title: 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.
authors.forename: Muhammad Ali
authors.initials: MA
authors.lastname: Shah
authors.forename: Ankur
authors.initials: A
authors.lastname: Mutreja
authors.forename: Nicholas
authors.initials: N
authors.lastname: Thomson
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Habib
authors.initials: H
authors.lastname: Bokhari
authors.forename: Brendan W
authors.initials: BW
authors.lastname: Wren
mesh_terms: D002771:Cholera / Q000453:epidemiology*; D055868:Floods; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D062306:Geography, Medical; D006801:Humans; D008826:Microbial Sensitivity Tests; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D041241:Vibrio cholerae O1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification
keywords: Pakistan; Vibrio cholerae O1; bacteria; cholera; floods; global phylogeny; single-nucleotide polymorphism; whole-genome sequencing