cholerae has played no detectable role in the evolution of the outbreak strain," Tarr and her colleagues noted.

Further studies, the investigators said, will uncover the mutation that prevents these strains from imbibing environmental DNA.

The Haiti strains, they added, are part of the atypical El Tor strains that are fast displacing the prototypical El Tor strains, and the new ones often are more virulent and resistant to drug treatments.

"With the tools such as WGS now being available for epidemiological surveillance and case tracking, we argue for renewed efforts aimed at cholera prevention to avert more widespread and difficult-to-treat cholera outbreaks," they added.