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Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS - MBio (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: mark.eppinger@utsa.edu paul.keim@nau.edu.

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Related in: MedlinePlus

Maximum parsimony tree of global V. cholerae O1 genomes. Comparisons of 116 genomes yielded 670 total SNPs of which 330 were parsimony informative. The tree shown is one of 20 equally parsimonious trees with a consistency index of 0.9651. Trees were recovered using a heuristic search in PAUP 4.0b10. The outgroup used for rooting was identified as basal following a larger analysis that included diverse non-O1 strain genomes (see Table S1 in the supplemental material). The branches (a to f) are arbitrarily labeled for discursive purposes; note the BEAST estimates for most recent common ancestors (MRCA) including the 95% confidence interval.
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fig2: Maximum parsimony tree of global V. cholerae O1 genomes. Comparisons of 116 genomes yielded 670 total SNPs of which 330 were parsimony informative. The tree shown is one of 20 equally parsimonious trees with a consistency index of 0.9651. Trees were recovered using a heuristic search in PAUP 4.0b10. The outgroup used for rooting was identified as basal following a larger analysis that included diverse non-O1 strain genomes (see Table S1 in the supplemental material). The branches (a to f) are arbitrarily labeled for discursive purposes; note the BEAST estimates for most recent common ancestors (MRCA) including the 95% confidence interval.

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).


Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS - MBio (2014)

Maximum parsimony tree of global V. cholerae O1 genomes. Comparisons of 116 genomes yielded 670 total SNPs of which 330 were parsimony informative. The tree shown is one of 20 equally parsimonious trees with a consistency index of 0.9651. Trees were recovered using a heuristic search in PAUP 4.0b10. The outgroup used for rooting was identified as basal following a larger analysis that included diverse non-O1 strain genomes (see Table S1 in the supplemental material). The branches (a to f) are arbitrarily labeled for discursive purposes; note the BEAST estimates for most recent common ancestors (MRCA) including the 95% confidence interval.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222100&req=5

fig2: Maximum parsimony tree of global V. cholerae O1 genomes. Comparisons of 116 genomes yielded 670 total SNPs of which 330 were parsimony informative. The tree shown is one of 20 equally parsimonious trees with a consistency index of 0.9651. Trees were recovered using a heuristic search in PAUP 4.0b10. The outgroup used for rooting was identified as basal following a larger analysis that included diverse non-O1 strain genomes (see Table S1 in the supplemental material). The branches (a to f) are arbitrarily labeled for discursive purposes; note the BEAST estimates for most recent common ancestors (MRCA) including the 95% confidence interval.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: mark.eppinger@utsa.edu paul.keim@nau.edu.

Show MeSH
Related in: MedlinePlus