title: Shigella sonnei genome sequencing and phylogenetic analysis indicate recent             global dissemination from Europe.
abstract: Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery(1,2), spreading efficiently via low-dose fecal-oral transmission(3,4). Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality(4-6). Classical approaches have shown that S. sonnei is genetically conserved and clonal(7). We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage.
authors.affiliation: Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia. kholt@unimelb.edu.au
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Andrew
authors.initials: A
authors.lastname: Kitchen
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Vartul
authors.initials: V
authors.lastname: Sangal
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Brown
authors.forename: John E
authors.initials: JE
authors.lastname: Coia
authors.forename: Dong Wook
authors.initials: DW
authors.lastname: Kim
authors.forename: Seon Young
authors.initials: SY
authors.lastname: Choi
authors.forename: Su Hee
authors.initials: SH
authors.lastname: Kim
authors.forename: Wanderley D
authors.initials: WD
authors.lastname: da Silveira
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Pickard
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Farrar
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D016000:Cluster Analysis; D018562:Disease Transmission, Infectious / Q000706:statistics & numerical data*; D004405:Dysentery, Bacillary / Q000453:epidemiology / Q000235:genetics / Q000382:microbiology* / Q000635:transmission*; D005060:Europe / Q000453:epidemiology; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012764:Shigella sonnei / Q000145:classification / Q000235:genetics*; D014871:Water Microbiology; D060753:Water Quality