Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.
Bottom Line: We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons.Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia.As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels.
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Mentions: We used the identified SNPs and metadata associated with each isolate to create a global phylogeny of the O1 serotype and to calibrate a molecular clock (see Table S2 in the supplemental material). A phylogenetic reconstruction of the evolutionary relationships among 116 V. cholerae strains was performed using maximum parsimony analysis to understand the dynamics of the Haitian outbreak and its phylogenetic position within the seventh epidemic relatives (Fig. 2). Of the 670 core genome SNPs analyzed, 330 were parsimony informative. The limited homoplasy in these data with only 22 homoplastic SNPs and a consistency index of 0.9651 is an indication of a highly accurate tree of a clonal organism without intraclade lateral gene transfer events (14, 15). A single tree is presented (Fig. 2), though there were 20 equally parsimonious hypotheses for the evolution of these strains. The phylogenetic ambiguity was restricted to only a few areas of the tree, which can be seen in the consensus tree shown in the supplemental material (see Fig. S3 in the supplemental material).