title: Comparative genomic analysis of two isolates of Vibrio cholerae O1 Ogawa El Tor isolated during outbreak in Mariupol in 2011.
abstract: Cholera is a water-borne, severe enteric infection essentially caused by toxigenic strains of Vibrio cholera O1 and O139 serogroups. An outbreak of cholera was registered during May-July 2011 in Mariupol, Ukraine, with 33 cholera cases and 25 carriers of cholera. Following this outbreak, the toxigenic strain of V. cholerae 2011EL-301 was isolated from seawater in the recreation area of Taganrog city on the territory of Russia. The aim of our study was to understand genomic features of Mariupol isolates as well as to evaluate hypothesis about possible interconnection between the outbreak of cholera in Mariupol and the single case of isolation of V. cholerae from the Sea of Azov in Russia. Mariupol isolates were phenotypically characterized and subsequently subjected to whole genome sequencing procedure. Phylogenetic analysis based on high-quality SNPs of V. cholera O1 El Tor isolates of the 7th pandemic clade from different regions showed that clinical and environmental isolates from Mariupol outbreak were attributable to a unique phylogenetic clade within wave 3 of V. cholera O1 El Tor isolates and characterized by six clade-specific SNPs. Whereas Taganrog isolate belonged to distantly related clade which allows us to reject the hypothesis of transmission the outbreak strain of V. cholerae O1 from Ukraine to Russia in 2011. Mariupol isolates shared a common ancestor with Haiti\Nepal-4\India clade indicating that outbreak progenitor strain most likely originated in the South Asia region and later was introduced to Ukraine. Moreover, genomic data both based on hqSNPs and similarity of virulence-associated mobile genomic elements of Mariupol isolates suggests that environmental and clinical isolates are a part of joint outbreak which confirms the role of contaminated domestic sewage, as an element of the complex chain of infection spread during cholera outbreak. In general, the genome-wide comparative analysis of both genes and genomic regions of epidemiological importance indicates accessory of this isolates to 'new' clone of toxigenic multiple drug resistance atypical variant of V. cholerae O1 El Tor.
authors.affiliation: Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow 111123, Russian Federation. Electronic address: konstantinkul@gmail.com.
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Kuleshov
authors.affiliation: InsideDNA Ltd, 5th Floor(740-750), Salisbury House, London Wall, London, UK. Electronic address: anna.kostikova@gmail.com.
authors.forename: Anna
authors.initials: A
authors.lastname: Kostikova
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: pisarenko_sv@mail.ru.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Pisarenko
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: alcheem@mail.ru.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Kovalev
authors.affiliation: Federal State Health Public Institutions "Anti-Plague Station of the Republic of Crimea", Republic of Crimea, Simferopol 295023, Russian Federation. Electronic address: krimpchs@mail.ru.
authors.forename: Sergey N
authors.initials: SN
authors.lastname: Tikhonov
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: saveleva1766@inbox.ru.
authors.forename: Irina V
authors.initials: IV
authors.lastname: Savelievа
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: savelev39@inbox.ru.
authors.forename: Vilory N
authors.initials: VN
authors.lastname: Saveliev
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: ksusha.vasilieva@gmail.com.
authors.forename: Oksana V
authors.initials: OV
authors.lastname: Vasilieva
authors.affiliation: Federal State Health Public Institutions "Anti-Plague Station of the Republic of Crimea", Republic of Crimea, Simferopol 295023, Russian Federation. Electronic address: liliia-zinich@rambler.ru.
authors.forename: Liliia S
authors.initials: LS
authors.lastname: Zinich
authors.affiliation: Federal State Health Public Institutions "Anti-Plague Station of the Republic of Crimea", Republic of Crimea, Simferopol 295023, Russian Federation. Electronic address: nadia2002@bk.ru.
authors.forename: Nadiia N
authors.initials: NN
authors.lastname: Pidchenko
authors.affiliation: Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation. Electronic address: kulichenko_an@list.ru.
authors.forename: Alexander N
authors.initials: AN
authors.lastname: Kulichenko
authors.affiliation: Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow 111123, Russian Federation. Electronic address: shipulin@pcr.ru.
authors.forename: German A
authors.initials: GA
authors.lastname: Shipulin
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002771:Cholera / Q000453:epidemiology* / Q000266:history / Q000382:microbiology*; D004196:Disease Outbreaks; D019008:Drug Resistance, Neoplasm; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics / Q000379:methods; D049674:History, 21st Century; D006801:Humans; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D014455:Ukraine / Q000453:epidemiology; D041241:Vibrio cholerae O1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D014774:Virulence
chemical_list: D000900:Anti-Bacterial Agents
keywords: Infectious disease transmission; Outbreak; Phylogeny; Single nucleotide polymorphism; Vibrio cholerae O1; Whole genome sequencing