Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010

Abstract

In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks.

Keywords: Pakistan; Vibrio cholerae O1; bacteria; cholera; floods; global phylogeny; single-nucleotide polymorphism; whole-genome sequencing.

Figure 1

Cholera during the floods, Pakistan, 2010. A) North-oriented map of Pakistan indicating the 8 locations of Vibrio cholerae O1 El Tor isolation (shown by individual circles; red outer shading indicates the 5 locations that had flooding during the study period). White arrows indicate the hypothesized directions of spread of the various subclades of V. cholerae O1 El Tor. B) Cumulative root-to-tip distances of subclade 2 and subclade 1 V. cholerae O1 El Tor isolates. Each colored circle corresponds with an individual V. cholerae O1 El Tor isolate; colors correspond with the locations shown in panel A. Shading corresponds with the month of V. cholerae O1 El Tor isolation: light gray, August; medium gray, September; dark gray, October.

Figure 2

Phylogenetic tree showing the relative position of Vibrio cholerae O1 El Tor from Pakistan in wave 3 of the seventh-pandemic lineage, based on single-nucleotide polymorphism differences. The blue, green, and red branches represent waves 1, 2, and 3 respectively. The colors of the subclade 1 and 2 isolates match the colors assigned to the strain isolation locations in Figure 1, panel A.

Figure 3

A single-nucleotide polymorphism–based maximum-likelihood phylogeny showing the position of Vibrio cholerae O1 El Tor from Pakistan in wave 3 of the seventh-pandemic lineage relative to the Haiti and Nepal strains of Hendriksen et al. (23). Waves 1, 2, and 3 are labeled in blue, green, and red respectively. Scale bar indicates substitutions per variable site.