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

Abstract

For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. 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. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade.

Importance: In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.

FIG 1

Geographic and phylogenetic locations of Haitian strains. One of two equally parsimonious trees showing relationships among Haitian strains is shown and is based upon 25 parsimony informative SNPs out of 71 total. Only one of the 25 SNPs is homoplastic, leading to a consistency index of 0.9615. The map is adapted from reference . Strain locations not depicted in the geographical map are indicated by an asterisk.

FIG 2

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.