title: Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae.
abstract: Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a "shift" between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a "drift" between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.
authors.affiliation: School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Grim
authors.forename: Nur A
authors.initials: NA
authors.lastname: Hasan
authors.forename: Je Hee
authors.initials: JH
authors.lastname: Lee
authors.forename: Seon Young
authors.initials: SY
authors.lastname: Choi
authors.forename: Bradd J
authors.initials: BJ
authors.lastname: Haley
authors.forename: Elisa
authors.initials: E
authors.lastname: Taviani
authors.forename: Yoon-Seong
authors.initials: YS
authors.lastname: Jeon
authors.forename: Dong Wook
authors.initials: DW
authors.lastname: Kim
authors.forename: Jae-Hak
authors.initials: JH
authors.lastname: Lee
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Brettin
authors.forename: David C
authors.initials: DC
authors.lastname: Bruce
authors.forename: Jean F
authors.initials: JF
authors.lastname: Challacombe
authors.forename: J Chris
authors.initials: JC
authors.lastname: Detter
authors.forename: Cliff S
authors.initials: CS
authors.lastname: Han
authors.forename: A Christine
authors.initials: AC
authors.lastname: Munk
authors.forename: Olga
authors.initials: O
authors.lastname: Chertkov
authors.forename: Linda
authors.initials: L
authors.lastname: Meincke
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Saunders
authors.forename: Ronald A
authors.initials: RA
authors.lastname: Walters
authors.forename: Anwar
authors.initials: A
authors.lastname: Huq
authors.forename: G Balakrish
authors.initials: GB
authors.lastname: Nair
authors.forename: Rita R
authors.initials: RR
authors.lastname: Colwell
mesh_terms: D001483:Base Sequence; D002772:Cholera Toxin / Q000235:genetics; D016000:Cluster Analysis; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D014644:Genetic Variation; D044404:Genomic Islands / Q000235:genetics; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D041241:Vibrio cholerae O1 / Q000235:genetics*
chemical_list: D002772:Cholera Toxin